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Sample records for collision-induced dissociation fragmentation

  1. 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.

  2. Collision-induced dissociation of aminophospholipids (PE, MMPE, DMPE, PS): an apparently known fragmentation process revisited.

    PubMed

    Pittenauer, Ernst; Rehulka, Pavel; Winkler, Wolfgang; Allmaier, Günter

    2015-07-01

    A new type of low-mass substituted 4-oxazolin product ions of [M + H](+) precursor ions of aminophospholipids (glycerophosphatidylethanolamine, glycerophosphatidyl-N-methylethanolamine, glycerophosphatidyl-N,N-dimethylethanolamine, glycerophosphatidylserine) resulting from high-energy collision-induced dissociation (matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry) and low-energy collision-induced dissociation (e.g., electrospray ionization quadrupole reflectron time-of-flight mass spectrometry) with accurate mass determination is described; these were previously misidentified as CHO-containing radical cationic product ions. The mechanism for the formation of these ions is proposed to be via rapid loss of water followed by cyclization to an 11-membered-ring transition state for the sn-1 fatty acid substituent and to a ten-membered-ring transition state for the sn-2 fatty acid substituent, and via final loss of monoacylglycerol phosphate, leading to substituted 4-oxazolin product ions. The minimum structural requirement for this interesting skeletal rearrangement fragmentation is an amino group linked to at least one hydrogen atom (i.e., ethanolamine, N-methylethanolamine, serine). Therefore, N,N-dimethylethanolamine derivates do not exhibit this type of fragmentation. The analytical value of these product ions is given by the fact that by post source decay and particularly high-energy collision-induced dissociation achieved via matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry, the sn-2-related substituted 4-oxazolin product ion is always significantly more abundant than the sn-1-related one, which is quite helpful for detailed structural analysis of complex lipids. All other important product ions found are described in detail (following our previously published glycerophospholipid product ion nomenclature; Pittenauer and Allmaier, Int. J. Mass. Spectrom

  3. 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.

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

    PubMed

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

    2016-04-01

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

  5. Low-Energy Collision-Induced Dissociation Fragmentation Analysis of Cysteinyl-Modified Peptides

    SciTech Connect

    Borisov, Oleg V.; Goshe, Michael B. ); Conrads, Thomas P. ); Rakov, Vsevolod S. ); Veenstra, Timothy D. ); Smith, Richard D. )

    2002-05-15

    The development of methods to chemically modify and isolate cysteinyl-residue containing peptides (Cys-peptides) for LC-MS/MS analysis has generated considerable interest in the field of proteomics. Methods using isotope-coded affinity tags (ICAT) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-PEO-biotin) employ similar Cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate Cys-containing peptides in conjunction with immobilized avidin. For these strategies to be effective on a proteome-wide level, the presence of the ICAT or acetyl-PEO-biotin tag should not interfere with the efficiency of induced dissociation in MS/MS experiments or with the identification of the modified Cys-peptides by automated database searching algorithms. We have compared the collision-induced dissociation (CID) fragmentation patterns of peptides labeled with iodoacetyl-PEO-biotin and the ICAT reagent to those of the unmodified peptides. CID of Cys-peptides modified with either reagent resulted in the formation of ions attributed to the modified Cys-peptides as well as those unique to the labeling reagent. As demonstrated by analyzing acetyl-PEO-biotin labeled peptides from ribonuclease A and the ICAT-labeled proteome of D. radiodurans, the presence of these labeled-specific product ions provides a useful identifier to discern whether a peptide has been modified with the Cys-specific reagent, especially when a number of peptides analyzed using these methods do not contain a modified Cys-residue, and to differentiate identical Cys-peptides labeled with either ICAT-D0 or ICAT-D8.

  6. Letter: Electron-capture dissociation and collision-induced dissociation fragmentation of the supermetallized complexes of Substance P with potassium, cesium and silver.

    PubMed

    Kostyukevich, Yury; Zherebker, Alexander; Kononikhin, Alexey; Indeykina, Maria; Popov, Igor; Nikolaev, Eugene

    2016-01-01

    We report the investigation of the collision-induced dissociation (CID) and electron-capture dissociation (ECD) product fragmentations of the supermetallized complexes of Substance P and several monovalent metals. The supermetallization is the phenomenon of the formation of the complex ion peptide-metals in the gas phase when the peptide accepts an unexpectedly large number of metals. We have obtained and investigated complexes with the incorporation of up to four cesium (Cs), up to five potassium (K) and up to six silver (Ag) atoms. The current research reveals crucial changes in the complex behavior in the cases of different metals. It was observed that in CID spectra of complexes with Cs and K is dominated by the peak corresponding to the loss of metal cation while ECD gives a rich fragmentation. In the case of complexes with Ag, the loss of Ag(+) occurs in ECD while the CID shows a good fragmentation. PMID:27419902

  7. High-Energy Collision-Induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

    NASA Astrophysics Data System (ADS)

    Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

    2014-08-01

    A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

  8. Collision-Induced Dissociation Fragmentation Inside Disulfide C-Terminal Loops of Natural Non-Tryptic Peptides

    NASA Astrophysics Data System (ADS)

    Samgina, Tatiana Y.; Vorontsov, Egor A.; Gorshkov, Vladimir A.; Artemenko, Konstantin A.; Zubarev, Roman A.; Ytterberg, Jimmy A.; Lebedev, Albert T.

    2013-07-01

    Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S-S bonds is often used in "bottom up" sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the "hidden" C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S-S bond rupture does not occur in this case.

  9. Fragmentation behavior of a thiourea-based reagent for protein structure analysis by collision-induced dissociative chemical cross-linking.

    PubMed

    Müller, Mathias Q; Dreiocker, Frank; Ihling, Christian H; Schäfer, Mathias; Sinz, Andrea

    2010-08-01

    The fragmentation behavior of a novel thiourea-based cross-linker molecule specifically designed for collision-induced dissociation (CID) MS/MS experiments is described. The development of this cross-linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross-linked products. The new derivatizing reagent for chemical cross-linking solely contains a thiourea moiety that is flanked by two amine-reactive N-hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N-termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities--a characteristic CNL of 85 u--ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross-linking studies. A detailed examination of the CID behavior of the presented thiourea-based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross-linking of proteins. PMID:20607845

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

    PubMed

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  12. Combined photoelectron, collision-induced dissociation, and computational studies of parent and fragment anions of N-paranitrophenylsulfonylalanine and N-paranitrophenylalanine

    SciTech Connect

    Lambert, Jason; Chen, Jing; Buonaugurio, Angela; Bowen, Kit H. E-mail: kbowen@jhu.edu; Do-Thanh, Chi-Linh; Wang, Yilin; Best, Michael D.; Compton, R. N. E-mail: kbowen@jhu.edu; Sommerfeld, Thomas

    2013-12-14

    After synthesizing the compounds N-paranitrophenylsulfonylalanine (NPNPSA) and N-paranitrophenylalanine (NPNPA), the photoelectron spectrum of the valence anion of N-paranitrophenylsulfonylalanine (NPNPSA){sup −}, was measured and the collision-induced dissociation (CID) pathways of deprotonated N-paranitrophenylsulfonylalanine (NPNPSA-H){sup −} and deprotonated N-paranitrophenylalanine (NPNPA-H){sup −} were determined. Pertinent calculations were conducted to analyze both sets of experimental data. From the valence anion photoelectron spectrum of (NPNPSA){sup −}, the adiabatic electron affinity (AEA) of NPNPSA was determined to be 1.7 ± 0.1 eV, while the vertical detachment energy (VDE) of (NPNPSA){sup −} was found to be 2.3 ± 0.1 eV. Calculations for four low lying conformers of (NPNPSA){sup −} gave AEA values in the range of 1.6–2.1 eV and VDE values in the range of 2.0–2.4 eV. These calculations are in very good agreement with the experimental values. While the NPNPA anion (NPNPSA){sup −} was not observed experimentally it was studied computationally. The six low lying (NPNPSA){sup −} conformers were identified and calculated to have AEA values in the range of 0.7–1.2 eV and VDE values in the range of 0.9–1.6 eV. CID was used to study the fragmentation patterns of deprotonated NPNPA and deprotonated NPNPSA. Based on the CID data and calculations, the excess charge was located on the delocalized π-orbitals of the nitrobenzene moiety. This is made evident by the fact that the dominant fragments all contained the nitrobenzene moiety even though the parent anions used for the CID study were formed via deprotonation of the carboxylic acid. The dipole-bound anions of both molecules are studied theoretically using the results of previous studies on nitrobenzene as a reference.

  13. 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.

  14. Collision-induced gas phase dissociation rates

    NASA Technical Reports Server (NTRS)

    Hansen, C. Frederick

    1990-01-01

    The Landau-Zener theory of reactive cross sections was applied to diatomic molecules dissociating from a ladder of vibrational states. The result predicts a dissociation rate that is quite well duplicated by an Arrhenius function having a preexponential temperature dependence of about T(sub -1/2), at least for inert collision partners. This relation fits experimental data reasonably well. The theory is then used to calculate the effect of vibrational nonequilibrium on dissociation rate. For Morse oscillators, the results are about the same as given by Hammerling, Kivel, and Teare in their analytic approximation for harmonic oscillators, though at very high temperature a correction for the partition function limit is included. The empirical correction for vibration nonequilibrium proposed by Park, which is a convenient algorithm for CFD calculations, is modified to prevent a drastic underestimation of dissociation rates that occurs with this method when vibrational temperature is much smaller than the kinetic temperature of the gas.

  15. Collision induced dissociation of alpha hydroxy acids

    NASA Astrophysics Data System (ADS)

    Bandu, Mary L.; Grubbs, Thomas; Kater, Marcus; Desaire, Heather

    2006-03-01

    Alpha hydroxy acids typically dissociate in tandem mass spectrometric experiments to produce product ions representing a neutral loss of 46 Da (CH2O2) in negative ion mode. Although it is widely accepted that the carboxylate group is lost in the dissociation process, the origin of the remaining two hydrogens is unclear. The current study utilizes an alpha hydroxy acid chemical library and deuterium labeling experiments to identify the origin of the two hydrogens lost during dissociation. Secondly, this study investigates the lower m/z region of the CID spectrum, a region previously unexplored, to aid in characterizing the dissociation mechanism. Further experiments testing the energy requirements and time parameters of the dissociation also are consistent with criteria previously defined for ion-neutral complex formation. In addition to describing the mechanism for the loss of CH2O2, we have conducted experiments that demonstrate the important chemical features of molecules that can prevent alpha hydroxy acids from undergoing the loss of 46 Da. By understanding the chemical composition of the 46 Da loss, the dissociation mechanism responsible for the loss, and the factors that hinder this mechanistic pathway, chemical information about alpha hydroxy acids can be obtained from their CID data.

  16. Formation, Fragmentation, and Structures of YxOy(+) (x = 1, 2, y = 1 - 13) Clusters: Collision-Induced Dissociation Experiments and Density Functional Theory Calculations.

    PubMed

    Glodić, Pavle; Mihesan, Claudia; Klontzas, Emmanouel; Velegrakis, Michalis

    2016-02-25

    Yttrium oxide cluster cations have been experimentally and theoretically studied. We produced small, oxygen-rich yttrium oxide clusters, YxOy+ (x = 1, 2, y = 1–13), by mixing the laser-produced yttrium plasma with a molecular oxygen jet. Mass spectrometry measurements showed that the most stable clusters are those consisting of one yttrium and an odd number of oxygen atoms of the form YO(+)(2k+1) (k = 0–6). Additionally, we performed collision induced dissociation experiments, which indicated that the loss of pairs of oxygen atoms down to a YO+ core is the preferred fragmentation channel for all clusters investigated. Furthermore, we conduct DFT calculations and we obtained two types of low-energy structures: one containing an yttrium cation core and the other composed of YO+ core and O2 ligands, being in agreement with the observed fragmentation pattern. Finally, from the fragmentation studies, total collision cross sections are obtained and these are compared with geometrical cross sections of the calculated structures. PMID:26812242

  17. Comparison of collision-induced dissociation and electron-induced dissociation of phillyrin using FT-ICR MS.

    PubMed

    Lin, Zhenguang; Lin, Zhiwei; Mu, Yingdi; Yan, Dong

    2016-10-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry using collision-induced dissociation (CID) and electron capture dissociation (ECD) at high mass resolution was first applied to investigate the characteristic fragment ions of phillyrin. The CID experimental results demonstrated the elemental composition of fragment ions unambiguously, so a reasonable fragmentation pathway of phillyrin was proposed. The ECD fragmentation mechanism was believed to be fundamentally different from the CID method. ECD could be used not only in the biological field but also as a powerful complement to the structural identification of small molecular compounds. The characteristic fragmentation pathways were helpful in analyzing and interpreting the stability and property of the parent ion. PMID:27258687

  18. Threshold collision induced dissociation experiment for azobenzene and its derivatives

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    In this study we investigated protonated azobenzene cation and properties of trans 2,2',6,6'-tetrafluoroazobenzene anion using the collision induced dissociation method and the results are compared with the results from ab initio electronic structure calculations. We measured the bond dissociation energies experimentally and found which theoretical quantum chemistry methods yield best results. Several high accuracy multi-level calculations such as CBS-QB3, G3 and G4 had been carried out to obtain reliable thermochemical information for azobenzene and several of its derivatives and their anion or cation. We also performed other experiments such as Raman spectroscopy to study these light sensitive molecules with promising applications such as photo-switching.

  19. 4-HNE Adduct Stability Characterized by Collision-Induced Dissociation and Electron Transfer Dissociation Mass Spectrometry

    PubMed Central

    Fritz, Kristofer S.; Kellersberger, Katherine A.; Gomez, Jose D.; Petersen, Dennis R.

    2012-01-01

    4-hydroxynonenal (4-HNE) alters numerous proteomic and genomic processes. Understanding chemical mechanisms of 4-HNE interactions with biomolecules and their respective stabilities may lead to new discoveries in biomarkers for numerous diseases of oxidative stress. Collision-induced dissociation (CID) and electron transfer dissociation (ETD) MS/MS were utilized to examine the stability of a 4-HNE-Cys Michael adduct. CID conditions resulted in the neutral loss of 4-HNE, also known as a retro-Michael addition reaction (RMA). Consequently, performing ETD fragmentation on this same adduct did not result in RMA. Interestingly, 4-HNE adduct reduction via sodium borohydride (NaBH4) treatment stabilized against the CID induced RMA. In a direct comparison of three forms of 4-HNE adducts, computational modeling revealed sizeable shifts in the shape and orientation of the lowest unoccupied molecular orbital (LUMO) density around the 4-HNE-Cys moiety. These findings demonstrate that ETD MS/MS analysis can be used to improve the detection of 4-HNE-protein modifications by preventing RMA reactions from occurring. PMID:22404378

  20. Collision-induced dissociation of H/sub 2/ and CO molecules

    SciTech Connect

    Roberge, W.; Dalgarno, A.

    1982-04-01

    A discussion is presented of the collision-induced dissociation of molecular hydrogen and carbonn monoxide in shock-heated regions of the interstellar medium. The modifications to the dissociation rate caused by radiative stabilization are considered, and estimates are presented of the effective rates of collision-induced dissociation as functions of density and temperature in gases in atomic and molecular hydrogen. Below a certain density, n/sub asterisk/, radiative stabilization greatly reduces the rate of collision-induced dissociation with substantial consequences for the thermal and chemical evolution of the postshock gas.

  1. Three-Body Collision Contributions to Recombination and Collision-Induced Dissociation. II. Kinetics

    SciTech Connect

    Kendrick, Brian; Pack, Russell T.; Walker, Robert B.

    1998-04-10

    Detailed rate constants for the reaction Ne + Ne + H {r_equilibrium} Ne{sub 2} + H are generated, and the master equations governing collision-induced dissociation (CID) and recombination are accurately solved numerically. The temperature and pressure dependence are explored. At all pressures, three-body (3B) collisions dominate. The sequential two-body energy-transfer (ET) mechanism gives a rate that is more than a factor of two too small at low pressures and orders of magnitude too small at high pressures. Simpler models are explored; to describe the kinetics they must include direct 3B rates connecting the continuum to the bound states and to the quasibound states. The relevance of the present reaction to more general CID/recombination reactions is discussed. For atomic fragments, the 3B mechanism usually dominates. For diatomic fragments,the 3B and ET mechanism are competitive, and for polyatomic fragments the ET mechanism usually dominates.

  2. Comparison of collision-induced dissociation and electron-induced dissociation of phillyrin using FT-ICR MS

    NASA Astrophysics Data System (ADS)

    Lin, Zhenguang; Lin, Zhiwei; Mu, Yingdi; Yan, Dong

    2016-10-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry using collision-induced dissociation (CID) and electron capture dissociation (ECD) at high mass resolution was first applied to investigate the characteristic fragment ions of phillyrin. The CID experimental results demonstrated the elemental composition of fragment ions unambiguously, so a reasonable fragmentation pathway of phillyrin was proposed. The ECD fragmentation mechanism was believed to be fundamentally different from the CID method. ECD could be used not only in the biological field but also as a powerful complement to the structural identification of small molecular compounds. The characteristic fragmentation pathways were helpful in analyzing and interpreting the stability and property of the parent ion. The ESI FT-ICR MS using CID and ECD methods was applied to investigate the characteristic fragment ions of Phillyrin for the first time. The fragmentation process of phillyrin which formation of the peroxide bond by CID, was discussed in detail. These characteristic fragmentation pathways were helpful to analyze and interpret the stability and property of the parent ion. It was clearly demonstrated that ECD can be not only used to Biological field but also a powerful complement to the structure identification of small molecules.

  3. Final report. Surface-induced dissociation versus collision-induced dissociation

    SciTech Connect

    Futrell, Jean H.

    2001-04-19

    A 7-Tesla Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer was modified to insert a surface inside the cell for ion-surface collisions leading to the dissociation of impacting ions. Modifications were made to the software/hardware to collide the ions brought into the cell and trap the resulting fragment and undissociated primary ions inside the cell. The trapping plates were also ramped to determine kinetic energy distributions of these ions. The surface-induced dissociation (SID) of benzene and chromium hexacarbonyl ions was first studied as test cases for the instrument. Then a systematic study of the SID of small protonated peptides formed by electrospray ionization was begun. A series of small alanine(A)-containing peptides, viz., AA, AAA, AAAA, AAAAA, and PAAAA were used in the study. In the absence of any direct comparisons of the SID processes with the commonly used technique of tandem mass spectrometry of collision-induced dissociations (CID) via collisions with a neutral gas, a comparative study of CID and SID using the same protonated peptides was made. Since multiple collisions are often used to enhance dissociation efficiency in CID, the CID was performed under single as well as multiple collisional activation conditions. Both on-resonance and sustained off-resonance irradiation excitation were used for CID experiments. Kinetic energy of the ions was varied by changing peak-to-peak voltage applied to the excitation plates. Results are shown in a series of graphs, and a simple theoretical model is presented. This direct comparison of the two activation techniques on the same instrument provided insights into the similarities and differences between these two. The results suggest that internal energy distributions of ions activated by ion-surface collision and multiple collision ion-gaseous neutral collisions are quite comparable. The results also suggest that, in ion-surface collisions, the ion collides with only a small fraction of th

  4. Identification of Proteins and Phosphoproteins Using Pulsed Q Collision Induced Dissociation (PQD)

    NASA Astrophysics Data System (ADS)

    Wu, Wells W.; Wang, Guanghui; Insel, Paul A.; Hsiao, Cheng-Te; Zou, Sige; Maudsley, Stuart; Martin, Bronwen; Shen, Rong-Fong

    2011-10-01

    Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.

  5. A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation.

    PubMed

    Webb, Ian K; Garimella, Sandilya V B; Norheim, Randolph V; Baker, Erin S; Ibrahim, Yehia M; Smith, Richard D

    2016-07-01

    A collision induced dissociation (CID) structure for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer. The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably with other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of nine peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied. Graphical Abstract ᅟ. PMID:27098413

  6. A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Webb, Ian K.; Garimella, Sandilya V. B.; Norheim, Randolph V.; Baker, Erin S.; Ibrahim, Yehia M.; Smith, Richard D.

    2016-07-01

    A collision induced dissociation (CID) structure for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer. The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably with other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of nine peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied.

  7. A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Webb, Ian K.; Garimella, Sandilya V. B.; Norheim, Randolph V.; Baker, Erin S.; Ibrahim, Yehia M.; Smith, Richard D.

    2016-04-01

    A collision induced dissociation (CID) structure for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer. The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably with other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of nine peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied.

  8. Implementation of Dipolar Resonant Excitation Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS

    SciTech Connect

    Webb, Ian K.; Chen, Tsung-Chi; Danielson, William F.; Ibrahim, Yehia M.; Tang, Keqi; Anderson, Gordon A.; Smith, Richard D.

    2014-01-28

    Under and overfragmentation are significant hurdles to the data independent “bottom-up” approach to proteomics. Another challenge to the data independent approach is the convolution of fragments from different peptides that coelute in reverse-phase liquid chromatography/mass spectrometry (RPLC/MS). The ion mobility/collision induced dissociation/time-of flight mass spectrometry (IMS/CID/TOF MS) approach gives drift-time aligned fragment ions that have the same arrival time distributions as precursor ions, greatly aiding in fragment and peptide ion identification. We have modified an IMS/TOF MS platform to allow for resonant excitation CID experiments. Resonant excitation CID leads to highly efficient, mass-resolved fragmentation without additional excitation of product ions, alleviating the overfragmentation problem. The ability to apply resonant waveforms in mobility-resolved windows has been demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS separation experiment.

  9. Comparison of Ultraviolet Photodissociation and Collision Induced Dissociation of Adrenocorticotropic Hormone Peptides

    NASA Astrophysics Data System (ADS)

    Robotham, Scott A.; Brodbelt, Jennifer S.

    2015-09-01

    In an effort to better characterize the fragmentation pathways promoted by ultraviolet photoexcitation in comparison to collision induced dissociation (CID), six adrenocorticotropic hormone (ACTH) peptides in a range of charge states were subjected to 266 nm ultraviolet photodissociation (UVPD), 193 nm UVPD, and CID. Similar fragment ions and distributions were observed for 266 nm UVPD and 193 nm UVPD for all peptides investigated. While both UVPD and CID led to preferential cleavage of the Y-S bond for all ACTH peptides [except ACTH (1-39)], UVPD was far less dependent on charge state and location of basic sites for the production of C-terminal and N-terminal ions. For ACTH (1-16), ACTH (1-17), ACTH (1-24), and ACTH (1-39), changes in the distributions of fragment ion types ( a, b, c, x, y, z, and collectively N-terminal ions versus C-terminal ions) showed only minor changes upon UVPD for all charge states. In contrast, CID displayed significant changes in the fragment ion type distributions as a function of charge state, an outcome consistent with the dependence on the number and location of mobile protons that is not prominent for UVPD. Sequence coverages obtained by UVPD showed less dependence on charge state than those determined by CID, with the latter showing a consistent decrease in coverage as charge state increased.

  10. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides*

    PubMed Central

    Giese, Sven H.; Fischer, Lutz; Rappsilber, Juri

    2016-01-01

    Cross-linking/mass spectrometry resolves protein–protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)-cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique cross-linked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotope-labeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary cross-linked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers. PMID:26719564

  11. An unprecedented rearrangement in collision-induced mass spectrometric fragmentation of protonated benzylamines.

    PubMed

    Bialecki, Jason; Ruzicka, Josef; Attygalle, Athula B

    2006-09-01

    The collision-induced dissociation (CID) mass spectra of several protonated benzylamines are described and mechanistically rationalized. Under collision-induced decomposition conditions, protonated dibenzylamine, for example, loses ammonia, thereby forming an ion of m/z 181. Deuterium labeling experiments confirmed that the additional proton transferred to the nitrogen atom during this loss of ammonia comes from the ortho positions of the phenyl rings and not from the benzylic methylene groups. A mechanism based on an initial elongation of a C--N bond at the charge center that eventually cleaves the C--N bond to form an ion/neutral complex of benzyl cation and benzylamine is proposed to rationalize the results. The complex then proceeds to dissociate in several different ways: (1) a direct dissociation to yield a benzyl cation observed at m/z 91; (2) an electrophilic attack by the benzyl cation within the complex on the phenyl ring of the benzylamine to remove a pair of electrons from the aromatic sextet to form an arenium ion, which either donates a ring proton (or deuteron when present) to the amino group forming a protonated amine, which undergoes a charge-driven heterolytic cleavage to eliminate ammonia (or benzylamine) forming a benzylbenzyl cation observed at m/z 181, or undergoes a charge-driven heterolytic cleavage to eliminate diphenylmethane and an immonium ion; and (3) a hydride abstraction from a methylene group of the neutral benzylamine to the benzylic cation to eliminate toluene and form a substituted immonium ion. Corresponding benzylamine and dibenzylamine losses observed in the spectra of protonated tribenzylamine and tetrabenzyl ammonium ion, respectively, indicate that the postulated mechanism can be widely applied. The postulated mechanisms enabled proper prediction of mass spectral fragments expected from protonated butenafine, an antifungal drug. PMID:16924596

  12. Peptide Scrambling During Collision-Induced Dissociation is Influenced by N-terminal Residue Basicity

    NASA Astrophysics Data System (ADS)

    Chawner, Ross; Holman, Stephen W.; Gaskell, Simon J.; Eyers, Claire E.

    2014-08-01

    `Bottom up' proteomic studies typically use tandem mass spectrometry data to infer peptide ion sequence, enabling identification of the protein whence they derive. The majority of such studies employ collision-induced dissociation (CID) to induce fragmentation of the peptide structure giving diagnostic b-, y-, and a- ions. Recently, rearrangement processes that result in scrambling of the original peptide sequence during CID have been reported for these ions. Such processes have the potential to adversely affect ion accounting (and thus scores from automated search algorithms) in tandem mass spectra, and in extreme cases could lead to false peptide identification. Here, analysis of peptide species produced by Lys-N proteolysis of standard proteins is performed and sequences that exhibit such rearrangement processes identified. The effect of increasing the gas-phase basicity of the N-terminal lysine residue through derivatization to homoarginine toward such sequence scrambling is then assessed. The presence of a highly basic homoarginine (or arginine) residue at the N-terminus is found to disfavor/inhibit sequence scrambling with a coincident increase in the formation of b(n-1)+H2O product ions. Finally, further analysis of a sequence produced by Lys-C proteolysis provides evidence toward a potential mechanism for the apparent inhibition of sequence scrambling during resonance excitation CID.

  13. Characteristics of Ion Activation and Collision Induced Dissociation Using Digital Ion Trap Technology.

    PubMed

    Xu, Fuxing; Dang, Qiankun; Dai, Xinhua; Fang, Xiang; Wang, Yuanyuan; Ding, Li; Ding, Chuan-Fan

    2016-08-01

    Collision induced dissociation (CID) is one of the most established techniques for tandem mass spectrometry analysis. The CID of mass selected ion could be realized by ion resonance excitation with a digital rectangular waveform. The method is simple, and highly efficient CID result could be obtained by optimizing the experimental parameters, such as digital waveform voltage, frequency, and q value. In this work, the relationship between ion trapping waveform voltage and frequency at preselected q value, the relationship between waveform frequency and the q value at certain ion trapping voltage for optimum CID efficiency were investigated. Experiment results showed that the max CID efficiency of precursor reserpine ions can be obtained at different trapping waveform voltage and frequency when q and β are different. Based on systematic experimental analysis, the optimum experimental conditions for high CID efficiency can be calculated at any selected β or q. By using digital ion trap technology, the CID process and efficient fragmentation of parent ions can be realized by simply changing the trapping waveform amplitude, frequency, and the β values in the digital ion trap mass spectrometry. The technology and method are simple. It has potential use in ion trap mass spectrometry. Graphical Abstract ᅟ. PMID:27150507

  14. Characteristics of Ion Activation and Collision Induced Dissociation Using Digital Ion Trap Technology

    NASA Astrophysics Data System (ADS)

    Xu, Fuxing; Dang, Qiankun; Dai, Xinhua; Fang, Xiang; Wang, Yuanyuan; Ding, Li; Ding, Chuan-Fan

    2016-08-01

    Collision induced dissociation (CID) is one of the most established techniques for tandem mass spectrometry analysis. The CID of mass selected ion could be realized by ion resonance excitation with a digital rectangular waveform. The method is simple, and highly efficient CID result could be obtained by optimizing the experimental parameters, such as digital waveform voltage, frequency, and q value. In this work, the relationship between ion trapping waveform voltage and frequency at preselected q value, the relationship between waveform frequency and the q value at certain ion trapping voltage for optimum CID efficiency were investigated. Experiment results showed that the max CID efficiency of precursor reserpine ions can be obtained at different trapping waveform voltage and frequency when q and β are different. Based on systematic experimental analysis, the optimum experimental conditions for high CID efficiency can be calculated at any selected β or q. By using digital ion trap technology, the CID process and efficient fragmentation of parent ions can be realized by simply changing the trapping waveform amplitude, frequency, and the β values in the digital ion trap mass spectrometry. The technology and method are simple. It has potential use in ion trap mass spectrometry.

  15. Characteristics of Ion Activation and Collision Induced Dissociation Using Digital Ion Trap Technology

    NASA Astrophysics Data System (ADS)

    Xu, Fuxing; Dang, Qiankun; Dai, Xinhua; Fang, Xiang; Wang, Yuanyuan; Ding, Li; Ding, Chuan-Fan

    2016-05-01

    Collision induced dissociation (CID) is one of the most established techniques for tandem mass spectrometry analysis. The CID of mass selected ion could be realized by ion resonance excitation with a digital rectangular waveform. The method is simple, and highly efficient CID result could be obtained by optimizing the experimental parameters, such as digital waveform voltage, frequency, and q value. In this work, the relationship between ion trapping waveform voltage and frequency at preselected q value, the relationship between waveform frequency and the q value at certain ion trapping voltage for optimum CID efficiency were investigated. Experiment results showed that the max CID efficiency of precursor reserpine ions can be obtained at different trapping waveform voltage and frequency when q and β are different. Based on systematic experimental analysis, the optimum experimental conditions for high CID efficiency can be calculated at any selected β or q. By using digital ion trap technology, the CID process and efficient fragmentation of parent ions can be realized by simply changing the trapping waveform amplitude, frequency, and the β values in the digital ion trap mass spectrometry. The technology and method are simple. It has potential use in ion trap mass spectrometry.

  16. Collision-induced dissociation reactions and pulsed field ionization photoelectron

    SciTech Connect

    Stimson, S.

    1999-02-12

    This report summarized the four parts of the research study and describes the general conclusions. Individual chapters have been removed for separate processing. The chapter titles are: A study of the dissociation of CH{sub 3}SH{sup +} by collisional activation: Observation of non-statistical behavior; High resolution vacuum ultraviolet pulsed field ionization photoelectron band for OCS{sup +}(X{sup 2}{Pi}): An experimental and theoretical study; Rotationally resolved pulsed field ionization photoelectron bands of H{sub 2}{sup +} ({Chi}{sup 2}{Sigma}{sup +}{sub g}, v{sup +} = 0--18); and Rotationally resolved pulsed field ionization photoelectron bands of HD{sup +} ({Chi}{sup 2}{Sigma}{sup +}, v{sup +} = 0--21).

  17. Identification and relative quantification of proteins in Escherichia coli proteome by "up-front" collision-induced dissociation.

    PubMed

    Arike, Liisa; Nahku, Ranno; Borrisova, Maria; Adamberg, Kaarel; Vilu, Raivu

    2010-01-01

    A method for identifying and quantifying proteins with relatively low-cost orthogonal acceleration time-of- flight mass spectrometry (oa-ToF-MS) was tested. Escherichia coli (E. coli) K12 MG1655 cell lysate was separated by 1D gel-electrophoresis; fractions were digested and separated fast and reproducibly by ultra-performance liquid chromatography (UPLC). Peptides were identified using oa-ToF-MS to measure exact masses of parent ions and the fragment ions generated by up-front collision-induced dissociation. Fragmentation of all compounds was achieved by rapidly cycling between high- and low values of energy applied to ions. More than 100 proteins from E. coli K12 proteome were identified and relatively quantified. Results were found to correlate with transcriptome data determined by DNA microarrays. PMID:20212332

  18. Electronic shell model contemplation of the dissociation dynamics of Al 8+: a collision-induced dissociation study

    NASA Astrophysics Data System (ADS)

    Ingólfsson, Oddur; Takeo, Harutoshi; Nonose, Shinji

    1999-10-01

    For the collision-induced dissociation of small cationic aluminum clusters, the release of Al + is known to dominate. An exception is Al 8+, where we find the neutral atom evaporation to be energetically favorable, and to couple strongly with the Al + release. These experimental results are discussed in the frame of the Clemenger-Nilsson electronic shell model. We find the electronic shell model to offer a consistent interpretation of the energy dependence of the dissociation dynamics of Al 8+, if the crucial role of collisional deformation is taken into account.

  19. Collision induced dissociation of protonated N-nitrosodimethylamine by ion trap mass spectrometry: Ultimate carcinogens in gas phase

    NASA Astrophysics Data System (ADS)

    Kulikova, Natalia; Baker, Michael; Gabryelski, Wojciech

    2009-12-01

    Collision induced dissociation of protonated N-nitrosodimethylamine (NDMA) and isotopically labeled N-nitrosodimethyl-d6-amine (NDMA-d6) was investigated by sequential ion trap mass spectrometry to establish mechanisms of gas phase reactions leading to intriguing products of this potent carcinogen. The fragmentation of (NDMA + H+) occurs via two dissociation pathways. In the alkylation pathway, homolytic cleavage of the N-O bond of N-dimethyl, N'-hydroxydiazenium ion generates N-dimethyldiazenium distonic ion which reacts further by a CH3 radical loss to form methanediazonium ion. Both methanediazonium ion and its precursor are involved in ion/molecule reactions. Methanediazonium ion showed to be capable of methylating water and methanol molecules in the gas phase of the ion trap and N-dimethyldiazenium distonic ion showed to abstract a hydrogen atom from a solvent molecule. In the denitrosation pathway, a tautomerization of N-dimethyl, N'-hydroxydiazenium ion to N-nitrosodimethylammonium intermediate ion results in radical cleavage of the N-N bond of the intermediate ion to form N-dimethylaminium radical cation which reacts further through [alpha]-cleavage to generate N-methylmethylenimmonium ion. Although the reactions of NDMA in the gas phase are different to those for enzymatic conversion of NDMA in biological systems, each activation method generates the same products. We will show that collision induced dissociation of N-nitrosodiethylamine (NDEA) and N-nitrosodipropylamine (NDPA) is also a feasible approach to gain information on formation, stability, and reactivity of alkylating agents originating from NDEA and NDPA. Investigating such biologically relevant, but highly reactive intermediates in the condensed phase is hampered by the short life-times of these transient species.

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

    PubMed Central

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

    2010-01-01

    The confidence in peptide (and protein) identifications with ion mobility spectrometry time-of-flight mass spectrometry (IMS-TOFMS) is expected to drastically improve with the addition of information from an efficient ion dissociation step prior to MS detection. High throughput IMS-TOFMS analysis imposes a strong need for multiplexed ion dissociation approaches where multiple precursor ions yield complex sets of fragment ions that are often intermingled with each other in both the drift time and m/z domains. We have developed and evaluated an approach for collision-induced dissociation (CID) using IMS-TOFMS instrument. It has been shown that precursor ions activated inside an rf-device with an axial dc-electric field produce abundant fragment ions which are radially confined with the rf-field and collisionally cooled at an elevated pressure, resulting in high CID efficiencies comparable or higher than those measured in triple-quadrupole instruments. We have also developed an algorithm for deconvoluting these complex multiplexed tandem MS spectra by clustering both the precursor and fragment ions into matching drift time profiles and by utilizing the high mass measurement accuracy achievable with TOFMS. In a single IMS separation from direct infusion of tryptic digest of bovine serum albumin (BSA), we have reliably identified 20 unique peptides using a multiplexed CID approach downstream of the IMS separation. Peptides were identified based upon the correlation between the precursor and fragment drift time profiles and by matching the profile representative masses to those of in silico BSA tryptic peptides and their fragments. The false discovery rate (FDR) of peptide identifications from multiplexed MS/MS spectra was less than 1%. PMID:20596241

  1. Collision-induced dissociation of Nb x O{/y +} ( x = 1, 2, y = 2-12) clusters: crossed molecular beams and collision cell studies

    NASA Astrophysics Data System (ADS)

    Mihesan, Claudia; Glodić, Pavle; Velegrakis, Michalis

    2015-03-01

    Oxygen-rich niobium oxide clusters are formed by mixing laser-produced Nb plasma with pure oxygen, and their stability is investigated by mass spectrometry and collision-induced dissociation. We use an experimental configuration recently developed by our group, where the cluster ions beam is crossed with a secondary beam of noble gas atoms, and the fragments are rejected by a retarding field energy analyzer. In this way, the relative collision cross sections of Nb x O{/y +} ( x = 1, 2, y = 2-12) clusters have been measured and information about their fragmentation channels has been obtained.

  2. Tetrapositive plutonium, neptunium, uranium, and thorium coordination complexes: chemistry revealed by electron transfer and collision induced dissociation.

    PubMed

    Gong, Yu; Tian, Guoxin; Rao, Linfeng; Gibson, John K

    2014-04-17

    The Pu(4+), Np(4+), and U(4+) ions, which have large electron affinities of ∼34.6, ∼33.6, and ∼32.6 eV, respectively, were stabilized from solution to the gas phase upon coordination by three neutral tetramethyl-3-oxa-glutaramide ligands (TMOGA). Both collision induced dissociation (CID) and electron transfer dissociation (ETD) of Pu(TMOGA)3(4+) reveal the propensity for reduction of Pu(IV) to Pu(III), by loss of TMOGA(+) in CID and by simple electron transfer in ETD. The reduction of Pu(IV) is in distinct contrast to retention of Th(IV) in both CID and ETD of Th(TMOGA)3(4+), where only the C-Oether bond cleavage product was observed. U(TMOGA)3(4+) behaves similarly to Th(TMOGA)3(4+) upon CID and ETD, while the fragmentation patterns of Np(TMOGA)3(4+) lie between those of Pu(TMOGA)3(4+) and U(TMOGA)3(4+). It is notable that the gas-phase fragmentation behaviors of these exceptional tetrapositive complexes parallel fundamental differences in condensed phase chemistry within the actinide series, specifically the tendency for reduction from the IV to III oxidation states. PMID:24660979

  3. Mechanistic Investigation of Phosphate Ester Bond Cleavages of Glycylphosphoserinyltryptophan Radical Cations under Low-Energy Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Quan, Quan; Hao, Qiang; Song, Tao; Siu, Chi-Kit; Chu, Ivan K.

    2013-04-01

    Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G p SW]•+) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G• p SW]+). The dissociation of [G• p SW]+ is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H]•+/y1 + pair as the minor products. In contrast, for [G p SW]•+, competitive cleavages along the peptide backbone, such as the formation of [G p SW - CO2]•+ and the [c2 + 2H]+/[z1 - H]•+ pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G• p SW]+ and [G p SW]•+ and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G• p SW]+ results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G p SW]•+.

  4. Collision-induced dissociation analysis of negative atmospheric ion adducts in atmospheric pressure corona discharge ionization mass spectrometry.

    PubMed

    Sekimoto, Kanako; Takayama, Mitsuo

    2013-05-01

    Collision-induced dissociation (CID) experiments were performed on atmospheric ion adducts [M + R](-) formed between various types of organic compounds M and atmospheric negative ions R(-) [such as O2(-), HCO3(-), COO(-)(COOH), NO2(-), NO3(-), and NO3(-)(HNO3)] in negative-ion mode atmospheric pressure corona discharge ionization (APCDI) mass spectrometry. All of the [M + R](-) adducts were fragmented to form deprotonated analytes [M - H](-) and/or atmospheric ions R(-), whose intensities in the CID spectra were dependent on the proton affinities of the [M - H](-) and R(-) fragments. Precursor ions [M + R](-) for which R(-) have higher proton affinities than [M - H](-) formed [M - H](-) as the dominant product. Furthermore, the CID of the adducts with HCO3(-) and NO3(-)(HNO3) led to other product ions such as [M + HO](-) and NO3(-), respectively. The fragmentation behavior of [M + R](-) for each R(-) observed was independent of analyte type (e.g., whether the analyte was aliphatic or aromatic, or possessed certain functional groups). PMID:23479312

  5. Do the O2 Schumann-Runge Bands Participate in keV Collision-Induced Dissociation Experiments?

    NASA Astrophysics Data System (ADS)

    Lin, Yawei; Mayer, Paul M.

    2011-01-01

    In high-energy (keV) CID experiments, oxygen has the unique ability to enhance specific ion fragmentation pathways that lie within a relatively narrow band of activation energy. It has been previously proposed that this oxygen-enhanced dissociation phenomenon is due to the participation of the {{O}_{{2}}}{B}{ ^{{3}}}{Σ_{{u}}}^{ + } - {X}{ ^{{3}}}{Σ_{{g}}}^{ - } (Schumann-Runge) system in the collision complex. During the collision, oxygen is first excited to its {B}{ ^{{3}}}{Σ_{{u}}}^{ + } state before it returns this energy to the projectile ion. This energy drives the nonstatistical dissociation of the projectile provided there is an energetically accessible pathway in resonance with the absorbed radiation. To probe the validity of this hypothesis, a modified VG-ZAB mass spectrometer was used to observe the photon emissions from keV collisions of a selection of projectile ions with O2 target gas. By studying the resulting collision-induced emission (CIE) spectra, a second potential mechanism came to light, one that involves the near-isoenergetic O2 +. A 2Πu→X 2 Πg state transition.

  6. Do the O2 Schumann-Runge bands participate in keV collision-induced dissociation experiments?

    PubMed

    Lin, Yawei; Mayer, Paul M

    2011-01-01

    In high-energy (keV) CID experiments, oxygen has the unique ability to enhance specific ion fragmentation pathways that lie within a relatively narrow band of activation energy. It has been previously proposed that this oxygen-enhanced dissociation phenomenon is due to the participation of the O(2) B(3)Σ(u)(+) - X(3)Σ(g)(-) (Schumann-Runge) system in the collision complex. During the collision, oxygen is first excited to its [Formula: see text] state before it returns this energy to the projectile ion. This energy drives the nonstatistical dissociation of the projectile provided there is an energetically accessible pathway in resonance with the absorbed radiation. To probe the validity of this hypothesis, a modified VG-ZAB mass spectrometer was used to observe the photon emissions from keV collisions of a selection of projectile ions with O(2) target gas. By studying the resulting collision-induced emission (CIE) spectra, a second potential mechanism came to light, one that involves the near-isoenergetic O(2) (+.) A (2)Π(u)→X (2) Π(g) state transition. PMID:21472546

  7. Generation of peptide radical dications via low-energy collision-induced dissociation of [CuII(terpy)(M + H)].3+ .

    PubMed

    Chu, Ivan K; Lam, Corey N W

    2005-11-01

    The first example of the formation of hydrogen-deficient radical cations of the type [M + H](.2+) is demonstrated to occur through a one-electron-transfer mechanism upon low-energy collision-induced dissociation (CID) of gas-phase triply charged [Cu(II)(terpy)(M + H)](.3+) complex ions (where M is an angiotensin III or enkephalin derivative; terpy = 2,2':6',2''-terpyridine). The collision-induced dissociation of doubly charged [M + H](.2+) radical cations generates similar product ions to those prepared through hot electron capture dissociation (HECD). Isomeric isoleucine and leucine residues were distinguished by observing the mass differences between [z(n) + H](.+) and w(n)(+) ions (having the same residue number, n) of the Xle residues. The product ion spectrum of [z(n) + H](.+) reveals that the w(n)(+) ions are formed possibly from consecutive fragmentations of [z(n) + H](.+) ions. Although only the first few [M + H](.2+) species have been observed using this approach, these hydrogen-deficient radical cations produce fragment ions that have more structure-informative patterns and are very different from those formed during the low-energy tandem mass spectrometry of protonated peptides. PMID:16198598

  8. Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry.

    PubMed

    Falick, A M; Hines, W M; Medzihradszky, K F; Baldwin, M A; Gibson, B W

    1993-11-01

    High-energy collision-induced dissociation (CID) mass spectrometry provides a rapid and sensitive means for determining the primary sequence of peptides. The low-mass region (below mass 300) of a large number of tandem CID spectra of peptides has been analyzed. This mass region contains several types of informative fragment ions, including dipeptide ions, immonium ions, and other related ions. Useful low-mass ions are also present in negative-ion CID spectra. Immonium ions (general structure [H2N=CH-R](+), where R is the amino acid side chain) and related ions characteristic of specific amino acid residues give information as to the presence or absence of these residues in the peptide being analyzed. Tables of observed immonium and reiated ions for the 20 standard amino acids and for a number of modified amino acids are presented. A database consisting of 228 high-energy CID spectra of peptides has been established, and the frequency of occurrence of various ions indicative of specific ammo acid residues has been determined. Two model computer-aided schemes for analysis of the ammo-acid content of unknown peptides have been developed and tested against the database. PMID:24227532

  9. Three-body collision contributions to recombination and collision-induced dissociation. 1: Cross sections

    SciTech Connect

    Pack, R.T.; Walker, R.B.; Kendrick, B.K.

    1998-04-10

    Atomic and molecular recombination and collision-induced dissociation (CID) reactions comprise two of the most fundamental types of chemical reactions. They are important in all gas phase chemistry; for example, about half of the 196 reactions identified as important in combustion chemistry are recombination or CID reactions. Many of the current chemical kinetics textbooks and kinetics papers treat atomic and molecular recombination and CID as occurring only via sequences of two-body collisions. Actually, there is considerable evidence from experiment and classical trajectory calculations for contributions by true three-body collisions to the recombination of atomic and diatomic radicals, and that evidence is reviewed. Then, an approximate quantum method treating both two-body and three-body collisions simultaneously and on equal footing is used to calculate cross sections for the reaction Ne{sub 2} + H {rightleftharpoons} Ne + Ne + H. The results provide clear quantum evidence that direct three-body collisions do contribute significantly to recombination and CID.

  10. Collision-Induced Dissociation Cross Sections Relevant to Atmospheric Loss from Mars

    NASA Astrophysics Data System (ADS)

    Williamson, Hayley N.; Tully, Cathy; Johnson, Robert

    2015-11-01

    The flow onto an atmosphere of the solar wind plasma, a plasma trapped in a planetary magnetic field, or a local pick-up ion plasma produces chemistry, heating and atmospheric loss. These processes, which affect its evolution, are often lumped together as atmospheric sputtering (Johnson 1994). When the atmosphere near the exobase is atomic, then laboratory data, calculations or scaled models for the collision cross sections are usually available for use in Monte Carlo simulations of atmospheric sputtering. However, atmospheres on a number of planetary bodies have molecules at the exobase and in the corona for which cross section data is often not available. Of particular interest are studies of the atmosphere of Mars in which there can be are significant levels of CO2 and CO in the exobase region. Here we present new calculations using improved potential energy surfaces of collision-induced dissociation of incident O atoms (~10eV-1keV), formed by neutralization of pick-up O+ incident on CO and CO2 molecules and compare their importance to our earlier estimates (e.g., Johnson and Liu 1998; Johnson et al. 2002) and discuss their relevance to simulations of atmospheric loss from Mars.

  11. Effects of transition metal ion coordination on the collision-induced dissociation of polyalanines.

    PubMed

    Watson, Heather M; Vincent, John B; Cassady, Carolyn J

    2011-11-01

    Transition metal-polyalanine complexes were analyzed in a high-capacity quadrupole ion trap after electrospray ionization. Polyalanines have no polar amino acid side chains to coordinate metal ions, thus allowing the effects metal ion interaction with the peptide backbone to be explored. Positive mode mass spectra produced from peptides mixed with salts of the first row transition metals Cr(III), Fe(II), Fe(III), Co(II), Ni(II), Cu(I), and Cu(II) yield singly and doubly charged metallated ions. These precursor ions undergo collision-induced dissociation (CID) to give almost exclusively metallated N-terminal product ions whose types and relative abundances depend on the identity of the transition metal. For example, Cr(III)-cationized peptides yield CID spectra that are complex and have several neutral losses, whereas Fe(III)-cationized peptides dissociate to give intense non-metallated products. The addition of Cu(II) shows the most promise for sequencing. Spectra obtained from the CID of singly and doubly charged Cu-heptaalanine ions, [M + Cu - H](+) and [M + Cu](2+) , are complimentary and together provide cleavage at every residue and no neutral losses. (This contrasts with [M + H](+) of heptaalanine, where CID does not provide backbone ions to sequence the first three residues.) Transition metal cationization produces abundant metallated a-ions by CID, unlike protonated peptides that produce primarily b- and y-ions. The prominence of metallated a-ions is interesting because they do not always form from b-ions. Tandem mass spectrometry on metallated (Met = metal) a- and b-ions indicate that [b(n)  + Met - H](2+) lose CO to form [a(n)  + Met - H](2+), mimicking protonated structures. In contrast, [a(n)  + Met - H](2+) eliminate an amino acid residue to form [a(n-1)  + Met - H](2+), which may be useful in sequencing. PMID:22124980

  12. Appropriate choice of collision-induced dissociation energy for qualitative analysis of notoginsenosides based on liquid chromatography hybrid ion trap time-of-flight mass spectrometry.

    PubMed

    Wang, Guang-Ji; Fu, Han-Xu; Xiao, Jing-Cheng; Ye, Wei; Rao, Tai; Shao, Yu-Hao; Kang, Dian; Xie, Lin; Liang, Yan

    2016-04-01

    Liquid chromatography hybrid ion trap/time-of-flight mass spectrometry possessesd both the MS(n) ability of ion trap and the excellent resolution of a time-of-flight, and has been widely used to identify drug metabolites and determine trace multi-components for in natural products. Collision energy, one of the most important factors in acquiring MS(n) information, could be set freely in the range of 10%-400%. Herein, notoginsenosides were chosen as model compounds to build a novel methodology for the collision energy optimization. Firstly, the fragmental patterns of the representatives for the authentic standards of protopanaxadiol-type and protopanaxatriol-type notoginsenosides authentic standards were obtained based on accurate MS(2) and MS(3) measurements via liquid chromatography hybrid ion trap/time-of-flight mass spectrometry. Then the extracted ion chromatograms of characteristic product ions of notoginsenosides in Panax Notoginseng Extract, which were produced under a series of collision energies and, were compared to screen out the optimum collision energies values for MS(2) and MS(3). The results demonstrated that the qualitative capability of liquid chromatography hybrid ion trap/time-of-flight mass spectrometry was greatly influenced by collision energies, and 50% of MS(2) collision energy was found to produce the highest collision-induced dissociation efficiency for notoginsenosides. BesidesAddtionally, the highest collision-induced dissociation efficiency appeared when the collision energy was set at 75% in the MS(3) stage. PMID:27114315

  13. Understanding collision-induced dissociation of dofetilide: a case study in the application of density functional theory as an aid to mass spectral interpretation.

    PubMed

    Wright, Patricia; Alex, Alexander; Harvey, Sophie; Parsons, Teresa; Pullen, Frank

    2013-11-21

    Fragmentation of molecules under collision-induced dissociation (CID) conditions is not well-understood. This may make interpretation of MSMS spectra difficult and limit the effectiveness of software tools intended to aid mass spectral interpretation. Density Functional Theory (DFT) has been successfully applied to explain the thermodynamics of fragmentation in the gas phase by the modelling the effect that protonation has on the bond lengths (and hence bond strengths). In this study, dofetilide and four methylated analogues were used to investigate further the potential for using DFT to understand and predict the CID fragmentation routes. The products ions present in the CID spectra of all five compounds were consistent with charge-directed fragmentation, with protonation adjacent to the cleavage site being required to initiate fragmentation. Protonation at the dissociative site may have occurred either directly or via proton migration. A correlation was observed between protonation-induced bond lengthening and the bonds which were observed to break in the CID spectra. This correlation was quantitative in that the bonds calculated to elongate to the greatest extent gave rise to the most abundant of the major product ions. Thus such quantum calculations may offer the potential for contributing to a predictive tool for aiding the accuracy and speed mass spectral interpretation by generating numerical data in the form of bond length increases to act as descriptors flagging potential bond cleavages. PMID:24071718

  14. Hg+Br-->HgBr recombination and collision-induced dissociation dynamics.

    PubMed

    Shepler, Benjamin C; Balabanov, Nikolai B; Peterson, Kirk A

    2007-10-28

    A global potential energy surface has been constructed for the system HgBr+Ar-->Hg+Br+Ar to determine temperature dependent rate constants for the collision-induced dissociation (CID) and recombination of Hg and Br atoms. The surface was decomposed using a many-body expansion. Accurate two-body potentials for HgBr, HgAr, and ArBr were calculated using coupled cluster theory with single and double excitations and a perturbative treatment of triple excitations [CCSD(T)], as well as the multireference averaged coupled pair functional method. Correlation consistent basis sets were used to extrapolate to the complete basis set limit and corrections were included to account for scalar and spin-orbit relativistic effects, core-valence correlation, and the Lamb shift. The three-body potential was computed with the CCSD(T) method and triple-zeta quality basis sets. Quasiclassical trajectories using the final analytical potential surface were directly carried out on the CID of HgBr by Ar for a large sampling of initial rotational, vibrational, and collision energies. The recombination rate of Hg and Br atoms is a likely first step in mercury depletion events that have been observed in the Arctic troposphere during polar sunrise. The effective second order rate constant for this process was determined in this work from the calculated CID rate as a function of temperature using the principle of detailed balance, which resulted in k(T) = 1.2 x 10(-12) cm(3) molecule(-1) s(-1) at 260 K and 1 bar pressure. PMID:17979335

  15. Structural analysis of ruthenium-arene complexes using ion mobility mass spectrometry, collision-induced dissociation, and DFT.

    PubMed

    Czerwinska, Izabella; Far, Johann; Kune, Christopher; Larriba-Andaluz, Carlos; Delaude, Lionel; De Pauw, Edwin

    2016-04-21

    Ion mobility mass spectrometry (IM-MS) and collision-induced dissociation (CID) techniques were used to investigate the influence of the phosphine ligand on the physicochemical properties of [RuCl2(p-cymene)(PCy3)] (), [RuCl2(p-cymene)(PPh3)] (), and [RuCl2(p-cymene)(PTA)] () in the gas phase (PTA is 1,3,5-triaza-7-phosphaadamantane). Electrospray ionization of complexes and led to the corresponding [RuCl(p-cymene)(PR3)](+) ions via the dissociation of a chlorido ligand, whereas RAPTA-C () afforded two molecular ions by in-source oxidation ([Ru(III)Cl2(p-cymene)(PTA)](+)) or protonation ([RuCl2(p-cymene)(PTA+H)](+)). Control experiments showed that the balance between these two ionization paths was strongly influenced by the nature of the solvent used for infusion. Collision cross sections (CCSs) of the four molecular ions accurately reflected the variations of steric bulk inferred from the Tolman steric parameters (θ) of the phosphine ligands. Moreover, DFT calculations combined with a model based on the kinetic theory of gases (the trajectory method of the IMoS software) afforded reliable CCS predictions. The almost two times higher dipole moment of [RuCl2(p-cymene)(PTA+H)](+) (μ = 13.75 D) compared to [Ru(III)Cl2(p-cymene)(PTA)](+) (μ = 7.18 D) was held responsible for increased ion-induced dipole interactions with a polarizable drift gas such as N2. Further experiments with He and CO2 confirmed that increasing the polarizability of the buffer gas improved the separation between the two molecular ions derived from complex . The fragmentation patterns of complexes were determined by CID. The sequence of collision voltages at which 50% of a precursor ion dissociates (V50) recorded for the molecular ions derived from compounds was in good agreement with simple electronic considerations based on the donor strength of the phosphine ligand. Thus, the CCS and V50 parameters used to determine the shape and stability of ionic species in the gas phase are complementary

  16. Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

    SciTech Connect

    Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

    2013-09-01

    Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of multiply charged vanadium oxide cluster anions including VxOyn- and VxOyCln- ions (x = 1 − 14, y= 2 − 36, n = 1 − 3), protonated clusters, and ligand-bound VxOyn- species. These cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L= Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms. Accurate mass measurement using high-resolution mass spectrometry (m/∆m = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy(1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions generated from solution. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster ions originating directly from solution produced comparatively complex CID spectra. These results indicate that low-energy CID results in formation of stable cage-like structures of VxOyCl and VxOy anions. Furthermore, solution-phase synthesis of one precursor cluster combined with gas-phase CID is an efficient approach for the top-down synthesis of a wide range of multiply charged gas-phase metal oxide clusters for subsequent investigations of structure and reactivity.

  17. Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

    2013-09-01

    Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a

  18. Collision-Induced Dissociation Ion Mobility Mass Spectrometry for the Elucidation of Unknown Structures in Strained Polycyclic Aromatic Hydrocarbon Macrocycles.

    PubMed

    Zhang, Wen; Quernheim, Martin; Räder, Hans Joachim; Müllen, Klaus

    2016-01-01

    Structure determination of unexpected products obtained during synthesis of large carbon nanotube sidewall segments with more than 200 carbon atoms represents a challenging task for traditional analytical methods. Herein, we investigate a homologous series of four products having the same number of carbon atoms but slightly different hydrogen numbers ranging from 168 to 162. We demonstrate that the combination of mass spectrometry, ion mobility separation, and collision-induced dissociation (CID) can be used to finally elucidate the complete structures with high certainty. The postulated 1,2-phenyl shift as origin for the side reaction could be proven by changes in the minimum fragment sizes. A combination of CID and ion mobility spectrometry was applied for the first time to prove the cyclic nature of all molecules by the significant size increase upon ring opening. Thereby, also, more compact molecules were discovered in the gas phase with thus far unknown structures. Finally, the potential presence of numerous isomers could be ruled out by drift time measurements and molecular modeling together with theoretical collision cross-section (CCS) calculations. Surprisingly, only one defined structure could be assigned to each macrocycle in the homologous series, most likely as a result of natural selection rules driven by ring strain and steric hindrance. With a decreasing hydrogen content, the macrocycles undergo a stepwise transition from a cylindrical to conical shape. Overall, ion mobility mass spectrometry together with molecular modeling shows great potential to analyze unknown structures, especially in cases where structure determination by X-ray single-crystal analysis is not applicable. PMID:26613508

  19. Evidence for zinc ion sharing in metallothionein dimers provided by collision-induced dissociation

    NASA Astrophysics Data System (ADS)

    Afonso, Carlos; Hathout, Yetrib; Fenselau, Catherine

    2004-02-01

    Nanospray and collisionally-induced dissociation are used to evaluate the presence and absence of interstrand co-chelation of zinc ions in dimers of metallothionein. As was reported in a previous publication from this laboratory, co-chelation stabilizes the dimer to collisional activation, and facilitates asymmetrical zinc ion transfers during fragmentation. In the case of metallothionein, dimers of the holoprotein are found to share zinc ions, while dimers of metallothionein, in which one domain has been denatured, do not. Zinc ions are silent to most physicochemical probes, e.g., NMR and Mossbauer spectroscopies, and the capability of mass spectrometry to provide information on zinc complexes has widespread potential application in biochemistry.

  20. Energy-resolved collision-induced dissociation of non-covalent ions: charge- and guest-dependence of decomplexation reaction efficiencies.

    PubMed

    Carroy, Glenn; Lemaur, Vincent; De Winter, Julien; Isaacs, Lyle; De Pauw, Edwin; Cornil, Jérôme; Gerbaux, Pascal

    2016-05-14

    Supramolecular chemistry, and especially host-guest chemistry, has been the subject of great interest in the past few decades leading to the synthesis of host cage molecules such as calixarenes, cyclodextrins and more recently cucurbiturils. Mass spectrometry methods are increasingly used to decipher at the molecular level the non-covalent interactions between the different associated molecules. The present article illustrates that the association between mass spectrometry and computational chemistry techniques proves very complementary to depict the gas-phase dissociation processes of ionic non-covalent complexes when subjected to collisional activation. The selected system associates a nor-seco-cucurbit[10]uril bitopic receptor with different amino compounds (adamantylamine, para-xylylenediamine, and para-phenylenediamine). When subjected to CID experiments, the ternary complexes undergo fragmentation via dissociation of non-covalently bound partners. Interestingly, depending on their charge state, the collisionally excited complexes can selectively expel either a neutral guest molecule or a protonated guest molecule. Moreover, based on energy-resolved CID experiments, it is possible to evaluate the guest molecule dependence on the gas phase dissociation efficiency. We observed that the relative order of gas phase dissociation is charge state dependent, with the adamantylamine-containing complexes being the weakest when triply charged and the strongest when doubly charged. The energetics of the gas-phase dissociation reactions have been estimated by density functional theory (DFT) calculations. We succeeded in theoretically rationalizing the experimental collision-induced dissociation results with a special emphasis on: (i) the charge state of the expelled guest molecule and (ii) the nature of the guest molecule. PMID:27086657

  1. Formation and collision-induced dissociation of adduct ions [matrix + C]+ (C = Li, Na, Cs and NH4) produced under fast atom bombardment conditions

    NASA Astrophysics Data System (ADS)

    Takayama, Mitsuo

    1994-09-01

    The formation of adduct ions of matrices B with organic/metallic cations C+, [B + C]+ (C = Li, Na, Cs and NH4), under fast atom bombardment (FAB) conditions has been examined. The cation affinity (CA) for various matrix materials, glycerol, thioglycerol, dithiothreitol, m-nitrobenzylalcohol and diethanolamine, was evaluated from the positive-ion FAB mass spectra obtained for the salts LiCl, NaCl, CsCl or NH4Cl added to matrix B. The order of the CA of matrices for relatively small cations Li+ and Na+ was in accordance with that of the proton affinity (PA) of the matrices used. The collision-induced dissociation (CID) spectra of [B + H]+ and [B + C]+ ions have been obtained. The PA differences between matrix B and ammonia (NH3) molecules were roughly estimated from the CID spectra of [B + NH4]+ ions. The CID spectra of [B + C]+ ions, which have different dissociation windows from [B + H]+ ions, were analyzed by proposing multidentate-binding structures of the adduct ions. Some dissociations of [B + C]+ ions could be explained by charge-remote fragmentations. The results obtained suggest that the binding energy for the coordination complex (B...C+) can be evaluated from the CID patterns.

  2. Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

  3. Linkage Determination of Linear Oligosaccharides by MSn (n > 2) Collision-Induced Dissociation of Z1 Ions in the Negative Ion Mode

    NASA Astrophysics Data System (ADS)

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2013-12-01

    Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MSn, n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides 18O-labeled on the reducing carbonyl group gave rise to Z1 product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS3 CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z1 ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MSn CID (n = 3 - 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z1 ions. CID data of these Z1 ions were collected and compared with the standard database of Z1 ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

  4. Selective Production of Electrostatically-Bound Adducts of Alkyl Cations/Polyoxoanions by the Collision-Induced Fragmentations of Their Quaternary Ammonium Counterparts

    NASA Astrophysics Data System (ADS)

    Cao, Jie; Xu, Chong; Fan, YanXuan; Fan, LinYuan; Zhang, XiuHui; Hu, ChangWen

    2013-06-01

    Solutions of the quaternary ammonium salts of a set of classic polyoxometalates (POMs) (Keggin [XM12O40]n-, Dawson [P2W18O62]6-, and Lindqvist [M6O19]2- (X = P, Si; M = W, Mo) were characterized by electrospray mass spectrometry. The gas-phase fragmentations of a series of quaternary ammonium-associated clusters were investigated by their collision-induced dissociations to elucidate their fragmentation mechanisms. It was found that the quaternary ammonium-associated clusters had distinctive dissociation characteristics. Moreover, the mono-quaternary ammonium-associated clusters, {NR4[POMs]}(n-1)-, shared a common fragmentation feature, that is, they decomposed exclusively into their respective alkyl cation-bound clusters irrespective of the different cation sizes and the different natures of the polyoxoanions. The optimized geometries and the binding energies of the mono cation-bound Lindqvist POM-based clusters were obtained by calculations. To the best of our knowledge, this is the first investigation of the gas-phase fragmentations of these noncovalent complexes between organic amines and inorganic POM anions by a combination of theory and mass spectrometry.

  5. Oxidation of 2-propanol ligands during collision-induced dissociation of a gas-phase uranyl complex

    NASA Astrophysics Data System (ADS)

    van Stipdonk, Michael J.; Chien, Winnie; Anbalagan, Victor; Gresham, Garold L.; Groenewold, Gary S.

    2004-10-01

    We demonstrate, by way of multi-stage tandem mass spectrometry and extensive deuterium labeling, that 2-propanol is converted to acetone, and 2-propoxide to acetaldehyde, when monopositive 2-propanol-coordinated uranyl-ligand cations are subjected to collision-induced dissociation in the gas-phase environment of an ion trap mass spectrometer. A species with formula [(UO2OCH(CH3)2)(HOCH(CH3)2)]+, derived from dissociation of the gas-phase precursor [(UO2NO3)(HOCH(CH3)2)3]+ eliminates two H atoms and CH3 in consecutive stages to generate a monopositive complex composed of the U(V) species UO2+ coordinated by acetone and acetaldehyde, i.e. [UO2+(OC(CH3)2)(OC(H)CH3)]. Dissociation of this latter ion resulted in elimination of the two coordinating carbonyl ligands in two consecutive dissociation stages to leave UO2+. Analogous reactions were not observed for uranyl complexes containing 1-propanol or 2-methyl-2-propanol, or for cationic complexes with divalent metals such as Ni2+, Co2+, Pb2+ and Ca2+. One explanation for these reactions is bond insertion by the metal center in the bis-ligated uranyl complex, which would be expected to have an LUMO consisting of unoccupied 6d-orbitals that would confer transition metal-like behavior on the complex.

  6. Exploring Salt Bridge Structures of Gas-Phase Protein Ions using Multiple Stages of Electron Transfer and Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Zhe; Browne, Shaynah J.; Vachet, Richard W.

    2014-04-01

    The gas-phase structures of protein ions have been studied by electron transfer dissociation (ETD) and collision-induced dissociation (CID) after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Because ETD can break covalent bonds while minimally disrupting noncovalent interactions, we have investigated the ability of this dissociation technique together with CID to probe the sites of electrostatic interactions in gas-phase protein ions. By comparing spectra from ETD with spectra from ETD followed by CID, we find that several proteins, including ubiquitin, CRABP I, azurin, and β-2-microglobulin, appear to maintain many of the salt bridge contacts known to exist in solution. To support this conclusion, we also performed calculations to consider all possible salt bridge patterns for each protein, and we find that the native salt bridge pattern explains the experimental ETD data better than nearly all other possible salt bridge patterns. Overall, our data suggest that ETD and ETD/CID of native protein ions can provide some insight into approximate location of salt bridges in the gas phase.

  7. Exploring Salt Bridge Structures of Gas-Phase Protein Ions using Multiple Stages of Electron Transfer and Collision Induced Dissociation

    PubMed Central

    Zhang, Zhe; Browne, Shaynah J.; Vachet, Richard W.

    2014-01-01

    The gas-phase structures of protein ions have been studied by electron transfer dissociation (ETD) and collision-induced dissociation (CID) after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Because ETD can break covalent bonds while minimally disrupting non-covalent interactions, we have investigated the ability of this dissociation technique together with CID to probe the sites of electrostatic interactions in gas phase protein ions. By comparing spectra from ETD with spectra from ETD followed by CID, we find that several proteins, including ubiquitin, CRABP I, azurin, and β-2-microglobulin, appear to maintain many of the salt bridge contacts known to exist in solution. To support this conclusion, we also performed calculations to consider all possible salt bridge patterns for each protein, and we find that the native salt bridge pattern explains the experimental ETD data better than nearly all other possible salt bridge patterns. Overall, our data suggest that ETD and ETD/CID of native protein ions can provide some insight into approximate location of salt bridges in the gas phase. PMID:24496600

  8. An isomer-specific high-energy collision-induced dissociation MS/MS database for forensic applications: a proof-of-concept on chemical warfare agent markers.

    PubMed

    Subramaniam, Raja; Östin, Anders; Nygren, Yvonne; Juhlin, Lars; Nilsson, Calle; Åstot, Crister

    2011-09-01

    Spectra database search has become the most popular technique for the identification of unknown chemicals, minimizing the need for authentic reference chemicals. In the present study, an isomer-specific high-energy collision-induced dissociation (CID) MS/MS spectra database of 12 isomeric O-hexyl methylphosphonic acids (degradation markers of nerve agents) was created. Phosphonate anions were produced by the electrospray ionization of phosphonic acids or negative-ion chemical ionization of their fluorinated derivatives and were analysed in a hybrid magnetic-sector-time-of-flight tandem mass spectrometer. A centre-of-mass energy (E(com)) of 65 eV led to an optimal sequential carbon-carbon bond breakage, which was interpreted in terms of charge remote fragmentation. The proposed mechanism is discussed in comparison with the routinely used low-energy CID MS/MS. Even-mass (odd-electron) charge remote fragmentation ion series were diagnostic of the O-alkyl chain structure and can be used to interpret unknown spectra. Together with the odd-mass ion series, they formed highly reproducible, isomer-specific spectra that gave significantly higher database matches and probability factors (by 1.5 times) than did the EI MS spectra of the trimethylsilyl derivatives of the same isomers. In addition, ionization by negative-ion chemical ionization and electrospray ionization resulted in similar spectra, which further highlights the general potential of the high-energy CID MS/MS technique. PMID:21915956

  9. Tandem crossed-beam collision-induced dissociation of CO{sub 2}{sup +}

    SciTech Connect

    Chawla, R.; Krishnamurthy, M.; Shukla, A.K.

    1995-12-31

    Angle and energy resolved CID provides valuable information about energy transfer reaction mechanisms and role of excited states in activation and dissociation steps. Recent studies from this laboratory have demonstrated that electronic excitation is a prominent mechanism in low and moderate collision energy CID of certain molecules (acetone, nitromethane) but others (enol acetone, methane, propane, methyl nitrite) dissociate predominantly on the ground state hypersurface. A current focus of this research is angle and energy resolved CID studies of triatomic cations whose potential surfaces are relatively well described. They are a logical bridge between diatomics (which dissociate in a single vibration) and more complex polyatomics (which generally follow RRKM/QET delayed dissociation mechanisms). In the accompanying poster the authors develop a prompt dissociation kinematics model and demonstrate that CID of CS{sub 2}{sup +} is well described by this model. Although the structure and energetics of CO{sub 2}{sup +} are similar to CS{sub 2}{sup +}, the authors find rather different dissociation dynamics for the analogous O{sup +} and CO{sup +} products.

  10. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

    NASA Astrophysics Data System (ADS)

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

  11. Collision-induced dissociation pathways of anabolic steroids by electrospray ionization tandem mass spectrometry.

    PubMed

    Guan, Fuyu; Soma, Lawrence R; Luo, Yi; Uboh, Cornelius E; Peterman, Scott

    2006-04-01

    Anabolic steroids are structurally similar compounds, and their product-ion spectra obtained by tandem mass spectrometry under electrospray ionization conditions are quite difficult to interpret because of poly-ring structures and lack of a charge-retaining center in their chemical structures. In the present study, the fragmentation of nine anabolic steroids of interest to the racing industry was investigated by using triple quadrupole mass spectrometer, Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and a linear ion trap instrument. With the aid of an expert system software (Mass Frontier version 3.0), accurate mass measurements, and multiple stage tandem mass spectrometric (MS(n)) experiments, fragmentation pathways were elucidated for boldenone, methandrostenolone, tetrahydrogestrinone (THG), trenbolone, normethandrolone and mibolerone. Small differences in the chemical structures of the steroids, such as an additional double-bond or a methyl group, result in significantly different fragmentation pathways. The fragmentation pathways proposed in this paper allow interpretation of major product ions of other anabolic steroids reported by other researchers in a recent publication. The proposed fragmentation pathways are helpful for characterization of new steroids. The approach used in this study for elucidation of the fragmentation pathways is helpful in interpretation of complicated product-ion spectra of other compounds, drugs and their metabolites. PMID:16488153

  12. Accurate Mass MS/MS/MS Analysis of Siderophores Ferrioxamine B and E1 by Collision-Induced Dissociation Electrospray Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sidebottom, Ashley M.; Karty, Jonathan A.; Carlson, Erin E.

    2015-11-01

    Siderophores are bacterially secreted, small molecule iron chelators that facilitate the binding of insoluble iron (III) for reuptake and use in various biological processes. These compounds are classified by their iron (III) binding geometry, as dictated by subunit composition and include groups such as the trihydroxamates (hexadentate ligand) and catecholates (bidentate). Small modifications to the core structure such as acetylation, lipid tail addition, or cyclization, make facile characterization of new siderophores difficult by molecular ion detection alone (MS1). We have expanded upon previous fragmentation-directed studies using electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS/MS) and identified diagnostic MS3 features from the trihydroxamate siderophore class for ferrioxamine B and E1 by accurate mass. Diagnostic features for MS3 include C-C, C-N, amide, and oxime cleavage events with proposed losses of water and -CO from the iron (III) coordination sites. These insights will facilitate the discovery of novel trihydroxamate siderophores from complex sample matrices.

  13. Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap-High-Energy Collision Induced Dissociation MS(3) Scan.

    PubMed

    Liu, Jane M; Sweredoski, Michael J; Hess, Sonja

    2016-08-01

    The use of tandem mass tags (TMT) as an isobaric labeling strategy is a powerful method for quantitative proteomics, yet its accuracy has traditionally suffered from interference. This interference can be largely overcome by selecting MS(2) fragment precursor ions for high-energy collision induced dissociation (HCD) MS(3) analysis in an Orbitrap scan. While this approach minimizes the interference effect, sensitivity suffers due to the high AGC targets and long acquisition times associated with MS(3) Orbitrap detection. We investigated whether acquiring the MS(3) scan in a linear ion trap with its lower AGC target would increase overall quantification levels with a minimal effect on precision and accuracy. Trypsin-digested proteins from Saccharomyces cerevisiae were tagged with 6-plex TMT reagents. The sample was subjected to replicate analyses using either the Orbitrap or the linear ion trap for the HCD MS(3) scan. HCD MS(3) detection in the linear ion trap vs Orbitrap increased protein identification by 66% with minor loss in precision and accuracy. Thus, the use of a linear ion trap-HCD MS(3) scan during a 6-plex TMT experiment can improve overall identification levels while maintaining the power of multiplexed quantitative analysis. PMID:27377715

  14. Bioassay-directed fractionation for discovery of bioactive neutral lipids guided by relative mass defect filtering and multiplexed collision-induced dissociation

    PubMed Central

    Stagliano, Michael C.; DeKeyser, Joshua G.; Omiecinski, Curtis J.; Jones, A. Daniel

    2014-01-01

    We report a synergistic method using bioassay-directed liquid chromatography fractionation and time-of-flight mass spectrometry to guide and accelerate bioactive compound discovery. To steer purification and assays toward anticipated neutral lipid activators of a constitutive androstane receptor splice variant, a relative mass defect filter was calculated, based on the ratio of the mass defect to the measured ion mass, and used to reduce the number of candidate ion masses. Mass measurements often lack sufficient accuracy to provide unambiguous assignments of elemental compositions, and since the relative mass defect reflects fractional hydrogen content of ions, this value is largely determined by the hydrogen content of a compound’s biosynthetic precursors. A relative mass defect window ranging from 600–1000 ppm, consistent with an assortment of lipids, was chosen to assess the number of candidate ions in fractions of fetal bovine serum. This filter reduced the number of candidate ion m/z values from 1345 to 892, which was further reduced to 21 by intensity and isotope filtering. Accurate mass measurements from time-of-flight mass spectrometry and fragment ion masses generated using nonselective collision-induced dissociation suggested dioctyl phthalate as one of few neutral lipid constituents in the active fraction. The identity of this compound was determined to be di(2-ethylhexyl) phthalate using GC/MS, and it was ranked as a promising candidate for reporter assay screening. PMID:21080510

  15. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond.

    PubMed

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates. PMID:26297186

  16. Hydration Enthalpies of Ba(2+)(H2O)x, x = 1-8: A Threshold Collision-Induced Dissociation and Computational Investigation.

    PubMed

    Wheeler, Oscar W; Carl, Damon R; Hofstetter, Theresa E; Armentrout, P B

    2015-04-23

    The sequential bond dissociation energies (BDEs) of Ba(2+)(H2O)x complexes, where x = 1-8, are determined using threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer. The electrospray ionization source generates complexes ranging in size from x = 6 to x = 8 with smaller complexes, x = 1-5, formed by an in-source fragmentation technique. The only products observed result from sequential loss of water ligands. Charge separation, a process in which both hydrated singly charged barium hydroxide and hydronium ion are formed, was not observed except for Ba(2+)(H2O)3 yielding BaOH(+) + H5O2(+). Modeling of the kinetic energy-dependent cross sections, taking into account the number of collisions, energy distributions, and lifetime effects for both primary and secondary water loss, provides 0 K BDEs. Experimental thermochemistry for the x = 1-3 complexes is obtained here for the first time. Hydration enthalpies and reaction coordinate pathways for charge separation are also examined computationally at several levels of theory. Our experimental and computational work are in excellent agreement in the x = 1-6 range. The present experimental values and theoretical calculations are also in reasonable agreement with the available literature values for experiment, x = 4-8, and theory, x = 1-6. Of the numerous calculations performed in the current study, B3LYP/DHF/def2-TZVPP calculations including counterpoise corrections reproduce our experimental values the best, although MP2(full)/DHF/def2-TZVPP//B3LYP/DHF/def2-TZVPP results are comparable. PMID:25822138

  17. Combined use of ion mobility and collision-induced dissociation to investigate the opening of disulfide bridges by electron-transfer dissociation in peptides bearing two disulfide bonds.

    PubMed

    Massonnet, Philippe; Upert, Gregory; Smargiasso, Nicolas; Gilles, Nicolas; Quinton, Loïc; De Pauw, Edwin

    2015-01-01

    Disulfide bonds are post-translational modifications (PTMs) often found in peptides and proteins. They increase their stability toward enzymatic degradations and provide the structure and (consequently) the activity of such folded proteins. The characterization of disulfide patterns, i.e., the cysteine connectivity, is crucial to achieve a global picture of the active conformation of the protein of interest. Electron-transfer dissociation (ETD) constitutes a valuable tool to cleave the disulfide bonds in the gas phase, avoiding chemical reduction/alkylation in solution. To characterize the cysteine pairing, the present work proposes (i) to reduce by ETD one of the two disulfide bridges of model peptides, resulting in the opening of the cyclic structures, (ii) to separate the generated species by ion mobility, and (iii) to characterize the species using collision-induced dissociation (CID). Results of this strategy applied to several peptides show different behaviors depending on the connectivity. The loss of SH· radical species, observed for all the peptides, confirms the cleavage of the disulfides during the ETD process. PMID:25915795

  18. Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

    PubMed

    Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

    2016-08-31

    Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. PMID:27506355

  19. Studies on high-energy collision-induced dissociation of endogenous cannabinoids: 2-arachidonoylglycerol and n-arachidonoylethanolamide in FAB-mass spectrometry.

    PubMed

    Kasai, Hiroko F; Tsubuki, Masayoshi; Honda, Toshio

    2006-07-01

    Analysis of 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamide (anandamide) via alkali or alkaline earth metal-adduct high-energy collision-induced dissociation (CID) in fast-atom bombardment (FAB) ionization-mass spectrometry (MS) is described. The CID-MS/MS of the [2-AG+Li](+) or [2-AG+Na](+) ion undergoes charge-remote fragmentation (CRF), which is useful for the determination of the double-bond positions in the hydrocarbon chain, while the CID-MS/MS of the [2-AG-H+Cat](+) (Cat = Mg(2+), Ca(2+), Ba(2+)) ion provides an abundant fragment ion of the cationized arachidonic acid species, which is derived from cleaving the ester bond via a McLafferty-type rearrangement in addition to structurally informative CRF ions in small amounts. On the other hand, the CID-MS/MS spectra of anandamide cationized with both alkali metal (Li(+) or Na(+)) and alkaline earth metal (Mg(2+), Ca(2+), or Ba(2+)) show CRF patterns: the spectra obtained in lithium or sodium adduct are more clearly visible than those in magnesium, calcium, or barium adduct. The McLafferty rearrangement is not observed with metal-adduct anandamide. The characteristics in each mass spectrum are useful for the detection of these endogenous ligands. m-Nitrobenzyl alcohol (m-NBA) is the most suitable matrix. A lithium-adduct [2-AG+Li](+) or [anandamide+Li](+) ion is observed to be the most abundant in each mass spectrum, since the affinity of lithium for m-NBA is lower than that for other matrices examined. PMID:16837740

  20. Ion Mobility-Mass Spectrometry Reveals Highly-Compact Intermediates in the Collision Induced Dissociation of Charge-Reduced Protein Complexes

    NASA Astrophysics Data System (ADS)

    Bornschein, Russell E.; Niu, Shuai; Eschweiler, Joseph; Ruotolo, Brandon T.

    2016-01-01

    Protocols that aim to construct complete models of multiprotein complexes based on ion mobility and mass spectrometry data are becoming an important element of integrative structural biology efforts. However, the usefulness of such data is predicated, in part, on an ability to measure individual subunits removed from the complex while maintaining a compact/folded state. Gas-phase dissociation of intact complexes using collision induced dissociation is a potentially promising pathway for acquiring such protein monomer size information, but most product ions produced are possessed of high charge states and elongated/string-like conformations that are not useful in protein complex modeling. It has previously been demonstrated that the collision induced dissociation of charge-reduced protein complexes can produce compact subunit product ions; however, their formation mechanism is not well understood. Here, we present new experimental evidence for the avidin (64 kDa) and aldolase (157 kDa) tetramers that demonstrates significant complex remodeling during the dissociation of charge-reduced assemblies. Detailed analysis and modeling indicates that highly compact intermediates are accessed during the dissociation process by both complexes. Here, we present putative pathways that describe the formation of such ions, as well as discuss the broader significance of such data for structural biology applications moving forward.

  1. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

    PubMed

    Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

    2016-06-16

    Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

  2. Fast transient analysis and first-stage collision-induced dissociation with the flowing atmospheric-pressure afterglow ionization source to improve analyte detection and identification.

    PubMed

    Shelley, Jacob T; Hieftje, Gary M

    2010-04-01

    The recent development of ambient desorption/ionization mass spectrometry (ADI-MS) has enabled fast, simple analysis of many different sample types. The ADI-MS sources have numerous advantages, including little or no required sample pre-treatment, simple mass spectra, and direct analysis of solids and liquids. However, problems of competitive ionization and limited fragmentation require sample-constituent separation, high mass accuracy, and/or tandem mass spectrometry (MS/MS) to detect, identify, and quantify unknown analytes. To maintain the inherent high throughput of ADI-MS, it is essential for the ion source/mass analyzer combination to measure fast transient signals and provide structural information. In the current study, the flowing atmospheric-pressure afterglow (FAPA) ionization source is coupled with a time-of-flight mass spectrometer (TOF-MS) to analyze fast transient signals (<500 ms FWHM). It was found that gas chromatography (GC) coupled with the FAPA source resulted in a reproducible (<5% RSD) and sensitive (detection limits of <6 fmol for a mixture of herbicides) system with analysis times of ca. 5 min. Introducing analytes to the FAPA in a transient was also shown to significantly reduce matrix effects caused by competitive ionization by minimizing the number and amount of constituents introduced into the ionization source. Additionally, MS/MS with FAPA-TOF-MS, enabling analyte identification, was performed via first-stage collision-induced dissociation (CID). Lastly, molecular and structural information was obtained across a fast transient peak by modulating the conditions that caused the first-stage CID. PMID:20349535

  3. GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to (13)C-metabolic flux analysis of Escherichia coli central metabolism.

    PubMed

    Okahashi, Nobuyuki; Kawana, Shuichi; Iida, Junko; Shimizu, Hiroshi; Matsuda, Fumio

    2016-09-01

    Stable isotope labeling experiments using mass spectrometry have been employed to investigate carbon flow levels (metabolic flux) in mammalian, plant, and microbial cells. To achieve a more precise (13)C-metabolic flux analysis ((13)C-MFA), novel fragmentations of tert-butyldimethylsilyl (TBDMS)-amino acids were investigated by gas chromatography-tandem mass spectrometry (GC-MS/MS). The product ion scan analyses of 15 TBDMS-amino acids revealed 24 novel fragment ions. The amino acid-derived carbons included in the five fragment ions were identified by the analyses of (13)C-labeled authentic standards. The identification of the fragment ion at m/z 170 indicated that the isotopic abundance of S-methyl carbon in methionine could be determined from the cleavage of C5 in the precursor of [M-159](+) (m/z 218). It was also confirmed that the precision of (13)C-MFA in Escherichia coli central carbon metabolism could be improved by introducing (13)C-labeling data derived from novel fragmentations. Graphical Abstract Novel collision-induced dissociation fragmentations of tert-butyldimethylsilyl amino acids were investigated and identified by GC-MS/MS. PMID:27342798

  4. Dissociation and Memory Fragmentation in Posttraumatic Stress Disorder: An Evaluation of the Dissociative Encoding Hypothesis

    PubMed Central

    Bedard-Gilligan, Michele; Zoellner, Lori A.

    2012-01-01

    Several prominent theories of posttraumatic stress disorder (PTSD) posit that peritraumatic dissociation results in insufficient encoding of the trauma memory and that persistent dissociation prevents memory elaboration, resulting in memory fragmentation and PTSD. In this review, we summarize the empirical literature on peritraumatic and trait dissociation and trauma narrative fragmentation as measured by meta-memory and rater/objective coding. Across 16 studies to date, the association between dissociation and fragmentation was most prominent when examining peritraumatic dissociation and patient's own ratings of memory fragmentation. This relationship did not hold when examining trait dissociation or rater-coded or computer-generated measures of fragmentation. Thus, initial evidence points more toward a strong self-reported association between constructs that is not supported on more objective fragmentation coding. Measurement overlap, construct ambiguity, and exclusion of potential confounds may underlie lack of a strong association between dissociation and objective-rated fragmentation. PMID:22348400

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

    NASA Astrophysics Data System (ADS)

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

    1989-03-01

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

  6. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation.

    PubMed

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A; Lambrecht, Marlies A; Koehler, Peter; Delcour, Jan A

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

  7. Formation of y + 10 and y + 11 Ions in the Collision-Induced Dissociation of Peptide Ions

    NASA Astrophysics Data System (ADS)

    Kilpatrick, Lisa E.; Neta, Pedatsur; Yang, Xiaoyu; Simón-Manso, Yamil; Liang, Yuxue; Stein, Stephen E.

    2012-04-01

    Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we investigate a class of fragment ions corresponding to yn-1 + 10 and yn-1 + 11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences in mass of the y ion were ascribed before to the masses of [+ CO - H2O] and [+ CO - NH3], respectively. The mechanism is suggested to involve dissociation of the N-terminal residue at the CH-CO bond following loss of H2O or NH3. MS3 spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The yn-1 + 10 ion is most often found in peptides with N-terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The yn-1 + 11 ion is observed predominantly with histidine and asparagine at the N-terminus, but also occurs with asparagine in positions two through four. The intensities of the yn-1 + 10 ions decrease with increasing peptide length. These data for yn-1 + 10 and yn-1 + 11 ion formation may be used to improve peptide identification from tandem mass spectra.

  8. Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]{sup 2+} gas phase unimolecular reactivity via chemical dynamics simulations

    SciTech Connect

    Spezia, Riccardo; Salpin, Jean-Yves; Cimas, Alvaro; Gaigeot, Marie-Pierre; Song, Kihyung; Hase, William L.

    2012-07-01

    In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)]{sup 2+}, in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar{sup +} [Ca(urea)]{sup 2+} collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex. (authors)

  9. Axial spatial distribution focusing: improving MALDI-TOF/RTOF mass spectrometric performance for high-energy collision-induced dissociation of biomolecules

    PubMed Central

    Belgacem, O; Pittenauer, E; Openshaw, M E; Hart, P J; Bowdler, A; Allmaier, G

    2016-01-01

    Rationale For the last two decades, curved field reflectron technology has been used in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometers, assisting in the generation of post-source-decay (PSD) or collision-induced dissociation (CID) without decelerating precursor ions, producing true high-energy CID spectra. The result was the generation of product ion mass spectra with product ions typical of high-energy (10 keV and beyond) collision processes. The disadvantage of this approach was the lack of resolution in CID spectra resulting from the excess laser energy deposition used to generate those MS/MS spectra. The work presented in this study overcomes this limitation and includes comprehensive examples of high-energy and high-resolution CID MALDI-MS/MS spectra of biomolecules. Methods The devices used in this study are TOF/RTOF instruments equipped with a high-vacuum MALDI ion source. High-resolution and high-energy CID spectra result from the use of axial spatial distribution focusing (ASDF) in combination with curved field reflectron technology. Results A CID spectrum of the P14R1 peptide exhibits product ion resolution in excess of 10,000 (FWHM) but at the same time yields typical high-energy product ions such as w- and [y–2]-type ion series. High-energy CID spectra of lipids, exemplified by a glycerophospholipid and triglyceride, demonstrate C–C backbone fragmentation elucidating the presence of a hydroxyl group in addition to double-bond positioning. A complex high mannose carbohydrate (Man)8(GlcNAc)2 was also studied at 20 keV collision energy and revealed further high-energy product ions with very high resolution, allowing unambiguous detection and characterization of cross-ring cleavage-related ions. Conclusions This is the first comprehensive study using a MALDI-TOF/RTOF instrument equipped with a curved field reflectron and an ASDF device prior to the reflectron. © 2015 The Authors. Rapid Communications in

  10. Tailored Noise Waveform/ Collision-Induced Dissociation of Ions Stored in a Linear Ion Trap Combined with Liquid Chromatography/Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    SciTech Connect

    Vilkov, Andrey N.; Bogdanov, Bogdan; Pasa-Tolic, Liljiana; Prior, David C.; Anderson, Gordon A.; Masselon, Christophe D.; Moore, Ronald J.; Smith, Richard D.

    2004-11-01

    A new collision-induced dissociation (CID) technique based on broadband tailored noise waveform (TNW) excitation of ions stored in a linear ion trap has been developed. In comparison with the conventional sustained off-resonance irradiation (SORI) CID method commonly used in Fourier transform ion cyclotron resonance mass spectrometry, this MS/MS technique increases throughput by eliminating the long pump-down delay associated with gas introduction into the high vacuum ICR cell region. In addition, the TNW-CID method speeds spectrum acquisition since it does not require Fourier transformation, calculation of resonant frequencies and generation of the excitation waveforms. We demonstrate TNW-CID coupled with on-line capillary reverse phase liquid chromatography separations for identification of peptides. The experimental results are compared with data obtained using conventional quadrupole ion trap MS/MS and SORI-CID MS/MS in an ICR cell.

  11. Collision induced dissociation of CsI and Cs2I2 to ion pairs by Kr, Xe, and SF6

    NASA Astrophysics Data System (ADS)

    Parks, E. K.; Inoue, M.; Wexler, S.

    1982-02-01

    Absolute cross sections as functions of collision energy have been determined for collision induced dissociation of cesium iodide monomer and dimer to ion pairs. In these studies a beam of accelerated Xe, Kr, or SF6 projectiles was crossed with a thermal beam of cesium iodide. The partial cross sections for each product-ion channel were determined by time-of-flight mass spectrometry. For the rare gas-monomer collisions, the dependence of each partial cross section on the internal temperature of the CsI was also obtained. Collisions of Xe with CsI produced three-body dissociation as well as the formation of the molecular ions CsXe+ and IXe-. The formation of both the positive and negative molecular ions is primarily a reflection of the similar masses of Cs+ and I-, and was not observed in previously studied systems. For the same reason, Cs2I+ and CsI-2 resulting from collisions of Xe with Cs2I2 were formed with comparable intensities. At energies well above threshold, the total dissociation cross section for the rare gases colliding with CsI or Cs2I2 is large (≳10 Å2). Those for SF6 are approximately a factor of 5 smaller for the monomer, but only slightly smaller for the dimer. No ions containing SF6 were observed. The cross sections for three-body dissociation as well as molecular ion formation are relatively small in the region of the thermodynamic threshold (decreasing in the series Xe, Kr, and Ar). Analysis of the experimental results indicates that dissociation in this region only occurs for CsI molecules having considerable internal excitation, an effect related almost entirely to the projectile-target relative masses. A model which takes into account the coupling of internal motion with relative translational motion is shown to give an excellent description of the dissociation in the threshold region. Collinear trajectory calculations of the rare gases colliding with CsI were also performed in order to determine the threshold for dissociation as a

  12. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation

    PubMed Central

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A.; Koehler, Peter; Delcour, Jan A.

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

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

    PubMed

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

    2016-03-01

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

  14. Development and Optimization of an UPLC-QTOF-MS/MS Method Based on an In-Source Collision Induced Dissociation Approach for Comprehensive Discrimination of Chlorogenic Acids Isomers from Momordica Plant Species

    PubMed Central

    Madala, N. E.; Tugizimana, F.; Steenkamp, P. A.

    2014-01-01

    Chlorogenic acids (CGA) have been profiled in the leaves of Momordica balsamina, Momordica charantia, and Momordica foetida. All three species were found to contain the trans and cis isomers of 4-acyl para-coumaroylquinic acid (pCoQA), caffeoylquinic acid (CQA), and feruloylquinic acid (FQA). To the best of our knowledge, this is the first report of pCoQA and FQA and their cis isomers in these Momordica species. These profiles were obtained by a newly developed UPLC-qTOF-MS method based on the in-source collision induced dissociation (ISCID) method optimized to mimic the MS2 and MS3 fragmentation of an ion trap-based MS. The presence of the cis isomers is believed to be due to high UV exposure of these plants. Furthermore, the absence of the 3-acyl and 5-acyl CGA molecules points to a metabolic mark that is unusual and represents a very interesting biochemical phenotype of these species. Our optimized ISCID method was also shown to be able to distinguish between the geometrical isomers of all three forms of CGA, a phenomenon previously deemed impossible with other common mass spectrometry systems used for CGA analyses. PMID:25295221

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

    PubMed

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

    2015-03-14

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

  16. Structural determination of cerebrosides isolated from Asterias amurensis starfish eggs using high-energy collision-induced dissociation of sodium-adducted molecules.

    PubMed

    Park, Taeseong; Park, Young Seung; Rho, Jung-Rae; Kim, Young Hwan

    2011-03-15

    Six cerebrosides were isolated from the eggs of the starfish Asterias amurensis using solvent extraction, silica gel column chromatography, and reversed-phase high-performance liquid chromatography. This study demonstrated that the structures of cerebrosides could be completely characterized, based on their sodium-adducted molecules, using fast atom bombardment (FAB) tandem mass spectrometry. The high-energy collision-induced dissociation of the sodium-adducted molecule, [M + Na](+), of each cerebroside molecular species generated abundant ions, providing information on the compositions of the 2-hydroxy fatty acids and long-chain sphingoid bases, as well as the sugar moiety polar head group. Each homologous ion series along the fatty acid and aliphatic chain of the sphingoid base was useful for locating the double-bond positions of both chains and the methyl branching position of the long-chain base. The N-fatty acyl portions were primarily long-chain saturated or monoenoic acids (C16 to C24) with an α-hydroxy group. The sphingoid long-chain base portions were aliphatic chains (C18 or C22) with two or three degrees of unsaturation and with or without methyl branching. PMID:21290443

  17. Influence of Equilibration Time in Solution on the Inclusion/Exclusion Topology Ratio of Host-Guest Complexes Probed by Ion Mobility and Collision-Induced Dissociation.

    PubMed

    Carroy, Glenn; Daxhelet, Charlotte; Lemaur, Vincent; De Winter, Julien; De Pauw, Edwin; Cornil, Jérôme; Gerbaux, Pascal

    2016-03-18

    Host-guest complexes are formed by the creation of multiple noncovalent bonds between a large molecule (the host) and smaller molecule(s) or ion(s) (the guest(s)). Ion-mobility separation coupled with mass spectrometry nowadays represents an ideal tool to assess whether the host-guest complexes, when transferred to the gas phase upon electrospray ionization, possess an exclusion or inclusion nature. Nevertheless, the influence of the solution conditions on the nature of the observed gas-phase ions is often not considered. In the specific case of inclusion complexes, kinetic considerations must be taken into account beside thermodynamics; the guest ingression within the host cavity can be characterized by slow kinetics, which makes the complexation reaction kinetically driven on the timescale of the experiment. This is particularly the case for the cucurbituril family of macrocyclic host molecules. Herein, we selected para-phenylenediamine and cucurbit[6]uril as a model system to demonstrate, by means of ion mobility and collision-induced dissociation measurements, that the inclusion/exclusion topology ratio varies as a function of the equilibration time in solution prior to the electrospray process. PMID:26880721

  18. Studies on the collision-induced dissociation of adipoR agonists after electrospray ionization and their implementation in sports drug testing.

    PubMed

    Dib, Josef; Schlörer, Nils; Schänzer, Wilhelm; Thevis, Mario

    2015-02-01

    AdipoR agonists are small, orally active molecules capable of mimicking the protein adiponectin, which represents an adipokine with antidiabetic and antiatherogenic effects. Two adiponectin receptors were reported in the literature referred to as adipoR1 and adipoR2. Activation of these receptors stimulates mitochondrial biogenesis and results in an improved oxidative metabolism (via adipoR1) and increased insulin sensitivity (via adipoR2). Hence, adipoR agonists are potentially performance enhancing substances and targets of proactive and preventive anti-doping measures. In this study, two adipoR agonists termed AdipoRon and 112254 as well as two isotopically labeled internal standards (ISTDs) were synthesized in three-step reactions. The products were fully characterized by nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS) and density functional theory (DFT) computation. Collision-induced dissociation pathways following electrospray ionization were suggested based on the determined elemental compositions of product ions, comparison to product ions derived from labeled analogs (ISTDs), H/D-exchange experiments and the results of DFT calculations. The most abundant product ions were found at m/z 174, tentatively assigned to protonated 1-benzyl-1,2,3,4-tetrahydropyridine for AdipoRon, and m/z 207, suggested as protonated 1-(4-methoxybenzyl)piperazine, for 112254. Notably, the loss of the heterocyclic ring (i.e. piperazine and piperidine, respectively) in a supposedly intramolecular elimination reaction was observed in both cases. A qualitative determination of both AdipoR agonists in human plasma was established and fully validated for doping control purposes. Validation items such as recovery (86-89%), specificity, linearity, lower limit of detection (1 ng/ml), intraday (3-18%) and interday (5-16%) precision as well as ion suppression or enhancement were determined. Based on these findings adipoR agonists can be implemented in sports drug

  19. High-energy collision-induced dissociation of [M+Na]+ ions desorbed by fast atom bombardment of ceramides isolated from the starfish Distolasterias nipon.

    PubMed

    Yoo, Ji Sun; Park, Taeseong; Bang, Geul; Lee, Chulhyun; Rho, Jung-Rae; Kim, Young Hwan

    2013-02-01

    Ten ceramides and four cerebrosides were extracted from the starfish Distolasterias nipon by solvent extraction, silica gel column chromatography and reversed-phase high-performance liquid chromatography. Structural identification was conducted using tandem mass spectrometry of monosodiated ions desorbed by fast atom bombardment. The complete structures of four cerebrosides were determined by a previously reported method. The high-energy collision-induced dissociation (CID) spectral characteristics of ceramides with various structures depend on the number and positions of double bonds on both the N-acyl and sphingoid chains, the presence of a hydroxyl group or a double bond at the C-4 position of the sphingoid chain and the presence of an α-hydroxy group on the N-acyl chain. The high-energy CID of the monosodiated ion, [M+Na](+), of each ceramide molecular species generated abundant ions, providing information on the composition of the fatty acyl chains and sphingoid long-chain bases. Each homologous ion series along the fatty acyl group and aliphatic chain of the sphingoid base was used for locating the double-bond positions of both chains and hydroxyl groups on the sphingoid base chain. The double-bond positions were also confirmed by the m/z values of abundant allylic even- and odd-electron ions, and the intensity ratio of the T ion peak relative to the O ion peak. This technique could determine the complete structures of ceramides and cerebrosides in an extract mixture and has great potential for determining other sphingolipids isolated from various biological sources. PMID:23378088

  20. Unique pentafluorobenzylation and collision-induced dissociation for specific and accurate GC-MS/MS quantification of the catecholamine metabolite 3,4-dihydroxyphenylglycol (DHPG) in human urine.

    PubMed

    Zoerner, Alexander A; Heusser, Karsten; Gutzki, Frank M; Mitschke, Anja; Tank, Jens; Stichtenoth, Dirk O; Jordan, Jens; Tsikas, Dimitrios

    2011-05-15

    In the human body, the catecholamine norepinephrine is mainly metabolized to 3,4-dihydroxyphenylglycol (DHPG) which therefore serves as an important biomarker for norepinephrine's metabolism. Most data on DHPG concentrations in human plasma and urine has been generated by using HPLC-ECD or GC-MS technologies. Here, we describe a stable-isotope dilution GC-MS/MS method for the quantitative determination of DHPG in human urine using trideutero-DHPG (d(3)-DHPG) as internal standard and a two-step derivatization process with pentafluorobenzyl bromide (PFB-Br) and N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA). Two pentafluorobenzyl (PFB) trimethylsilyl (TMS) derivatives were obtained and identified, i.e., two isomeric DHPG-PFB-(TMS)(3) derivatives and the later eluting DHPG-tetrafluorobenzyl-(TMS)(2) derivative, i.e., DHPG-TFB-(TMS)(2). To our knowledge the DHPG-TFB-(TMS)(2) derivative and the underlying reaction have not been reported previously. In this reaction both vicinal aromatic hydroxyl groups of DHPG react with PFB-Br to form a heterocyclic seven-membered [1,4]dioxepin compound. The DHPG-TFB-(TMS)(2) derivative was used for quantitative GC-MS/MS analysis in the electron-capturing negative-ion chemical ionization mode by selected-reaction monitoring of m/z 351 from m/z 401 for DHPG and of m/z 352 from m/z 404 for d(3)-DHPG. Validation experiments on human urine samples spiked with DHPG in a narrow (0-33 nM) and a wide range (0-901 nM) revealed high recovery (86-104%) and low imprecision (RSD; 0.01-2.8%). LOD and relative LLOQ (rLLOQ) values of the method for DHPG were determined to be 76 amol and 9.4%, respectively. In urine of 28 patients suffering from chronic inflammatory rheumatic diseases, DHPG was measured at a mean concentration of 238 nM (38.3 μg/g creatinine). The DHPG concentration in the respective control group of 40 healthy subjects was measured to be 328 nM (39.2 μg/g creatinine). Given the unique derivatization reaction and collision-induced

  1. Studies of two-center three-electron S...S bonds in [n-Pr{sub 2}S...Sn-Pr{sub 2}]{sup +} and [i-Pr{sub 2}S...Si-Pr{sub 2}]{sup +}: Thermochemistry of adduct formation and MS/MS metastable and collision-induced dissociation spectra of the adducts

    SciTech Connect

    James, M.A.; Illies, A.J.

    1996-09-26

    Gas-phase ion-molecule association reactions of n-propyl sulfide radical cation ([n-Pr{sub 2}S]{sup +}) with n-propyl sulfide (n-Pr{sub 2}S) were studied by equilibrium methods in CO{sub 2} bath gas to investigate the bond energy of the 2c-3e bond. The 2c-3e S...S bond enthalpy in [n-Pr{sub 2}S...Sn-Pr{sub 2}]{sup +} was determined to be 119 kJ/mol at 507 K. This results in a scaled S...S bond energy of 123 kJ/mol. The S...S bond enthalpy in the i-propyl sulfide dimer cation ([i-Pr{sub 2}S...Si-Pr{sub 2}]{sup +}) could not be determined due to a fragmentation reaction, the loss of an i-propyl group. MS/MS metastable and collision-induced dissociation experiments were carried out to determine metastable fragmentation pathways and to aid in structure analysis. The results are consistent with association products containing 2c-3e bonds; statistical unimolecular metastable fragmentation of the association adduct, [i-Pr{sub 2}S...Si-Pr{sub 2}]{sup +}, confirms the loss of the i-propyl group, which prevented the equilibrium experiments. 21 refs., 11 figs., 1 tab.

  2. Electromagnetic Dissociation Cross Sections for High LET Fragments

    NASA Technical Reports Server (NTRS)

    Norbury, John

    2016-01-01

    Nuclear interaction cross sections are used in space radiation transport codes to calculate the probability of fragment emission in high energy nucleus-nucleus collisions. Strong interactions usually dominate in these collisions, but electromagnetic (EM) interactions can also sometimes be important. Strong interactions typically occur when the projectile nucleus hits a target nucleus, with a small impact parameter. For impact parameters larger than the sum of the nuclear radii, EM reactions dominate and the process is called electromagnetic dissociation (EMD) if one of the nuclei undergo fragmentation. Previous models of EMD have been used to calculate single proton (p) production, single neutron (n) production or light ion production, where a light ion is defined as an isotope of hydrogen (H) or helium (He), such as a deuteron (2H), a triton (3H), a helion (3He) or an alpha particle (4He). A new model is described which can also account for multiple nucleon production, such as 2p, 2n, 1p1n, 2p1n, 2p2n, etc. in addition to light ion production. Such processes are important to include for the following reasons. Consider, for example, the EMD reaction 56Fe + Al --> 52Cr + X + Al, for a 56Fe projectile impacting Al, which produces the high linear energy transfer (LET) fragment 52Cr. In this reaction, the most probable particles representing X are either 2p2n or 4He. Therefore, production of the high LET fragment 52Cr, must include the multiple nucleon production of 2p2n in addition to the light ion production of 4He. Previous models, such as the NUCFRG3 model, could only account for the 4He production process in this reaction and could not account for 2p2n. The new EMD model presented in this work accounts for both the light ion and multiple nucleon processes, and is therefore able to correctly account for the production of high LET products such as 52Cr. The model will be described and calculations will be presented that show the importance of light ion and multiple

  3. Improving Collision Induced Dissociation (CID), High Energy Collision Dissociation (HCD), and Electron Transfer Dissociation (ETD) Fourier Transform MS/MS Degradome-Peptidome Identifications Using High Accuracy Mass Information

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Purvine, Samuel O.; Smith, Richard D.

    2012-02-03

    Identification of peptides through analysis of peptide ion fragmentation mass spectra is key to proteomic/peptidomic studies. Advanced mass spectrometry has enabled measurement of peptide fragments with {approx}ppm mass error levels; however, mass accuracy has not been widely utilized in broad aspects of peptide identification. In this work we describe how peptide high-precision fragments measured with Fourier transform mass spectrometry can provide a powerful discriminative capability to distinguish true peptide 'hits' from possible incorrect peptides. For identification of peptides having multiple termini and carrying multiple charges, we show that the simple utilization of high-precision mass fragments information results in improved peptide analysis coverage and consistency, with coverage of >95% peptides identified totally from different spectral scoring and peptide statistic probability methods developed for moderate accuracy mass spectral peptide identification.

  4. Ultrasensitive characterization of site-specific glycosylation of affinity-purified haptoglobin from lung cancer patient plasma using 10 μm i.d. porous layer open tubular liquid chromatography-linear ion trap collision-induced dissociation/electron transfer dissociation mass spectrometry.

    PubMed

    Wang, Dongdong; Hincapie, Marina; Rejtar, Tomas; Karger, Barry L

    2011-03-15

    Site-specific analysis of protein glycosylation is important for biochemical and clinical research efforts. Glycopeptide analysis using liquid chromatography-collision-induced dissociation/electron transfer dissociation mass spectrometry (LC-CID/ETD-MS) allows simultaneous characterization of the glycan structure and attached peptide site. However, due to the low ionization efficiency of glycopeptides during electrospray ionization, 200-500 fmol of sample per injection is needed for a single LC-MS run, which makes it challenging for the analysis of limited amounts of glycoprotein purified from biological matrixes. To improve the sensitivity of LC-MS analysis for glycopeptides, an ultranarrow porous layer open tubular (PLOT) LC column (2.5 m × 10 μm i.d.) was coupled to a linear ion trap (LTQ) collision-induced dissociation/electron transfer dissociation mass spectrometer to provide sensitive analysis of N-linked protein glycosylation heterogeneity. The potential of the developed method is demonstrated by the characterization of site-specific glycosylation using haptoglobin (Hpt) as a model protein. To limit the amount of haptoglobin to low picomole amounts of protein, we affinity purified it from 1 μL of pooled lung cancer patient plasma. A total of 26 glycoforms/glycan compositions on three Hpt tryptic glycopeptides were identified and quantified from 10 LC-MS runs with a consumption of 100 fmol of Hpt digest (13 ng of protein, 10 fmol per injection). Included in this analysis was the determination of the glycan occupancy level. At this sample consumption level, the high sensitivity of the PLOT LC-LTQ-CID/ETD-MS system allowed glycopeptide identification and structure determination, along with relative quantitation of glycans presented on the same peptide backbone, even for low abundant glycopeptides at the ∼100 amol level. The PLOT LC-MS system is shown to have sufficient sensitivity to allow characterization of site-specific protein glycosylation from trace

  5. Fragment appearance energies in dissociative ionization of a sulfur hexafluoride molecule by electron impact

    NASA Astrophysics Data System (ADS)

    Demesh, Sh. Sh.; Zavilopulo, A. N.; Shpenik, O. B.; Remeta, E. Yu.

    2015-06-01

    Theoretical analysis of the fragment appearance energies corresponding to possible channels of formation of SF{/k +} fragments in dissociative ionization of the SF6 molecule by an electron impact is carried out. The total energies of neutral and ion molecular and atomic fragments are calculated using the theoretical methods of the GAMESS program complex. It is concluded that apart from dissociative ionization via autoionizing repulsive electronic states of the SF6 molecule, the excitation channels for SF{/k +} fragments and F2 molecules play a significant role, which leads to higher values of the observed fragment appearance energy as compared to theoretical values. The dependence of the energy corresponding to the formation of SF{/k +} c fragments on the number k of fluorine atoms is considered.

  6. 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.

  7. Affective Association: An Effective Intervention in Countering Fragmentation and Dissociation

    ERIC Educational Resources Information Center

    Hart, Carolyn

    2008-01-01

    This paper is concerned with the processes, both psychoanalytic and neuroscientific, involved in the undoing of dissociation in a 3-year-old, who was seen weekly over a nine month period. A neuroscientific and psychoanalytic developmental framework is used to follow a sequence of phenomena that emerged over the duration of relatively brief once…

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

    NASA Astrophysics Data System (ADS)

    Demesh, Shandor Sh.; Remeta, Eugene Yu.

    2015-07-01

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

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

    PubMed

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

    2015-05-01

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

  10. 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.

  11. Experimental and data analysis techniques for deducing collision-induced forces from photographic histories of engine rotor fragment impact/interaction with a containment ring

    NASA Technical Reports Server (NTRS)

    Yeghiayan, R. P.; Leech, J. W.; Witmer, E. A.

    1973-01-01

    An analysis method termed TEJ-JET is described whereby measured transient elastic and inelastic deformations of an engine-rotor fragment-impacted structural ring are analyzed to deduce the transient external forces experienced by that ring as a result of fragment impact and interaction with the ring. Although the theoretical feasibility of the TEJ-JET concept was established, its practical feasibility when utilizing experimental measurements of limited precision and accuracy remains to be established. The experimental equipment and the techniques (high-speed motion photography) employed to measure the transient deformations of fragment-impacted rings are described. Sources of error and data uncertainties are identified. Techniques employed to reduce data reading uncertainties and to correct the data for optical-distortion effects are discussed. These procedures, including spatial smoothing of the deformed ring shape by Fourier series and timewise smoothing by Gram polynomials, are applied illustratively to recent measurements involving the impact of a single T58 turbine rotor blade against an aluminum containment ring. Plausible predictions of the fragment-ring impact/interaction forces are obtained by one branch of this TEJ-JET method; however, a second branch of this method, which provides an independent estimate of these forces, remains to be evaluated.

  12. Energetics and Dynamics of Dissociation of Deprotonated Peptides: Fragmentation of Angiotensin Analogs

    SciTech Connect

    Laskin, Julia; Yang, Zhibo

    2011-12-01

    We present a first study of the energetics and dynamics of dissociation of deprotonated peptides using time- and collision-energy resolved surface-induced dissociation (SID) experiments. SID of four model peptides: RVYIHPF, HVYIHPF, DRVYIHPF, and DHVYIHPF was studied using a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for studying ion-surface collisions. Energy and entropy effects for the overall decomposition of the precursor ion were deduced by modeling the time- and collision energy-resolved survival curves using an RRKM based approach developed in our laboratory. The results were compared to the energetics and dynamics of dissociation of the corresponding protonated species. We demonstrate that acidic peptides are less stable in the negative mode because of the low threshold associated with the kinetically hindered loss of H2O from [M-H]- ions. Comparison between the two basic peptides indicates that the lower stability of the [M-H]- ion of RVYIHPF as compared to HVYIHPF towards fragmentation is attributed to the differences in fragmentation mechanisms. Specifically, threshold energy associated with losses of NH3 and NHCNH from RVYIHPF is lower than the barrier for backbone fragmentation that dominates gas-phase decomposition of HVYIHPF. The results provide a first quantitative comparison between the energetics and dynamics of dissociation of [M+H]+ and [M-H]- ions of acidic and basic peptides.

  13. Dissociative ionization at high laser intensities: importance of resonances and relaxation for fragmentation

    NASA Astrophysics Data System (ADS)

    Trushin, S. A.; Fuß, W.; Schmid, W. E.

    2004-10-01

    We investigated dissociative single and double ionization of the metal carbonyls Ni(CO)4, Fe(CO)5 and Cr(CO)6 in the gas phase by means of laser pulses of different durations (30-110 fs) and wavelengths (0.8 and 1.35 µm) at intensities of 2 × 1012-2 × 1014 W cm-2. The mass spectra show striking differences: for example, Fe(CO)5 strongly fragments at 0.8 µm but little at 1.35 µm, whereas for Ni(CO)4 fragmentation is higher at 1.35 µm than at 0.8 µm chromium carbonyl shows little fragmentation at both wavelengths. In other cases, fragmentation first decreases and then increases again with intensity. These and other phenomena, also published ones, can readily be understood from long-known principles, namely resonances in the parent ions, sometimes also in the neutral molecules, in particular if relaxations are also taken into account. We emphasize that fragmentation and ionization are two separate processes. We also point out that in the process of dissociative ionization in intense laser radiation, one should generally consider intermediate states, even if there is no one-photon resonance.

  14. Identifying fragment vuv excitations with dissociation channels from the strong-field ionization of N{sub 2}

    SciTech Connect

    Coffee, Ryan N.; Gibson, George N.

    2005-07-15

    Along with attosecond pulses comes a growing need for broadband amplification in the extreme ultraviolet spectral regime. Ultrafast laser pulses interacting with high symmetry molecules produce electronic excitations that are approaching this energy regime. Although there is some theoretical work regarding such excitation, experimental progress had been hampered in a fundamental way. Ion time-of-flight spectroscopy measures dissociation pathways but provides no specific information regarding the final state of the fragments. Vacuum-ultraviolet spectroscopy provides complete information about excited fragments but says nothing of the dissociation channel. In this paper we measure the internal states of nitrogen ion fragments and we associate them with specific dissociation pathways.

  15. Profiling monoterpenol glycoconjugation in Vitis vinifera L. cv. Muscat of Alexandria using a novel putative compound database approach, high resolution mass spectrometry and collision induced dissociation fragmentation analysis.

    PubMed

    Hjelmeland, Anna K; Zweigenbaum, Jerry; Ebeler, Susan E

    2015-08-01

    In this work we present a novel approach for the identification of plant metabolites using ultrahigh performance liquid chromatography coupled to accurate mass time-of-flight mass spectrometry. The workflow involves developing an in-house compound database consisting of exact masses of previously identified as well as putative compounds. The database is used to screen accurate mass spectrometry (MS) data to identify possible compound matches. Subsequent tandem MS data is acquired for possible matches and used for structural elucidation. The methodology is applied to profile monoterpene glycosides in Vitis vinifera cv. Muscat of Alexandria grape berries over three developmental stages. Monoterpenes are a subclass of terpenes, the largest class of plant secondary metabolites, and are found in two major forms in the plant, "bound" to one or more sugar moieties or "free" of said sugar moieties. In the free form, monoterpenes are noted for their fragrance and play important roles in plant defense and as attractants for pollinators. However, glycoconjugation renders these compounds odorless, and it is this form that the plant uses for monoterpene storage. In order to gain insight into monoterpene biochemistry and their fate in the plant an analysis of intact glycosides is essential. Eighteen monoterpene glycosides were identified including a monoterpene trisaccharide glycoside, which is tentatively identified here for this first time in any plant. Additionally, while previous studies have identified monoterpene malonylated glucosides in other grapevine tissue, we tentatively identify them for the first time in grape berries. This analytical approach can be readily applied to other plants and the workflow approach can also be used for other classes of compounds. This approach, in general, provides researchers with data to support the identification of putative compounds, which is especially useful when no standard is available. PMID:26320795

  16. Fast dissociation kinetics between individual E-cadherin fragments revealed by flow chamber analysis

    PubMed Central

    Perret, Emilie; Benoliel, Anne-Marie; Nassoy, Pierre; Pierres, Anne; Delmas, Véronique; Thiery, Jean-Paul; Bongrand, Pierre; Feracci, Hélène

    2002-01-01

    E-cadherin is the predominant adhesion molecule of epithelia. The interaction between extracellular segments of E-cadherin in the membrane of opposing cells is homophilic and calcium dependent. Whereas it is widely accepted that the specificity of the adhesive interaction is localized to the N-terminal domain, the kinetics of the recognition process are unknown. We report the first quantitative data describing the dissociation kinetics of individual E-cadherin interactions. Aggregation assays indicate that the two outermost domains of E-cadherin (E/EC1–2) retain biological activity when chemically immobilized on glass beads. Cadherin fragment trans-interaction was analysed using a flow chamber technique. Transient tethers had first-order kinetics, suggesting a unimolecular interaction. The unstressed lifetime of individual E-cadherin interactions was as brief as 2 s. A fast off rate and the low tensile strength of the E-cadherin bond may be necessary to support the high selectivity and plasticity of epithelial cell interactions. PMID:12032067

  17. Fragmentation of deprotonated d-ribose and d-fructose in MALDI--Comparison with dissociative electron attachment

    NASA Astrophysics Data System (ADS)

    Bald, Ilko; Flosadóttir, Helga D.; Kopyra, Janina; Illenberger, Eugen; Ingólfsson, Oddur

    2009-02-01

    We present a detailed, collaborative study on the fragmentation of deprotonated native d-ribose and d-fructose and the isotopically labelled 1-13C-d-ribose, 5-13C-d-ribose and C-1-d-d-ribose. The fragmentation is studied in a matrix assisted laser desorption/ionization time of flight mass spectrometer (MALDI ToF MS), both in in-source decay (ISD) and post-source decay (PSD) mode and compared with fragmentation through dissociative electron attachment (DEA). Fragmentation of deprotonated monosaccharides formed in the MALDI process, as well as their transient molecular anions formed upon electron attachment are characterized by loss of different numbers of H2O and CH2O units. Two different fragmentation pathways leading to cross-ring cleavage are identified. Metastable decay of deprotonated d-ribose proceeds either via an X-type cleavage yielding fragment anions at m/z = 119, 100 and 89, or via an A-type cleavage resulting in m/z = 89, 77 and 71. A fast and early metastable cross-ring cleavage of deprotonated d-ribose observed in in-source decay is dominated by X-type cleavage leading mainly to m/z = 100 and 71. For dissociative electron attachment to d-ribose a sequential dissociation was identified that includes metastable decay of the dehydrogenated molecular anion leading to m/z = 89. All other fragmentation reactions in DEA to d-ribose are likely to proceed directly and on a faster timescale (below 400 ns).

  18. Studies of negative ions by collision-induced decomposition and hydrogen-deuterium exchange techniques.

    PubMed Central

    Hunt, D F; Sethi, S K; Shabanowitz, J

    1980-01-01

    Development of two new techniques for studying the gas phase chemistry of negative ions is reported. Collision induced dissociation (CID) of (M-1)- ions has been accomplished in a newly constructed triple stage quadrupole mass spectrometer. This instrument was assembled by adding two additional Finnigan quadrupole mass filters to a Finnigan Model 3200 CI mass spectrometer. Generation of (M-1)- ions is accomplished by allowing OH- and sample to react under CI conditions in the ion source. The first quadrupole mass filter, Q1, is then employed to selectively pass the (M-1)- ion into a second quadrupole filter containing argon or neon at 10(-3) torr. On collision with the inert gas the (M-1)- ions dissociate into fragments which are then mass analyzed in the third quadrupole filter, CID spectra of (M-1)- ions from twelve carbonyl compounds are presented in this paper. Ion molecule isotope exchange reactions in the CI ion source can be used to count the number of hydrogen atoms in many different chemical environments. Collisions between sample (M-1)- ions and deuterium-labeled reagent gases (ND3, D2O, EtOD) facilitate incorporation of deuterium into the negative ion if the basicities of the sample and reagent anions are similar. Thus it is possible to selectively incorporate deuterium into many organic samples by controlling the exothermicity of the acid base, ion-molecule chemistry. PMID:7428745

  19. Postmortem changes in actomyosin dissociation, myofibril fragmentation and endogenous enzyme activities of grass carp (Ctenopharyngodon idellus) muscle.

    PubMed

    Wang, Daoying; Zhang, Muhan; Deng, Shaoying; Xu, Weimin; Liu, Yuan; Geng, Zhiming; Sun, Chong; Bian, Huan; Liu, Fang

    2016-04-15

    The changes of actomyosin, proteolytic activities and myofibril fragmentation during the postmortem aging of grass carp were studied. The study revealed dramatically increased actomyosin dissociation within 6 h of storage postmortem in grass carp, and it was associated with the drop of pH from 6.9 to 6.7, while liberated actin remained almost unchanged after 6 h postmortem. The myofibril fragmentation also increased significantly with the storage time in 6 h, and a highly positive correlation (P<0.01) existed between MFI and cathepsin B, D, H activities. The study indicated both actomyosin dissociation and cathepsin B, D, H played a role in postmortem tenderization and textural changes in grass carp. PMID:26616958

  20. Development and the fragmented self: longitudinal study of dissociative symptomatology in a nonclinical sample.

    PubMed

    Ogawa, J R; Sroufe, L A; Weinfield, N S; Carlson, E A; Egeland, B

    1997-01-01

    Dissociative behaviors and their relation to both the self and self-organization were examined using the developmental psychopathology perspective in a prospective longitudinal study of high-risk children. Participants were 168 young adults (n = 79 females, n = 89 males, age = 18-19 years) considered high-risk for poor developmental outcomes at birth due to poverty. The present study investigated whether trauma, sense of self, quality of early mother-child relationship, temperament, and intelligence were related to dissociative symptomatology measured at four times across 19 years. Findings were (a) age of onset, chronicity and severity of trauma were highly correlated and predicted level of dissociation; (b) both the avoidant and disorganized patterns of attachment were strong predictors of dissociation; (c) dissociation in childhood may be a more normative response to disruption and stress, while dissociation in adolescence and young adulthood may be more indicative of psychopathology; (d) preliminary support was found for a model proposed by G. Liotti that links disorganized attachment, later trauma, and dissociation in adulthood; and (e) strong support was found for N. Waller, F. W. Putnam, and E. B. Carlson's contention that psychopathological dissociation should not be viewed as the top end of a continuum of dissociative symptomatology, but as a separate taxon that represents an extreme deviation from normal development. PMID:9449009

  1. Effect of Basic Residue on the Kinetics of Peptide Fragmentation Examined Using Surface-Induced Dissociation Combined with Resonant Ejection

    SciTech Connect

    Laskin, Julia

    2015-11-30

    In this work, resonant ejection coupled with surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer is used to examine fragmentation kinetics of two singly protonated hexapeptides, RYGGFL and KYGGFL, containing the basic arginine residue and less basic lysine residue at the N-terminus. The kinetics of individual reaction channels at different collision energies are probed by applying a short ejection pulse (1 ms) in resonance with the cyclotron frequency of a selected fragment ion and varying the delay time between ion-surface collision and resonant ejection while keeping total reaction delay time constant. Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental data provides accurate threshold energies and activation entropies of individual reaction channels. Substitution of arginine with less basic lysine has a pronounced effect on the observed fragmentation kinetics of several pathways, including the b2 ion formation, but has little or no effect on formation of the b5+H2O fragment ion. The combination of resonant ejection SID, time- and collision energy-resolved SID, and RRKM modeling of both types of experimental data provides a detailed mechanistic understanding of the primary dissociation pathways of complex gaseous ions.

  2. Deprotonated purine dissociation: experiments, computations, and astrobiological implications.

    PubMed

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

    2015-01-15

    A central focus of astrobiology is the determination of abiotic formation routes to important biomolecules. The dissociation mechanisms of these molecules lend valuable insights into their synthesis pathways. Because of the detection of organic anions in the interstellar medium (ISM), it is imperative to study their role in these syntheses. This work aims to experimentally and computationally examine deprotonated adenine and guanine dissociation in an effort to illuminate potential anionic precursors to purine formation. Collision-induced dissociation (CID) products and their branching fractions are experimentally measured using an ion trap mass spectrometer. Deprotonated guanine dissociates primarily by deammoniation (97%) with minor losses of carbodiimide (HNCNH) and/or cyanamide (NH2CN), and isocyanic acid (HNCO). Deprotonated adenine fragments by loss of hydrogen cyanide and/or isocyanide (HCN/HNC; 90%) and carbodiimide (HNCNH) and/or cyanamide (NH2CN; 10%). Tandem mass spectrometry (MS(n)) experiments reveal that deprotonated guanine fragments lose additional HCN and CO, while deprotonated adenine fragments successively lose HNC and HCN. Every neutral fragment observed in this study has been detected in the ISM, highlighting the potential for nucleobases such as these to form in such environments. Lastly, the acidity of abundant fragment ions is experimentally bracketed. Theoretical calculations at the B3LYP/6-311++G(d,p) level of theory are performed to delineate the mechanisms of dissociation and analyze the energies of reactants, intermediates, transition states, and products of these CID processes. PMID:25559322

  3. A novel method for the analysis of the substitution pattern of O-methyl-[alpha]- and [beta]-1,4-glucans by means of electrospray ionisation-mass spectrometry/collision induced dissociation

    NASA Astrophysics Data System (ADS)

    Adden, Roland; Mischnick, Petra

    2005-03-01

    The substitution pattern of O-methyl amylose and O-methyl cellulose was analysed after per-O-methylation (Me-d3), and partial hydrolysis by subsequent ESI-MS/CID of the sodium (MS2) and the lithium adducts (MS3). Based on previous studies about the influence of regioselective O-methylation on the fragmentation pathways of malto- and cello-oligosaccharides, we could calculate the contribution of a certain methyl pattern to a distinct signal in the reproducible ESI-MS2 daughter spectrum. Signal intensities obtained from each O-methyl-O-methyl-d3 disaccharide were distributed on the corresponding methyl patterns and accumulated for all peaks of the mother mass spectrum. Data from ESI-MS2 were not sufficient for disaccharides bearing methyl and deuteromethyl groups in the combination 2 and 4, 3 and 3, or 4 and 2. Further independent information was obtained by ESI-MS3 of the lithium adducts. Monomer composition of methyl celluloses and methyl amyloses obtained by this novel approach were in very good agreement with reference data from GLC of the partially methylated glucitol acetates after complete hydrolysis, reduction and acetylation.

  4. The dynamic Auger Doppler effect in HF and DF: control of fragment velocities in femtosecond dissociation through photon energy detuning

    NASA Astrophysics Data System (ADS)

    Wiesner, K.; Naves de Brito, A.; Sorensen, S. L.; Burmeister, F.; Gisselbrecht, M.; Svensson, S.; Björneholm, O.

    2002-03-01

    The Auger-Doppler effect in the experimental spectra of HF and DF is presented, and the dynamics of ultra-fast dissociation in the core-excited state are discussed. The Doppler splitting of the atomic Auger peak is calculated and simulated using a classical model and a very good agreement is found between experiment and simulation. It is shown that the difference in photon energy relative to the resonance is transferred completely into the kinetic energy release (KER). This is expected to be a general phenomenon, but is clearly illuminated in the HF/DF case. Thus the fragment velocity can be controlled through photon energy detuning.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  6. HRMS studies on the fragmentation pathways of metallapentalyne

    NASA Astrophysics Data System (ADS)

    Lin, Zhiwei; Zhu, Congqing; Xia, Haiping

    2015-02-01

    The electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) using collision-induced dissociation (CID) method was applied to investigate the characteristic fragment ions of metalla-aromatic complexes for the first time. The fragmentation process of osmapentalyne, which contained metal-carbon triple bond in a five-membered ring, was discussed in detail. The ESI FT-ICR MS CID experimental results at high resolution mass spectra (HRMS) demonstrated the elemental composition of fragment ions unambiguously, thus a reasonable fragmentation pathway of osmapentalyne was proposed. In addition, the characteristic fragment ions have been investigated, which were specific and useful for the identification of some osmapentalynes complexes. These characteristic fragmentation pathways were helpful to analyze and interpret the stability and property of the parent ion. Also, this method could be used for the characterization of other organometallic complexes, especially containing characteristic isotopic peaks.

  7. New Approach for Studying Slow Fragmentation Kinetics in FT-ICR: Surface-Induced Dissociation Combined with Resonant Ejection

    SciTech Connect

    Laskin, Julia; Futrell, Jean H.

    2015-02-01

    We introduce a new approach for studying the kinetics of large ion fragmentation in the gas phase by coupling surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer with resonant ejection of selected fragment ions using a relatively short (5 ms) ejection pulse. The approach is demonstrated for singly protonated angiotensin III ions excited by collisions with a self-assembled monolayer of alkylthiol on gold (HSAM). The overall decomposition rate and rate constants of individual reaction channels are controlled by varying the kinetic energy of the precursor ion in a range of 65–95 eV. The kinetics of peptide fragmentation are probed by varying the delay time between resonant ejection and fragment ion detection at a constant total reaction time. RRKM modeling indicates that the shape of the kinetics plots is strongly affected by the shape and position of the energy deposition function (EDF) describing the internal energy distribution of the ion following ion-surface collision. Modeling of the kinetics data provides detailed information on the shape of the EDF and energy and entropy effects of individual reaction channels.

  8. Dissociation and Re-Aggregation of Multicell-Ensheathed Fragments Responsible for Rapid Production of Massive Clumps of Leptothrix Sheaths.

    PubMed

    Kunoh, Tatsuki; Nagaoka, Noriyuki; McFarlane, Ian R; Tamura, Katsunori; El-Naggar, Mohamed Y; Kunoh, Hitoshi; Takada, Jun

    2016-01-01

    Species of the Fe/Mn-oxidizing bacteria Leptothrix produce tremendous amounts of microtubular, Fe/Mn-encrusted sheaths within a few days in outwells of groundwater that can rapidly clog water systems. To understand this mode of rapid sheath production and define the timescales involved, behaviors of sheath-forming Leptothrix sp. strain OUMS1 were examined using time-lapse video at the initial stage of sheath formation. OUMS1 formed clumps of tangled sheaths. Electron microscopy confirmed the presence of a thin layer of bacterial exopolymer fibrils around catenulate cells (corresponding to the immature sheath). In time-lapse videos, numerous sheath filaments that extended from the periphery of sheath clumps repeatedly fragmented at the apex of the same fragment, the fragments then aggregated and again elongated, eventually forming a large sheath clump comprising tangled sheaths within two days. In this study, we found that fast microscopic fragmentation, dissociation, re-aggregation and re-elongation events are the basis of the rapid, massive production of Leptothrix sheaths typically observed at macroscopic scales. PMID:27490579

  9. Measuring fragmentation in dissociative identity disorder: the integration measure and relationship to switching and time in therapy

    PubMed Central

    Barlow, M. Rose; Chu, James A.

    2014-01-01

    Background Some people with dissociative identity disorder (DID) have very little communication or awareness among the parts of their identity, while others experience a great deal of cooperation among alternate identities. Previous research on this topic has been sparse. Currently, there is no empirical measure of integration versus fragmentation in a person with DID. In this study, we report the development of such a measure. Objective The goal of this study was to pilot the integration measure (IM) and to address its psychometric properties and relationships to other measures. The IM is the first standardized measure of integration in DID. Method Eleven women with DID participated in an experiment that included a variety of tasks. They filled out questionnaires about trauma and dissociation as well as the IM. They also provided verbal results about switching among alternate identities during the study sessions. Results Participants switched among identities an average of 5.8 times during the first session, and switching was highly correlated with trauma. Integration was related to switching, though this relationship may be non-linear. Integration was not related to time in psychotherapy. Conclusions The IM provides a useful beginning to quantify and study integration and fragmentation in DID. Directions for future research are also discussed, including expanding the IM from this pilot. The IM may be useful in treatment settings to assess progress or change over time. PMID:24396569

  10. Surface Induced Dissociation Yields Quaternary Substructure of Refractory Noncovalent Phosphorylase B and Glutamate Dehydrogenase Complexes

    NASA Astrophysics Data System (ADS)

    Ma, Xin; Zhou, Mowei; Wysocki, Vicki H.

    2014-03-01

    Ion mobility (IM) and tandem mass spectrometry (MS/MS) coupled with native MS are useful for studying noncovalent protein complexes. Collision induced dissociation (CID) is the most common MS/MS dissociation method. However, some protein complexes, including glycogen phosphorylase B kinase (PHB) and L-glutamate dehydrogenase (GDH) examined in this study, are resistant to dissociation by CID at the maximum collision energy available in the instrument. Surface induced dissociation (SID) was applied to dissociate the two refractory protein complexes. Different charge state precursor ions of the two complexes were examined by CID and SID. The PHB dimer was successfully dissociated to monomers and the GDH hexamer formed trimeric subcomplexes that are informative of its quaternary structure. The unfolding of the precursor and the percentages of the distinct products suggest that the dissociation pathways vary for different charge states. The precursors at lower charge states (+21 for PHB dimer and +27 for GDH hexamer) produce a higher percentage of folded fragments and dissociate more symmetrically than the precusors at higher charge states (+29 for PHB dimer and +39 for GDH hexamer). The precursors at lower charge state may be more native-like than the higher charge state because a higher percentage of folded fragments and a lower percentage of highly charged unfolded fragments are detected. The combination of SID and charge reduction is shown to be a powerful tool for quaternary structure analysis of refractory noncovalent protein complexes, as illustrated by the data for PHB dimer and GDH hexamer.

  11. Combustion pathways of the alkylated heteroaromatics: bond dissociation enthalpies and alkyl group fragmentations

    SciTech Connect

    Hayes, C.J.; Hadad, C.M.

    2009-11-15

    The bond dissociation enthalpies (BDEs) of the alkyl groups of the alkyl-substituted heterocycles have been studied and compiled using DFT methodology, with the intent of modeling the larger heterocyclic functionalities found in coal. DFT results were calibrated against CBS-QB3 calculations, and qualitative trends were reproduced between these methods. Loss of hydrogen at the benzylic position provided the most favorable route to radical formation, for both the azabenzenes and five-membered heterocycles. The ethyl derivatives had lower BDE values than the methyl derivatives due to increased stabilization of the corresponding radicals. Calculated spin densities correlated well with bond dissociation enthalpies for these compounds, while geometric effects were minimal with respect to the heterocycles themselves. Temperature effects on the bond dissociation enthalpies were minor, ranging by about 5 kcal/mol from 298 to 2000 K; the free energies of reaction dropped significantly over the same range due to entropic effects. Monocyclic heteroaromatic rings were seen to replicate the chemistry of multicyclic heteroaromatic systems.

  12. MALDI-TOF/TOF CID Study of Poly(1,4-dihydroxybenzene terephthalate) Fragmentation Reactions

    PubMed Central

    Gies, Anthony P.; Stow, Sarah M.; McLean, John A.; Hercules, David M.

    2015-01-01

    MALDI-TOF/TOF collision-induced dissociation (CID) experiments were conducted on model aromatic polyester oligomers. CID fragmentation studies identified initial fracture of the ester bond and subsequent CO loss as a major pathway, consistent with the general fragmentation mechanism used to explain the origin of poly(p-phenylenediamine terephthalamide) (PPD-T) fragment ions. Specifically, both charge-remote and charge-site fragmentation were observed. Different parent-ion species were observed, the major ones being carboxyl-hydroxyl, di-carboxyl, di-hydroxyl, and phenyl-carboxyl terminated. One species observed was hydroxyl-diethylamine terminated caused by reaction of carboxyl groups with triethylamine added to the synthesis reaction mixture. Fragment ions reflected the end groups of the parent oligomers. Some MALDI fragment-ion spectra were obtained for species showing exchange between Li and H at the carboxyl end group. Bond energy calculations provide further insight into suggested fragmentation mechanisms. PMID:26195848

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  14. Dissociation of CH4 by electron impact: Production of metastable hydrogen and carbon fragments

    NASA Technical Reports Server (NTRS)

    Finn, T. G.; Carnahan, B. L.; Zipf, E. C.

    1974-01-01

    Metastable fragments produced by electron impact excitation of CH4 have been investigated for incident electron energies from threshold to 300 eV. Only metastable hydrogen and carbon atoms were observed. Onset energies for the production of metastable hydrogen atoms were observed at electron impact energies of 22.0 + or - .5 eV, 25.5 + or - .6 eV, 36.7 + or - .6 eV and 66 + or - 3 eV, and at 26.6 + or - .6 eV for the production of metastable carbon atoms. Most of the fragments appear to have been formed in high-lying Rydberg states. The total metastable hydrogen cross section reaches a maximum value of approximately 1 X 10 to the minus 18th power sq cm at 100 eV. At the same energy, the metastable carbon cross section is 2 x 10 to the minus 19th power sq cm.

  15. Temperature dependence of the cross section for the fragmentation of thymine via dissociative electron attachment

    SciTech Connect

    Kopyra, Janina; Abdoul-Carime, Hassan

    2015-05-07

    Providing experimental values for absolute Dissociative Electron Attachment (DEA) cross sections for nucleobases at realistic biological conditions is a considerable challenge. In this work, we provide the temperature dependence of the cross section, σ, of the dehydrogenated thymine anion (T − H){sup −} produced via DEA. Within the 393-443 K temperature range, it is observed that σ varies by one order of magnitude. By extrapolating to a temperature of 313 K, the relative DEA cross section for the production of the dehydrogenated thymine anion at an incident energy of 1 eV decreases by 2 orders of magnitude and the absolute value reaches approximately 6 × 10{sup −19} cm{sup 2}. These quantitative measurements provide a benchmark for theoretical prediction and also a contribution to a more accurate description of the effects of ionizing radiation on molecular medium.

  16. Reliable Determination of Site-Specific In Vivo Protein N-Glycosylation Based on Collision-Induced MS/MS and Chromatographic Retention Time

    NASA Astrophysics Data System (ADS)

    Wang, Benlian; Tsybovsky, Yaroslav; Palczewski, Krzysztof; Chance, Mark R.

    2014-05-01

    Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures.

  17. Differentiation of Isomeric Ginsenosides by Using Electron-Induced Dissociation Mass Spectrometry.

    PubMed

    Wong, Y-L Elaine; Chen, Xiangfeng; Li, Wan; Wang, Ze; Hung, Y-L Winnie; Wu, Ri; Chan, T-W Dominic

    2016-06-01

    Current phytochemical research on ginsengs focuses on the structural characterization and isomer differentiation of ginsenosides. In this Letter, electron-induced dissociation (EID) was initially investigated by analyzing isomeric ginsenosides. EID provided more structural information on their differentiation than collision-induced dissociation (CID) did. Glycosyl group migration previously observed in the CID of oligosaccharide ions could also be found in the EID of protonated Rg1. This rearrangement reaction would show substantial ambiguities in differentiating Rg1 from Rf. Although other charge carriers could alleviate this problem, the use of EID in dissociating deprotonated ginsenoside ions was superior to other techniques in terms of eliminating glycosyl group migration and generating diagnostic fragment ions for the differentiation of structural isomers. This study demonstrates a potential method to analyze natural products and thus help discover and evaluate novel compounds. PMID:27181402

  18. Surface induced dissociation yields substructure of Methanosarcina thermophila 20S proteasome complexes

    PubMed Central

    Ma, Xin; Loo, Joseph A.; Wysocki, Vicki H.

    2015-01-01

    Native mass spectrometry (MS) and surface induced dissociation (SID) have been applied to study the stoichiometry and quaternary structure of non-covalent protein complexes. In this study, Methanosarcina thermophila 20S proteasome, which consists of four stacked heptameric rings (α7β7β7α7 symmetry), has been selected to explore the SID dissociation pattern of a complicated stacked ring protein complex. SID produces both α and β subunits while collision induced dissociation (CID) produces only highly charged α subunit. In addition, the charge reduced 20S proteasome produces the α7β7 fragment, reflecting the stacked ring topology of the complex. The combination of SID and charge reduction is shown to be a powerful tool for the study of protein complex structure. PMID:26005366

  19. Nonthermal rotational distribution of CO/A 1Pi/ fragments produced by dissociative excitation of CO2 by electron impact. [in Mars atmosphere

    NASA Technical Reports Server (NTRS)

    Mumma, M. J.; Stone, E. J.; Zipf, E. C.

    1975-01-01

    Measurements were made of the rotational profiles of specific bands of the CO fourth-positive group (4PG). The CO 4PG bands were excited by electron impact dissociative excitation of CO2. The results are applicable to analysis of the Mariner observations of the CO 4PG in the dayglow of Mars. The results indicate that dissociative excitation of CO2 by electron impact leads to CO(A 1Pi) fragments with a rotational distribution that is highly nonthermal. The parent CO2 temperature was about 300 K in the experiment, while the fragment CO(A 1Pi) showed emission band profiles consistent with a rotational temperature greater than about 1500 K. Laboratory measurement of the reduced transmission of the hot bands by thermal CO appears to be the most direct way of determining the column density responsible for the CO(v',0) absorption of Mars.

  20. Photo and Collision Induced Isomerization of a Cyclic Retinal Derivative: An Ion Mobility Study.

    PubMed

    Coughlan, Neville J A; Scholz, Michael S; Hansen, Christopher S; Trevitt, Adam J; Adamson, Brian D; Bieske, Evan J

    2016-09-01

    A cationic degradation product, formed in solution from retinal Schiff base (RSB), is examined in the gas phase using ion mobility spectrometry, photoisomerization action spectroscopy, and collision induced dissociation (CID). The degradation product is found to be N-n-butyl-2-(β-ionylidene)-4-methylpyridinium (BIP) produced through 6π electrocyclization of RSB followed by protonation and loss of dihydrogen. Ion mobility measurements show that BIP exists as trans and cis isomers that can be interconverted through buffer gas collisions and by exposure to light, with a maximum response at λ = 420 nm.Graphical Abstract. PMID:27278825

  1. Photo and Collision Induced Isomerization of a Cyclic Retinal Derivative: An Ion Mobility Study

    NASA Astrophysics Data System (ADS)

    Coughlan, Neville J. A.; Scholz, Michael S.; Hansen, Christopher S.; Trevitt, Adam J.; Adamson, Brian D.; Bieske, Evan J.

    2016-06-01

    A cationic degradation product, formed in solution from retinal Schiff base (RSB), is examined in the gas phase using ion mobility spectrometry, photoisomerization action spectroscopy, and collision induced dissociation (CID). The degradation product is found to be N-n-butyl-2-(β-ionylidene)-4-methylpyridinium (BIP) produced through 6π electrocyclization of RSB followed by protonation and loss of dihydrogen. Ion mobility measurements show that BIP exists as trans and cis isomers that can be interconverted through buffer gas collisions and by exposure to light, with a maximum response at λ = 420 nm.

  2. Photo and Collision Induced Isomerization of a Cyclic Retinal Derivative: An Ion Mobility Study

    NASA Astrophysics Data System (ADS)

    Coughlan, Neville J. A.; Scholz, Michael S.; Hansen, Christopher S.; Trevitt, Adam J.; Adamson, Brian D.; Bieske, Evan J.

    2016-09-01

    A cationic degradation product, formed in solution from retinal Schiff base (RSB), is examined in the gas phase using ion mobility spectrometry, photoisomerization action spectroscopy, and collision induced dissociation (CID). The degradation product is found to be N- n-butyl-2-(β-ionylidene)-4-methylpyridinium (BIP) produced through 6π electrocyclization of RSB followed by protonation and loss of dihydrogen. Ion mobility measurements show that BIP exists as trans and cis isomers that can be interconverted through buffer gas collisions and by exposure to light, with a maximum response at λ = 420 nm.

  3. Anionic derivatives of uracil: fragmentation and reactivity.

    PubMed

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

    2014-09-01

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

  4. Effects of molecular rotation after ionization and prior to fragmentation on observed recoil-frame photoelectron angular distributions in the dissociative photoionization of nonlinear molecules

    NASA Astrophysics Data System (ADS)

    López-Domínguez, Jesús A.; Lucchese, Robert R.

    2016-03-01

    Experimental angle-resolved photoelectron-photoion coincidence experiments measure photoelectron angular distributions (PADs) in dissociative photoionization (DPI) in the reference frame provided by the momenta of the emitted heavy fragments. By extension of the nomenclature used with DPI of diatomic molecules, we refer to such a PAD as a recoil-frame PAD (RFPAD). When the dissociation is fast compared to molecular rotational and bending motions, the emission directions of the heavy fragments can be used to determine the orientation of the bonds that are broken in the DPI at the time of the ionization, which is known as the axial-recoil approximation (ARA). When the ARA is valid, the RFPADs correspond to molecular-frame photoelectron angular distributions (MFPADs) when the momenta of a sufficient number of the heavy fragments are determined. When only two fragments are formed, the experiment cannot measure the orientation of the fragments about the recoil axes so that the resulting measured PAD is an azimuthally averaged RFPAD (AA-RFPAD). In this study we consider how the breakdown of the ARA due to rotation will modify the observed RFPADs for DPI processes in nonlinear molecules for ionization by light of arbitrary polarization. This model is applied to the core C 1 s DPI of CH4, with the results compared to experimental measurements and previous theoretical calculations done within the ARA. The published results indicate that there is a breakdown in the ARA for two-fragment events where the heavy-fragment kinetic energy release was less than 9 eV. Including the breakdown of the ARA due to rotation in our calculations gives very good agreement with the experimental AA-RFPAD, leading to an estimate of upper bounds on the predissociative lifetimes as a function of the kinetic energy release of the intermediate ion states formed in the DPI process.

  5. Measurements of the Coulomb dissociation cross section of 156 MeV sup 6 Li projectiles at extremely low relative fragment energies of astrophysical interest

    SciTech Connect

    Kiener, J.; Gils, H.J.; Rebel, H.; Zagromski, S.; Gsottschneider, G.; Heide, N.; Jelitto, H.; Wentz, J. ); Baur, G. )

    1991-11-01

    Coulomb dissociation of light nuclear projectiles in the electric field of heavy target nuclei has been experimentally investigated as an alternative access to radiative capture cross sections at low relative energies of the fragments, which are of astrophysical interest. As a pilot experiment the breakup of 156 MeV {sup 6}Li projectiles at {sup 208}Pb with small emission angles of the {alpha} particle and deuteron fragments has been studied. Both fragments were coincidentally detected in the focal plane of a magnetic spectrograph at several reaction angles well below the grazing angle and with relative angles between the fragments of 0{degree}--2{degree}. The experimental cross sections have been analyzed on the basis of the Coulomb breakup theory. The results for the resonant breakup give evidence for the strong dominance of the Coulomb dissociation mechanism and the absence of nuclear distortions, while the cross section for the nonresonant breakup follows theoretical predictions of the astrophysical {ital S} factor and extrapolations of corresponding radiative capture reaction cross section to very low c.m. energies of the {alpha} particle and deuteron. Various implications of the approach are discussed.

  6. Dissociation reactions of protonated anthracycline antibiotics following electrospray ionization-tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Sleno, Lekha; Campagna-Slater, Valerie; Volmer, Dietrich A.

    2006-09-01

    Fragmentation pathways of doxorubicin, a common cancer therapy agent, and three closely related analogs (epirubicin, daunorubicin, idarubicin) were compared using electrospray ionization with tandem mass spectrometry. This class of antibiotics with anti-tumour activity has important structural features, with a tetracyclic aromatic, polyketide portion, which is glycosylated with an amino sugar in order to exhibit its biological activity. Collision-induced dissociation spectra revealed very similar product ions for each analog, however, important differences were seen in the relative abundances and the ease at which certain fragments were formed. Fragment ions observed included those from cleavage of the glycosidic bond, loss of the side chain from the aglycone moiety, water losses and loss of a methyl radical. Following cleavage of the glycosidic bond, the charge can either reside on the aglycone portion or the sugar moiety, and each of these primary fragments undergoes several secondary dissociation pathways, depending on the collision energy. By ramping the collision voltage, we were able to correlate the changes in fragmentation behavior with small alterations in the structure of the precursor ion. The detailed study of the fragmentation behavior of doxorubicin was supported by accurate mass measurements, using an electrospray-time of flight instrument, as well as MS3 data from a quadrupole-linear ion trap mass spectrometer. Computational studies were also performed to help explain the role of certain functional groups in the fragmentation reactions.

  7. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

    PubMed Central

    Vaniya, Arpana

    2015-01-01

    Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations. PMID:26213431

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

    PubMed

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

    2016-03-01

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

  9. 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.

  10. Detailed glycan structural characterization by electronic excitation dissociation.

    PubMed

    Yu, Xiang; Jiang, Yan; Chen, Yajie; Huang, Yiqun; Costello, Catherine E; Lin, Cheng

    2013-11-01

    The structural complexity and diversity of glycans parallel their multilateral functions in living systems. To better understand the vital roles glycans play in biological processes, it is imperative to develop analytical tools that can provide detailed glycan structural information. This was conventionally achieved by multistage tandem mass spectrometry (MS(n)) analysis using collision-induced dissociation (CID) as the fragmentation method. However, the MS(n) approach lacks the sensitivity and throughput needed to analyze complex glycan mixtures from biological sources, often available in limited quantities. We define herein the critical parameters for a recently developed fragmentation technique, electronic excitation dissociation (EED), which can yield rich structurally informative fragment ions during liquid chromatographic (LC)-MS/MS analysis of glycans. We further demonstrate that permethylation, reducing end labeling and judicious selection of the metal charge carrier, can greatly facilitate spectral interpretation. With its high sensitivity, throughput, and compatibility with online chromatographic separation techniques, EED appears to hold great promise for large-scale glycomics studies. PMID:24080071

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  13. 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.

  14. Trajectory study of energy transfer and unimolecular dissociation of highly excited allyl with argon.

    PubMed

    Conte, Riccardo; Houston, Paul L; Bowman, Joel M

    2014-09-11

    The influence of rotational excitation on energy transfer in single collisions of allyl with argon and on allyl dissociation is investigated. About 90,000 classical scattering simulations are performed in order to determine collision-induced changes in internal energy and in allyl rotational angular momentum. Dissociation is studied by means of about 50,000 additional trajectories evolved for the isolated allyl under three different conditions: allyl with no angular momentum (J = 0); allyl with the same microcanonically sampled initial conditions used for the collisions (J*); allyl evolving from the corresponding exit conditions after the collision. The potential energy surface is the sum of an intramolecular potential and an interaction one, and it has already been used in a previous work on allyl-argon scattering (Conte, R.; Houston, P. L.; Bowman, J. M. J. Phys. Chem. A 2013, 117, 14028-14041). Energy transfer data show that increased initial rotation favors, on average, increased relaxation of the excited molecule. The availability of a high-level intramolecular potential energy surface permits us to study the dependence of energy transfer on the type of starting allyl isomer. A turning point analysis is presented, and highly efficient collisions are detected. Collision-induced variations in the allyl rotational angular momentum may be quite large and are found to be distributed according to three regimes. The roles of rotational angular momentum, collision, and type of isomer on allyl unimolecular dissociation are considered by looking at dissociations times, kinetic energies of the fragments, and branching ratios. Generally, rotational angular momentum has a strong influence on the dissociation dynamics, while the single collision and the type of starting isomer are less influential. PMID:25116695

  15. Fragmentation reactions of deprotonated peptides containing proline. The proline effect.

    PubMed

    Harrison, Alex G; Young, Alex B

    2005-09-01

    The collision-induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS(2) and MS(3) experiments, deuterium labelling and accurate mass measurements when necessary. The [M--H--CO(2)](-) (a(2)) ion derived from H-Pro-Xxx-OH dipeptides shows an unusual fragmentation involving loss of C(2)H(4); this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with an N-terminal proline are formation of a(3) and y(1) ions. When proline is in the central position of tripeptides, a(3), y(2) and y(1) ions are the primary fragmentation products of [M--H](-), while when the proline is in the C-terminal position, a(3)and y(1) ions are the major primary products. In the latter case, the a(3) ion fragments primarily to the ''b(2) ion; further evidence is presented that the ''b(2) ions have a deprotonated oxazolone structure. Larger deprotonated peptides having at least two amino acid residues N-terminal to proline show a distinct preference for cleavage of the amide bond N-terminal to proline to form, mainly, the appropriate y ion. This proline effect is compared and contrasted with the similar proline effect observed in the fragmentation of protonated peptides containing proline. PMID:16041740

  16. Electron capture dissociation mass spectrometry of metallo-supramolecular complexes.

    PubMed

    Kaczorowska, Malgorzata A; Hotze, Anna C G; Hannon, Michael J; Cooper, Helen J

    2010-02-01

    The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe(2)L(3)(4+) ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu(I) or Ag(I). The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS(3) of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu(I) and Ag(I) complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe(I)(2)L(2)(2+) and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution. PMID:20004114

  17. EVALUATION OF THE EXPERIMENTAL PARAMETERS WHICH CONTROL ELECTRON DETACHMENT DISSOCIATION, AND THEIR EFFECT ON THE FRAGMENTATION EFFICIENCY OF GLYCOSAMINOGLYCAN CARBOHYDRATES

    PubMed Central

    Leach, Franklin E.; Wolff, Jeremy J.; Laremore, Tatiana N.; Linhardt, Robert J.; Amster, I. Jonathan

    2008-01-01

    The efficiency of conversion of precursor ions to observable products for electron detachment dissociation (EDD) was measured as a function of the key experimental parameters to determine their optimal values for the Fourier transform mass spectrometry analysis of anionic glycosaminoglycan carbohydrates. These parameters include electron current, electron energy, dispenser cathode heater current, electron beam duration, charge state of the precursor ion, oligomer length, and precursor ion number accumulated in an external radio frequency multipole trap. Precursor conversion is most efficient at an electron current of 15 µA, and decreases at higher and lower values. The conversion of precursor to product ions increases in efficiency as the electron pulse duration is increased. Together, these data suggest that a radially repulsive electric field is produced between the electron beam and negative ions during EDD which causes the reaction cross section to decrease at higher values of electron current (>15 µA). Elevating the heater current of the dispenser cathode increases the electron flux, but also causes ion activation, presumably by blackbody infrared irradiation. An electronic circuit is described that allows the electron current produced by the dispenser cathode to be measured during an EDD or electron capture dissociation (ECD) experiment. PMID:19802340

  18. EVALUATION OF THE EXPERIMENTAL PARAMETERS WHICH CONTROL ELECTRON DETACHMENT DISSOCIATION, AND THEIR EFFECT ON THE FRAGMENTATION EFFICIENCY OF GLYCOSAMINOGLYCAN CARBOHYDRATES.

    PubMed

    Leach, Franklin E; Wolff, Jeremy J; Laremore, Tatiana N; Linhardt, Robert J; Amster, I Jonathan

    2008-10-01

    The efficiency of conversion of precursor ions to observable products for electron detachment dissociation (EDD) was measured as a function of the key experimental parameters to determine their optimal values for the Fourier transform mass spectrometry analysis of anionic glycosaminoglycan carbohydrates. These parameters include electron current, electron energy, dispenser cathode heater current, electron beam duration, charge state of the precursor ion, oligomer length, and precursor ion number accumulated in an external radio frequency multipole trap. Precursor conversion is most efficient at an electron current of 15 µA, and decreases at higher and lower values. The conversion of precursor to product ions increases in efficiency as the electron pulse duration is increased. Together, these data suggest that a radially repulsive electric field is produced between the electron beam and negative ions during EDD which causes the reaction cross section to decrease at higher values of electron current (>15 µA). Elevating the heater current of the dispenser cathode increases the electron flux, but also causes ion activation, presumably by blackbody infrared irradiation. An electronic circuit is described that allows the electron current produced by the dispenser cathode to be measured during an EDD or electron capture dissociation (ECD) experiment. PMID:19802340

  19. Evaluation of the experimental parameters which control electron detachment dissociation, and their effect on the fragmentation efficiency of glycosaminoglycan carbohydrates

    NASA Astrophysics Data System (ADS)

    Leach, Franklin E., III; Wolff, Jeremy J.; Laremore, Tatiana N.; Linhardt, Robert J.; Amster, I. Jonathan

    2008-10-01

    The efficiency of conversion of precursor ions to observable products for electron detachment dissociation (EDD) was measured as a function of the key experimental parameters to determine their optimal values for the Fourier transform mass spectrometry analysis of anionic glycosaminoglycan carbohydrates. These parameters include electron current, electron energy, dispenser cathode heater current, electron beam duration, charge state of the precursor ion, oligomer length, and precursor ion number accumulated in an external radio frequency multipole trap. Precursor conversion is most efficient at an electron current of 15 [mu]A, and decreases at higher and lower values. The conversion of precursor to product ions increases in efficiency as the electron pulse duration is increased. Together, these data suggest that a radially repulsive electric field is produced between the electron beam and negative ions during EDD which causes the reaction cross-section to decrease at higher values of electron current (>15 [mu]A). Elevating the heater current of the dispenser cathode increases the electron flux, but also causes ion activation, presumably by blackbody infrared irradiation. An electronic circuit is described that allows the electron current produced by the dispenser cathode to be measured during an EDD or electron capture dissociation (ECD) experiment.

  20. Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization

    PubMed Central

    Lloyd, John R.; Hess, Sonja

    2010-01-01

    Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M]+•, thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: 1. Complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; 2. Electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e− → Fe +•); 3. Radical fragmentation of the complexed compound. 4. Electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

  1. Peptide fragmentation by corona discharge induced electrochemical ionization.

    PubMed

    Lloyd, John R; Hess, Sonja

    2010-12-01

    Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M](+·), thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides, and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: (1) complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; (2) electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e(-) → Fe(+·)); (3) radical fragmentation of the complexed compound; (4) electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

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

    DOE PAGESBeta

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; et al

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  3. 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.

  4. Wavepacket theory of collisional dissociation in molecules

    SciTech Connect

    Kulander, K.

    1980-01-01

    An explicit integration scheme is used to solve the time dependent Schroedinger equation for wavepackets which model collisions in the collinear H + H/sub 2/ system. A realistic LEPS-type potential energy surface is used. Collision energies considered are above the dissociation threshold and probabilities for collision induced dissociation are reported. Also quantum mechanical state-to-state transition probabilities are generated. These results are compared to extensive classical trajectory calculations performed on this same system. The time evolution of the wavepacket densities is studied to understand the dynamics of the collinear collisional dissociation process.

  5. The Formation and Fragmentation of Primordial Protostellar Discs

    NASA Astrophysics Data System (ADS)

    Clark, Paul C.; Glover, Simon C. O.; Smith, Rowan J.; Greif, Thomas H.; Klessen, Ralf S.; Bromm, Volker

    2010-11-01

    We study the formation and evolution of the protostellar discs that form around the first stars in the Universe. Using sink particles, we replace the gravitationally bound gas at densities higher than 1015 cm-3 and radii greater than 3 AU from the central protostellar core, with an accreting point mass that is able to gravitationally interact with the surrounding gas. We find the disc is gravitationally (or `Toomre') unstable, and is dominated by a strong m = 2 spiral mode. Although the angular momentum transport is dominated by a combination of gravitational torques and Reynolds stresses, which are extremely efficient mechanisms, the disc is unable to process the infalling material and grows increasingly gravitationally unstable. During the build-up of the disc, the temperature in the gas is regulated by a combination of H2 line cooling, collision-induced emission and H2 dissociation, which together help to offset heating from the gravitational collapse and feedback from the protostar. Once the disc starts to fragment, H2 dissociation keeps the gas almost isothermal as the collapse of the fragment progresses. The fragmentation occurs when the protostar/disc system is only 230 yr old and at a distance of ~20 AU from its sibling, by which point the central protostar has a mass of ~1 Msolar. Given the angular momentum of the new protostellar system, it is likely that the protostars will grow to become a massive binary system.

  6. Structural identification of electron transfer dissociation products in mass spectrometry using infrared ion spectroscopy.

    PubMed

    Martens, Jonathan; Grzetic, Josipa; Berden, Giel; Oomens, Jos

    2016-01-01

    Tandem mass spectrometry occupies a principle place among modern analytical methods and drives many developments in the 'omics' sciences. Electron attachment induced dissociation methods, as alternatives for collision-induced dissociation have profoundly influenced the field of proteomics, enabling among others the top-down sequencing of entire proteins and the analysis of post-translational modifications. The technique, however, produces more complex mass spectra and its radical-driven reaction mechanisms remain incompletely understood. Here we demonstrate the facile structural characterization of electron transfer dissociation generated peptide fragments by infrared ion spectroscopy using the tunable free-electron laser FELIX, aiding the elucidation of the underlying dissociation mechanisms. We apply this method to verify and revise previously proposed product ion structures for an often studied model tryptic peptide, [AlaAlaHisAlaArg+2H](2+). Comparing experiment with theory reveals that structures that would be assigned using only theoretical thermodynamic considerations often do not correspond to the experimentally sampled species. PMID:27277826

  7. Structural identification of electron transfer dissociation products in mass spectrometry using infrared ion spectroscopy

    PubMed Central

    Martens, Jonathan; Grzetic, Josipa; Berden, Giel; Oomens, Jos

    2016-01-01

    Tandem mass spectrometry occupies a principle place among modern analytical methods and drives many developments in the ‘omics' sciences. Electron attachment induced dissociation methods, as alternatives for collision-induced dissociation have profoundly influenced the field of proteomics, enabling among others the top-down sequencing of entire proteins and the analysis of post-translational modifications. The technique, however, produces more complex mass spectra and its radical-driven reaction mechanisms remain incompletely understood. Here we demonstrate the facile structural characterization of electron transfer dissociation generated peptide fragments by infrared ion spectroscopy using the tunable free-electron laser FELIX, aiding the elucidation of the underlying dissociation mechanisms. We apply this method to verify and revise previously proposed product ion structures for an often studied model tryptic peptide, [AlaAlaHisAlaArg+2H]2+. Comparing experiment with theory reveals that structures that would be assigned using only theoretical thermodynamic considerations often do not correspond to the experimentally sampled species. PMID:27277826

  8. Collision--induced absorption in dense atmospheres of cool stars

    SciTech Connect

    Borysow, Aleksandra; Joergensen, Uffe Graae

    1999-04-01

    In the atmosphere of the Sun the major interaction between the matter and the radiation is through light absorption by ions (predominantly the negative ion of hydrogen atoms), neutral atoms and a small amount of polar molecules. The majority of stars in the universe are, however, cooler and denser than our Sun, and for a large fraction of these, the above absorption processes are very weak. Here, collision-induced absorption (CIA) becomes the dominant opacity source. The radiation is absorbed during very short mutual passages ('collisions') of two non-polar molecules (and/or atoms), while their electric charge distributions are temporarily distorted which gives rise to a transient dipole moment. We present here a review of the present-day knowledge about the impact of collision-induced absorption processes on the structure and the spectrum of such stars.

  9. Water vapor continuum: Whether collision-induced absorption is involved?

    NASA Astrophysics Data System (ADS)

    Vigasin, A. A.

    2014-11-01

    In a series of recent publications, the idea is pursued to shed a new light on the theory of the water vapor continuum absorption invoking the mechanism of collision-induced absorption. In the opinion of the present author, a portion of theoretical suggestions on this subject is biased and may thus lead to untenable conclusions about the nature of the continuum. The most typical drawback consists of improper consideration of statistics in the ensemble of interacting monomers that lead to embedding incorrect statistical weights to various types of molecular pairs which can form. The current note aims at clarifying the term “collision-induced absorption” in order to avoid incongruity in understanding the nature of the water vapor continuum.

  10. Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies.

    PubMed

    Tamara, Sem; Dyachenko, Andrey; Fort, Kyle L; Makarov, Alexander A; Scheltema, Richard A; Heck, Albert J R

    2016-08-31

    Tandem mass spectrometry can provide structural information on intact protein assemblies, generating mass fingerprints indicative of the stoichiometry and quaternary arrangement of the subunits. However, in such experiments, collision-induced dissociation yields restricted information due to simultaneous subunit unfolding, charge rearrangement, and subsequent ejection of a highly charged unfolded single subunit. Alternative fragmentation strategies can potentially overcome this and supply a deeper level of structural detail. Here, we implemented ultraviolet photodissociation (UVPD) on an Orbitrap mass spectrometer optimized for native MS and benchmark its performance to HCD fragmentation using various protein oligomers. We investigated dimeric β-lactoglobulin, dimeric superoxide dismutase, dimeric and tetrameric concanavalin A, and heptameric GroES and Gp31; ranging in molecular weight from 32 to 102 kDa. We find that, for the investigated systems, UVPD produces more symmetric charge partitioning than HCD. While HCD spectra show sporadic fragmentation over the full protein backbone sequence of the subunits with a bias toward fragmenting labile bonds, UVPD spectra provided higher sequence coverage. Taken together, we conclude that UVPD is a strong addition to the toolbox of fragmentation methods for top-down proteomics experiments, especially for native protein assemblies. PMID:27480281

  11. Photodissociation of CH3CHO at 248 nm by time-resolved Fourier-transform infrared emission spectroscopy: Verification of roaming and triple fragmentation

    NASA Astrophysics Data System (ADS)

    Hung, Kai-Chan; Tsai, Po-Yu; Li, Hou-Kuan; Lin, King-Chuen

    2014-02-01

    By using time-resolved Fourier-transform infrared emission spectroscopy, the HCO fragment dissociated from acetaldehyde (CH3CHO) at 248 nm is found to partially decompose to H and CO. The fragment yields are enhanced by the Ar addition that facilitates the collision-induced internal conversion. The channels to CH2CO + H2 and CH3CO + H are not detected significantly. The rotational population distribution of CO, after removing the Ar collision effect, shows a bimodal feature comprising both low- and high-rotational (J) components, sharing a fraction of 19% and 81%, respectively, for the vibrational state v = 1. The low-J component is ascribed to both roaming pathway and triple fragmentation. They are determined to have a branching ratio of <0.13 and >0.06, respectively, relative to the whole v = 1 population. The CO roaming is accompanied by a highly vibrational population of CH4 that yields a vibrational bimodality.

  12. 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

  13. Gas-Phase Unimolecular Dissociation Reveals Dominant Base Property of Protonated Homocysteine Sulfinyl Radical Ions.

    PubMed

    Love-Nkansah, Chasity B; Tan, Lei; Francisco, Joseph S; Xia, Yu

    2016-01-18

    Homocysteine sulfinyl radical ((SO⋅) Hcy) is a reactive intermediate involved during oxidative damage of DNA in the presence of high concentrations of homocysteine (Hcy). The short lifetime of (SO⋅) Hcy makes its preparation, isolation, and characterization challenging using traditional chemical measurement tools. Herein, we demonstrate the first study on mass-selected protonated (SO⋅) Hcy ions in the gas phase by investigating its unimolecular dissociation pathways from low energy collision-induced dissociation (CID). Tandem mass spectrometry (MS/MS), stable-isotope labeling, and theoretical calculations were employed to rationalize the observed fragmentation pathways. The dominant dissociation channel of protonated (SO⋅) Hcy was a charge-directed H2 O loss from the protonated sulfinyl radical (-SO⋅) moiety, forming a thiyl radical (-S⋅), which further triggered sequential radical-directed ⋅SH loss through multiple pathways. Compared to cysteine sulfinyl radical ((SO⋅) Cys), the small structural change induced by one additional methylene group in the side chain of (SO⋅) Hcy significantly promotes its base property while reducing the radical reactivity of sulfinyl radical. This observation provides new insight into studying reactions of (SO⋅) Hcy with biomolecules, which are critical in understanding toxicity induced by high levels of Hcy in biological conditions. PMID:26531146

  14. Top-Down Mass Analysis of Protein Tyrosine Nitration: Comparison of Electron Capture Dissociation with “Slow-Heating” Tandem Mass Spectrometry Methods

    PubMed Central

    2010-01-01

    Tyrosine nitration in proteins is an important post-translational modification (PTM) linked to various pathological conditions. When multiple potential sites of nitration exist, tandem mass spectrometry (MS/MS) methods provide unique tools to locate the nitro-tyrosine(s) precisely. Electron capture dissociation (ECD) is a powerful MS/MS method, different in its mechanisms to the “slow-heating” threshold fragmentation methods, such as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). Generally, ECD provides more homogeneous cleavage of the protein backbone and preserves labile PTMs. However recent studies in our laboratory demonstrated that ECD of doubly charged nitrated peptides is inhibited by the large electron affinity of the nitro group, while CID efficiency remains unaffected by nitration. Here, we have investigated the efficiency of ECD versus CID and IRMPD for top-down MS/MS analysis of multiply charged intact nitrated protein ions of myoglobin, lysozyme, and cytochrome c in a commercial Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. CID and IRMPD produced more cleavages in the vicinity of the sites of nitration than ECD. However the total number of ECD fragments was greater than those from CID or IRMPD, and many ECD fragments contained the site(s) of nitration. We conclude that ECD can be used in the top-down analysis of nitrated proteins, but precise localization of the sites of nitration may require either of the “slow-heating” methods. PMID:20677807

  15. Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides

    SciTech Connect

    Zhang, Qibin; Frolov, Andrej; Tang, Ning; Hoffman, Ralf; van der Goor, Tom; Metz, Thomas O.; Smith, Richard D.

    2007-03-15

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in diabetes mellitus research, particularly in the context of development of diabetic complications. The fragmentation behavior of glycated peptides produced from reaction of D-glucose with lysine residues was investigated by electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was found that high abundance ions corresponding to various degrees of neutral water losses, as well as furylium ion production, dominate the CID spectra, and that the sequence informative b and y ions were rarely observed when Amadori-modified peptides were fragmented. Contrary to what was observed under CID conditions, ions corresponding to neutral losses of water or furylium ion production were not observed in the ETD spectra. Instead, abundant and almost complete series of c and z type ions were observed regardless of whether the modification site was located in the middle of the sequence or close to the N-terminus, greatly facilitating the peptide sequencing. This study strongly suggests that ETD is a better technique for proteomics studies of non-enzymatically glycated peptides and proteins.

  16. Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines

    PubMed Central

    van der Hooft, Justin J. J.; Ridder, Lars; Barrett, Michael P.; Burgess, Karl E. V.

    2015-01-01

    Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software1. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context

  17. Fragmentation pathways of 2,3-dimethyl-2,3-dinitrobutane cations in the gas phase.

    PubMed

    Paine, Martin R L; Kirk, Benjamin B; Ellis-Steinborner, Simon; Blanksby, Stephen J

    2009-09-01

    2,3-Dimethyl-2,3-dinitrobutane (DMNB) is an explosive taggant added to plastic explosives during manufacture making them more susceptible to vapour-phase detection systems. In this study, the formation and detection of gas-phase [M+H](+), [M+Li](+), [M+NH(4)](+) and [M+Na](+) adducts of DMNB was achieved using electrospray ionisation on a triple quadrupole mass spectrometer. The [M+H](+) ion abundance was found to have a strong dependence on ion source temperature, decreasing markedly at source temperatures above 50 degrees C. In contrast, the [M+Na](+) ion demonstrated increasing ion abundance at source temperatures up to 105 degrees C. The relative susceptibility of DMNB adduct ions toward dissociation was investigated by collision-induced dissociation. Probable structures of product ions and mechanisms for unimolecular dissociation have been inferred based on fragmentation patterns from tandem mass (MS/MS) spectra of source-formed ions of normal and isotopically labelled DMNB, and quantum chemical calculations. Both thermal and collisional activation studies suggest that the [M+Na](+) adduct ions are significantly more stable toward dissociation than their protonated analogues and, as a consequence, the former provide attractive targets for detection by contemporary rapid screening methods such as desorption electrospray ionisation mass spectrometry. PMID:19670345

  18. Review: Formation of Peptide Radical Ions Through Dissociative Electron Transfer in Ternary Metal-Ligand-Peptide Complexes

    SciTech Connect

    Chu, Ivan K.; Laskin, Julia

    2011-12-31

    The formation and fragmentation of odd-electron ions of peptides and proteins is of interest to applications in biological mass spectrometry. Gas-phase redox chemistry occurring during collision-induced dissociation of ternary metal-ligand-peptide complexes enables the formation of a variety of peptide radicals including the canonical radical cations, M{sup +{sm_bullet}}, radical dications, [M{sup +}H]{sup 2+{sm_bullet}}, radical anions, [M-2H]{sup -{sm_bullet}}. In addition, odd-electron peptide ions with well-defined initial location of the radical site are produced through side chain losses from the radical ions. Subsequent fragmentation of these species provides information on the role of charge and the location of the radical site on the competition between radical-induced and proton-driven fragmentation of odd-electron peptide ions. This account summarizes current understanding of the factors that control the efficiency of the intramolecular electron transfer (ET) in ternary metal-ligand-peptide complexes resulting in formation of odd-electron peptide ions. Specifically, we discuss the effect of the metal center, the ligand and the peptide structure on the competition between the ET, proton transfer (PT), and loss of neutral peptide and neutral peptide fragments from the complex. Fundamental studies of the structures, stabilities, and the energetics and dynamics of fragmentation of such complexes are also important for detailed molecular-level understanding of photosynthesis and respiration in biological systems.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  20. Collision induced ultraviolet structure in nitrogen radar REMPI spectra

    SciTech Connect

    McGuire, S. Miles, R.

    2014-12-28

    We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a{sup 1}Π{sub g} ← X{sup 1}Σ{sub g}{sup +} electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a{sup ″1}Σ{sub g}{sup +} electronic state.

  1. Low Mass MS/MS Fragments of Protonated Amino Acids Used for Distinction of Their 13C- Isotopomers in Metabolic Studies

    NASA Astrophysics Data System (ADS)

    Ma, Xin; Dagan, Shai; Somogyi, Árpád; Wysocki, Vicki H.; Scaraffia, Patricia Y.

    2013-04-01

    Glu, Gln, Pro, and Ala are the main amino acids involved in ammonia detoxification in mosquitoes. In order to develop a tandem mass spectrometry method (MS2) to monitor each carbon of the above isotopically-labeled 13C-amino acids for metabolic studies, the compositions and origins of atoms in fragments of the protonated amino acid should be first elucidated. Thus, various electrospray (ESI)-based MS2 tools were employed to study the fragmentation of these unlabeled and isotopically-labeled amino acids and better understand their dissociation pathways. A broad range of fragments, including previously-undescribed low m/z fragments was revealed. The formulae of the fragments (from m/z 130 down to m/z 27) were confirmed by their accurate masses. The structures and conformations of the larger fragments of Glu were also explored by ion mobility mass spectrometry (IM-MS) and gas-phase hydrogen/deuterium exchange (HDX) experiments. It was found that some low m/z fragments ( m/z 27-30) are common to Glu, Gln, Pro, and Ala. The origins of carbons in these small fragments are discussed and additional collision induced dissociation (CID) MS2 fragmentation pathways are proposed for them. It was also found that small fragments (≤ m/z 84) of protonated, methylated Glu, and methylated Gln are the same as those of the underivatized Glu and Gln. Taken together, the new approach of utilizing low m/z fragments can be applied to distinguish, identify, and quantify 13C-amino acids labeled at various positions, either in the backbone or side chain.

  2. Conversion of 3-nitrotyrosine to 3-aminotyrosine residues facilitates mapping of tyrosine nitration in proteins by electrospray ionization-tandem mass spectrometry using electron capture dissociation.

    PubMed

    Guo, Jia; Prokai, Laszlo

    2012-12-01

    Protein tyrosine nitration is associated with oxidative stress and various human diseases. Tandem mass spectrometry has been the method of choice for the identification and localization of this posttranslational modification to understand the underlying mechanisms and functional consequences. Due to the electron predator effect of the nitro group limiting fragmentation of the peptide backbone, electron-based dissociation has not been applicable, however, to nitrotyrosine-containing peptides. A straightforward conversion of the nitrotyrosine to the aminotyrosine residues is introduced to address this limitation. When tested with nitrated ubiquitin and human serum albumin as model proteins in top-down and bottom-up approaches, respectively, this chemical derivatization enhanced backbone fragmentation of the corresponding nitroproteins and nitropeptides by electron capture dissociation (ECD). Increased sequence coverage has been obtained by combining in the bottom-up strategy the conversion of nitrotyrosine to aminotyrosine and introducing, in addition to trypsin, a further digesting enzyme of complementary specificity, when protein nitration was mapped by liquid chromatography-electrospray ionization tandem mass spectrometry using both collision-induced dissociation (CID) and ECD. PMID:23280749

  3. Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

    NASA Astrophysics Data System (ADS)

    Viglino, Emilie; Lai, Cheuk Kuen; Mu, Xiaoyan; Chu, Ivan K.; Tureček, František

    2016-09-01

    We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H]+● and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS3 dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in CuII(2,2 ':6 ',2 ″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR]+● that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates.

  4. Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals.

    PubMed

    Viglino, Emilie; Lai, Cheuk Kuen; Mu, Xiaoyan; Chu, Ivan K; Tureček, František

    2016-09-01

    We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H](+●) and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS(3) dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in Cu(II)(2,2':6',2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR](+●) that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates. Graphical Abstract ᅟ. PMID:27278824

  5. Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

    NASA Astrophysics Data System (ADS)

    Viglino, Emilie; Lai, Cheuk Kuen; Mu, Xiaoyan; Chu, Ivan K.; Tureček, František

    2016-06-01

    We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H]+● and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS3 dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in CuII(2,2':6',2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR]+● that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates.

  6. Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry

    SciTech Connect

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John; Smith, Richard D.; Metz, Thomas O.

    2007-06-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resulted in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.

  7. Using Electron Induced Dissociation (EID) on an LC Time-Scale to Characterize a Mixture of Analogous Small Organic Molecules

    NASA Astrophysics Data System (ADS)

    Prakash, Aruna S.; Smith, Michael J. P.; Kaabia, Zied; Hurst, Glenn; Yan, Ci; Sims, Martin; Bristow, Anthony W. T.; Stokes, Peter; Parker, David; Mosely, Jackie A.

    2012-05-01

    LC ESI FTICR MS of a sample of cediranib identified this pharmaceutical target molecule plus an additional 10 compounds of interest, all of which were less than 10% total ion current (TIC) peak intensity relative to cediranib. LC FTICR tandem mass spectrometry using electron induced dissociation (EID) has been achieved and has proven to be the best way to generate useful product ion information for all of these singly protonated molecules. Cediranib [M + H]+ fragmented by EID to give 29 product ions whereas QTOF-CID generated only one very intense product ion, and linear ion trap-CID, which generated 10 product ions, but all with poor S/N. Twenty-six of the EID product ions were unique to this fragmentation technique alone. By considering the complementary LC-EID and LC-CID data together, all 10 unknown compounds were structurally characterized and proven to be analogous to cediranib. Of particular importance, EID produced unique product ion information for one of the low level cediranib analogues that enabled full characterization of the molecule such that the presence of an extra propylpyrrolidine group was discovered and proven to be located on the pyrrolidine ring of cediranib, solving an analytical problem that could not be solved by collision induced dissociation (CID). Thus, it has been demonstrated that EID is in harmony with the chromatography duty-cycle and the dynamic concentration range of synthetic compounds containing trace impurities, providing crucial analytical information that cannot be obtained by more traditional methodologies.

  8. Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides.

    PubMed

    Giese, Sven H; Belsom, Adam; Rappsilber, Juri

    2016-08-16

    Cross-linking/mass spectrometry has evolved into a robust technology that reveals structural insights into proteins and protein complexes. We leverage a new tribrid instrument with improved fragmentation capacities in a systematic comparison to identify which fragmentation method would be best for the identification of cross-linked peptides. Specifically, we explored three fragmentation methods and two combinations: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), ETciD, and EThcD. Trypsin-digested, SDA-cross-linked human serum albumin (HSA) served as a test sample, yielding over all methods and in triplicate analysis in total 2602 matched PSMs and 1390 linked residue pairs at 5% false discovery rate, as confirmed by the crystal structure. HCD wins in number of matched peptide-spectrum-matches (958 PSMs) and identified links (446). CID is most complementary, increasing the number of identified links by 13% (58 links). HCD wins together with EThcD in cross-link site calling precision, with approximately 62% of sites having adjacent backbone cleavages that unambiguously locate the link in both peptides, without assuming any cross-linker preference for amino acids. Overall quality of spectra, as judged by sequence coverage of both peptides, is best for EThcD for the majority of peptides. Sequence coverage might be of particular importance for complex samples, for which we propose a data dependent decision tree, else HCD is the method of choice. The mass spectrometric raw data has been deposited in PRIDE (PXD003737). PMID:27454319

  9. Spectral lineshapes of collision-induced absorption (CIA) and collision-induced light scattering (CILS) for molecular nitrogen using isotropic intermolecular potential. New insights and perspectives

    NASA Astrophysics Data System (ADS)

    El-Kader, M. S. A.; Mostafa, S. I.; Bancewicz, T.; Maroulis, G.

    2014-08-01

    The rototranslational collision-induced absorption (CIA) at different temperatures and collision-induced light scattering (CILS) at room temperature of nitrogen gas are analyzed in terms of new isotropic intermolecular potential, multipole-induced dipole functions and interaction-induced pair polarizability models, using quantum spectral lineshape computations. The irreducible spherical form for the induced operator of light scattering mechanisms was determined. The high frequency wings are discussed in terms of the collision-induced rotational Rayleigh effect and estimates for the dipole-octopole polarizability E4, is obtained and checked with the ab initio theoretical value. The quality of the present potential has been checked by comparing between calculated and experimental thermo-physical and transport properties over a wide temperature range, which are found to be in good agreement.

  10. Electron capture dissociation mass spectrometric analysis of lysine-phosphorylated peptides

    PubMed Central

    Kowalewska, Karolina; Stefanowicz, Piotr; Ruman, Tomasz; Frączyk, Tomasz; Rode, Wojciech; Szewczuk, Zbigniew

    2010-01-01

    Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by 1H NMR and 31P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD–MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested. PMID:20144148

  11. Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Kjeldsen, Frank; Haselmann, Kim F; Sørensen, Esben S; Zubarev, Roman A

    2003-03-15

    In hot electron capture dissociation (HECD), multiply protonated polypeptides fragment upon capturing approximately 11-eV electrons. The excess of energy upon the primary c, z* cleavage induces secondary fragmentation in z* fragments. The resultant w ions allow one to distinguish between the isomeric Ile and Leu residues. The analytical utility of HECD is evaluated using tryptic peptides from the bovine milk protein PP3 containing totally 135 amino acid residues. Using a formal procedure for Ile/Leu (Xle) residue assignment, the identities of 20 out of 25 Xle residues (80%) were determined. The identity of an additional two residues could be correctly guessed from the absence of the alternative w ions, and only two residues, for which neither expected nor alternative w ions were observed, remained unassigned. Reinspection of conventional ECD spectra also revealed the presence of Xle w ions, although at lower abundances, with 44% of all Xle residues distinguished. Using a dispenser cathode as an electron source, identification of four out of five Xle residues in a 2.7-kDa peptide was possible with one acquisition 2 s long, with identification of all five residues by averaging of five such acquisitions. Unlike the case of high-energy collision-induced dissociation, no d ions were observed in the HECD of tryptic peptides. PMID:12659185

  12. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode.

    PubMed

    Enjalbert, Quentin; Simon, Romain; Salvador, Arnaud; Antoine, Rodolphe; Redon, Sébastien; Ayhan, Mehmet Menaf; Darbour, Florence; Chambert, Stéphane; Bretonnière, Yann; Dugourd, Philippe; Lemoine, Jérôme

    2011-11-30

    Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides. PMID:22002689

  13. Dissociation of CH4 and CD4 by electron impact - Production of metastable and high-Rydberg hydrogen and carbon fragments

    NASA Technical Reports Server (NTRS)

    Finn, T. G.; Carnahan, B. L.; Wells, W. C.; Zipf, E. C.

    1975-01-01

    Production of hydrogen and carbon atoms in metastable and high-lying Rydberg states by electron-impact dissociation of methane and deuterated methane is investigated for incident electron energies ranging from threshold values to 300 eV. Threshold energies for five different processes resulting in metastable hydrogen and carbon atoms are determined in the energy range from 20 to 70 eV, and it is shown that metastable hydrogen atoms are produced in four of these collisional processes while metastable carbon atoms are produced in the other. The nature of each collisional process is described, differential cross sections are derived for the dissociative excitation of both types of atoms to metastable and high-Rydberg states at 100 eV, and the onset energy for UV photon production is measured. Much of the data is interpreted in terms of the ion core model suggested by Kupriyanov (1968) and developed by Freund (1971).

  14. Competition of charge- versus radical-directed fragmentation of gas-phase protonated cysteine sulfinyl radicals.

    PubMed

    Love, Chasity B; Tan, Lei; Francisco, Joseph S; Xia, Yu

    2013-04-24

    The fragmentation behavior of various cysteine sulfinyl ions (intact, N-acetylated, and O-methylated), new members of the gas-phase amino acid radical ion family, was investigated by low-energy collision-induced dissociation (CID). The dominant fragmentation channel for the protonated cysteine sulfinyl radicals ((SO•)Cys) was the radical-directed Cα-Cβ homolytic cleavage, resulting in the formation of glycyl radical ions and loss of CH2SO. This channel, however, was not observed for protonated N-acetylated cysteine sulfinyl radicals (Ac-(SO•)Cys); instead, charge-directed H2O loss followed immediately by SH loss prevailed. Counterintuitively, the H2O loss did not derive from the carboxyl group but involved the sulfinyl oxygen, a proton, and a Cβ hydrogen atom. Theoretical calculations suggested that N-acetylation significantly increases the barrier (~14 kcal mol(-1)) for the radical-directed fragmentation channel because of its reduced capability to stabilize the thus-formed glycyl radical ions via the captodative effect. N-Acetylation also assists in moving the proton to the sulfinyl site, which reduces the barrier for H2O loss. Our studies demonstrate that for cysteine sulfinyl radical ions, the stability of the product ions (glycyl radical ions) and the location of the charge (proton) can significantly modulate the competition between radical- and charge-directed fragmentation. PMID:23527556

  15. Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry.

    PubMed

    Schwarzenberg, Adrián; Ichou, Farid; Cole, Richard B; Machuron-Mandard, Xavier; Junot, Christophe; Lesage, Denis; Tabet, Jean-Claude

    2013-05-01

    Organophosphorus compounds have played important roles as pesticides, chemical warfare agents and extractors of radioactive material. Structural elucidation of phosphonates poses a particular challenge because their initial forms can be hydrolyzed, thus, degradation products may predominate in samples acquired in the field. The analysis of non-volatile organophosphorus compounds and their degradation products is possible using electrospray tandem mass spectrometry ESI-MS/MS. Here, we present a generic strategy that allows the unambiguous identification of substituents for two families of organophosphorus compounds: the phosphonates and phosphates. General fragmentation rules were deduced based on the study of decomposition pathways of 55 organophosphorus esters, including examples found in the literature. Multistage MS (MS(n)) experiments at high resolution in a hybrid mass spectrometer provide accurate mass measurements, whereas collision-induced dissociation experiments in a triple quadrupole give access to small fragment ions. The creation of a specific nomenclature for each possible structure of organophosphorus compound, depending on the alkyl side chain linked to the oxygen, was achieved by applying these fragmentation rules. This led to the creation of an 'identification tree' based upon the unique consecutive decomposition pathways uncovered for each individual compound. Hence, seven structural motifs were created that orient an unequivocal identification using the 'identification tree'. Despite the similar structures of the ensemble of phosphate and phosphonate esters, distinct identifications based upon characteristic neutral losses and diagnostic fragment ions were possible in all cases. PMID:23674282

  16. Intermetallic Competition in the Fragmentation of Trimetallic Au-Zn-Alkali Complexes.

    PubMed

    Lang, Johannes; Cayir, Merve; Walg, Simon P; Di Martino-Fumo, Patrick; Thiel, Werner R; Niedner-Schatteburg, Gereon

    2016-02-12

    Cationization is a valuable tool to enable mass spectrometric studies on neutral transition-metal complexes (e.g., homogenous catalysts). However, knowledge of potential impacts on the molecular structure and catalytic reactivity induced by the cationization is indispensable to extract information about the neutral complex. In this study, we cationize a bimetallic complex [AuZnCl3 ] with alkali metal ions (M(+) ) and investigate the charged adducts [AuZnCl3 M](+) by electrospray ionization mass spectrometry (ESI-MS). Infrared multiple photon dissociation (IR-MPD) in combination with density functional theory (DFT) calculations reveal a μ(3) binding motif of all alkali ions to the three chlorido ligands. The cationization induces a reorientation of the organic backbone. Collision-induced dissociation (CID) studies reveal switches of fragmentation channels by the alkali ion and by the CID amplitude. The Li(+) and Na(+) adducts prefer the sole loss of ZnCl2 , whereas the K(+) , Rb(+) , and Cs(+) adducts preferably split off MCl2 ZnCl. Calculated energetics along the fragmentation coordinate profiles allow us to interpret the experimental findings to a level of subtle details. The Zn(2+) cation wins the competition for the nitrogen coordination sites against K(+) , Rb(+) , and Cs(+) , but it loses against Li(+) and Na(+) in a remarkable deviation from a naive hard and soft acids and bases (HSAB) concept. The computations indicate expulsion of MCl2 ZnCl rather than of MCl and ZnCl2 . PMID:26785330

  17. Identification and Characterization of Citrulline-modified Brain Proteins by Combining HCD and CID Fragmentation

    PubMed Central

    Jin, Zhicheng; Fu, Zongming; Yang, Jun; Troncosco, Juan; Everett, Allen D.; Van Eyk, Jennifer E.

    2016-01-01

    Citrullination is a protein post-translational modification of arginine residues catalyzed by peptidylarginine deiminase. Protein citrullination has been detected in the central nervous system and associated with a number of neurological diseases. However, identifying citrullinated proteins from complex mixtures and pinpointing citrullinated residues has been limited. Using reversed-phase liquid chromatography and high resolution mass spectrometry, this study determined in vitro citrullination sites of glial fibrillary acid protein (GFAP) and myelin basic protein (MBP) and in vivo sites in brain protein extract. Human GFAP has five endogenous citrullination sites, R30, R36, R270, R406, and R416, and MBP has fourteen in vivo citrullination sites. Human neurogranin (NRGN/RC3) was found citrullinated at residue R68. The sequence of citrullinated peptides and citrullination sites were confirmed from peptides identified in trypsin, Lys-C, and Glu-C digests. The relative ratio of citrullination was estimated by simultaneous identification of citrullinated and unmodified peptides from Alzheimer’s and control samples. The site occupancy of citrullination at the residue R68 of NRGN ranged from 1.6% to 9.5%. Compared to collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) mainly produced protein backbone fragmentation for citrullinated peptides. CID triggered HCD fragmentation is an optimal approach for the identification of citrullinated peptides in complex protein digests. PMID:23828821

  18. Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator*

    PubMed Central

    Wright, James C.; Collins, Mark O.; Yu, Lu; Käll, Lukas; Brosch, Markus; Choudhary, Jyoti S.

    2012-01-01

    Peptide identification using tandem mass spectrometry is a core technology in proteomics. Latest generations of mass spectrometry instruments enable the use of electron transfer dissociation (ETD) to complement collision induced dissociation (CID) for peptide fragmentation. However, a critical limitation to the use of ETD has been optimal database search software. Percolator is a post-search algorithm, which uses semi-supervised machine learning to improve the rate of peptide spectrum identifications (PSMs) together with providing reliable significance measures. We have previously interfaced the Mascot search engine with Percolator and demonstrated sensitivity and specificity benefits with CID data. Here, we report recent developments in the Mascot Percolator V2.0 software including an improved feature calculator and support for a wider range of ion series. The updated software is applied to the analysis of several CID and ETD fragmented peptide data sets. This version of Mascot Percolator increases the number of CID PSMs by up to 80% and ETD PSMs by up to 60% at a 0.01 q-value (1% false discovery rate) threshold over a standard Mascot search, notably recovering PSMs from high charge state precursor ions. The greatly increased number of PSMs and peptide coverage afforded by Mascot Percolator has enabled a fuller assessment of CID/ETD complementarity to be performed. Using a data set of CID and ETcaD spectral pairs, we find that at a 1% false discovery rate, the overlap in peptide identifications by CID and ETD is 83%, which is significantly higher than that obtained using either stand-alone Mascot (69%) or OMSSA (39%). We conclude that Mascot Percolator is a highly sensitive and accurate post-search algorithm for peptide identification and allows direct comparison of peptide identifications using multiple alternative fragmentation techniques. PMID:22493177

  19. Collision-induced vibrational absorption in molecular hydrogens

    SciTech Connect

    Reddy, S.P.

    1993-05-01

    Collision induced absorption (CIA) spectra of the first overtone bands of H{sub 2}, D{sub 2}, and HD have been recorded for gas densities up to 500 amagat at 77-300 K. Analyses of these spectra reveal that (1) contrary to the observations in the fundamental bands, the contribution of the isotropic overlap interaction to the first overtone bands is negligible, (2) the squares of the matrix elements B{sub 32}(R)/ea{sub o} [= {lambda}{sub 32} exp(-(R-{sigma})/{rho}{sub 32}) + 3 (R/a{sub o}){sup -4}] where the subscripts 3 and 2 represent L and {lambda}, respectively, account for the absorption intensity of the bands and (3) the mixed term, 2,3 {lambda}{sub 32} exp (-(R-{sigma})/{rho}{sub 32}) <{vert_bar}Q{vert_bar}> <{alpha}> (R/a){sup -4}, gives a negative contribution. In the CIA spectra of H{sub 2} in its second overtone region recorded at 77, 201 and 298 K for gas densities up to 1000 amagat, a dip in the Q branch with characteristic Q{sub p} and Q{sub R} components has been observed. The analysis of the absorption profiles reveals, in addition to the previously known effects, the occurrence of the triple-collision transitions of H{sub 2} of the type Q{sub 1}(J) + Q{sub 1}(J) + Q{sub 1}(J) for the first time. From the profile analysis the absorption coefficient of these transitions is obtained.

  20. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize phytochemicals in plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. New methods a...

  1. Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly

    PubMed Central

    Cui, Weidong; Zhang, Hao; Blankenship, Robert E; Gross, Michael L

    2015-01-01

    Native spray has the potential to probe biophysical properties of protein assemblies. Here we report an investigation using both ECD top-down sequencing with an FTICR mass spectrometer and ion mobility (IM) measurements on a Q-TOF to investigate the collisionally induced unfolding of a native-like heterogeneous tetrameric assembly, human hemoglobin (hHb), in the gas phase. To our knowledge, this is the first report combining ECD and ion-mobility data on the same target protein assembly to delineate the effects of collisional activation on both assembly size and the extent and location of fragmentation. Although the collision-induced unfolding of the hemoglobin assembly is clearly seen by both IMMS and ECD, the latter delineates the regions that increasingly unfold as the collision energy is increased. The results are consistent with previous outcomes for homogeneous protein assemblies and reinforce our interpretation that activation opens the structure of the protein assembly from the flexible regions to make available ECD fragmentation, without dissociating the component proteins. PMID:26032343

  2. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes.

    PubMed

    Lermyte, Frederik; Sobott, Frank

    2015-08-01

    Top-down sequencing approaches are becoming ever more popular for protein characterization, due to the ability to distinguish and characterize different protein isoforms. Under non-denaturing conditions, electron transfer dissociation (ETD) can furthermore provide important information on the exposed surface of proteins or complexes, thereby contributing to the characterization of their higher-order structure. Here, we investigate this approach using top-down ETD of tetrameric hemoglobin, concanavalin A, and alcohol dehydrogenase combined with ion mobility (IM) on a commercially available quadrupole/ion mobility/time-of-flight instrument (Waters Synapt G2). By applying supplemental activation in the transfer cell (post-IM), we release ETD fragments and attain good sequence coverage in the exposed terminal regions of the protein. We investigate the correlation between observed sites of fragmentation with regions of solvent accessibility, as derived from the crystal structure. Ion acceleration prior to ETD is also used to cause collision-induced unfolding (CIU) of the complexes without monomer ejection, as evidenced by the IM profiles. These partially unfolded tetramers show efficient fragmentation in some regions which are not sequenced under more gentle MS conditions. We show that by increasing CIU in small increments and monitoring the changes in the fragmentation pattern, it is possible to follow the initial steps of gas-phase protein unfolding. Fragments from partially unfolded protein complexes are released immediately after electron transfer, prior to IM (they do not share the drift time of their precursor), and observed without the need for supplemental activation. This is further evidence that the higher-order structure in these protein regions has been disrupted. PMID:26081219

  3. THE DISSOCIATIVE TURN IN PSYCHOANALYSIS.

    PubMed

    Itzkowitz, Sheldon

    2015-06-01

    In his response to the Roundtable Discussions on what is effective in psychoanalytic psychotherapy, the author focuses on the renewed interest in the concept of dissociation that began to emerge toward the end of the 20th century. A contemporary psychoanalytic position informed by the impact of developmental trauma has led to an understanding of and interest in the dissociative mind. The actuality of trauma during infancy and early childhood is recognized as a key factor leading to the emergence of dissociative processes, the potential dissociative structuring of the mind, and mind being characterized by multiple, discontinuous, centers of consciousness. The therapeutic goal in the psychoanalytic work with fragmented patients is to establish communication and understanding between the dissociated self-states. The author offers two brief clinical examples of working with dissociated self-states. PMID:26177756

  4. A fragmentation study of an isoflavone glycoside, genistein-7-O-glucoside, using electrospray quadrupole time-of-flight mass spectrometry at high mass resolution

    NASA Astrophysics Data System (ADS)

    March, Raymond E.; Miao, Xiu-Sheng; Metcalfe, Chris D.; Stobiecki, Maciej; Marczak, Lukasz

    2004-03-01

    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 genistein-7-O-[beta]--glucoside (5,7,4'-trihydroxyisoflavone). The product ion mass spectrum of [M-H]- ions shows neutral losses of the glycan residue (162 Da) and of the glycan residue + H[radical sign] (163 Da) by rearrangement and scission, respectively, where the latter loss dominates at higher collision energies. The genistein moiety remained intact and only minor fragmentation of the glucose moiety was observed. The low-energy product ion mass spectrum of [M+H]+ ions shows extensive fragmentation of the glucose moiety, though at low ion signal intensity, loss of the glycan residue, and simple fragmentation of the genistein moiety that permits characterization of the substituents in the A and B rings. The use of elevated cone voltages permitted observation of product ion mass spectra of selected primary fragment ions. Product ion mass spectra examined at high mass resolution allowed unambiguous determination of the elemental composition of fragment ions. Fragmentation mechanisms and ion structures have been proposed.

  5. 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.

  6. 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.

  7. Tandem mass spectrometry approach for the investigation of the steroidal metabolism: structure-fragmentation relationship (SFR) in anabolic steroids and their metabolites by ESI-MS/MS analysis.

    PubMed

    Musharraf, Syed Ghulam; Ali, Arslan; Khan, Naik Tameem; Yousuf, Maria; Choudhary, Muhammad Iqbal; Atta-ur-Rahman

    2013-02-01

    Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to investigate the effect of different substitutions introduced during metabolism on fragmentation patterns of four anabolic steroids including methyltestosterone, methandrostenolone, cis-androsterone and adrenosterone, along with their metabolites. Collision-induced dissociation (CID) analysis was performed to correlate the major product ions of 19 steroids with structural features. The analysis is done to portray metabolic alteration, such as incorporation or reduction of double bonds, hydroxylations, and/or oxidation of hydroxyl moieties to keto functional group on steroidal skeleton which leads to drastically changed product ion spectra from the respective classes of steroids, therefore, making them difficult to identify. The comparative ESI-MS/MS study also revealed some characteristic peaks to differentiate different steroidal metabolites and can be useful for the unambiguous identification of anabolic steroids in biological fluid. Moreover, LC-ESI-MS/MS analysis of fermented extract of methyltestosterone, obtained by Macrophomina phaseolina was also investigated. PMID:23159734

  8. Photodissociation of gaseous CH3COSH at 248 nm by time-resolved Fourier-transform infrared emission spectroscopy: Observation of three dissociation channels

    NASA Astrophysics Data System (ADS)

    Hu, En-Lan; Tsai, Po-Yu; Fan, He; Lin, King-Chuen

    2013-01-01

    Upon one-photon excitation at 248 nm, gaseous CH3C(O)SH is dissociated following three pathways with the products of (1) OCS + CH4, (2) CH3SH + CO, and (3) CH2CO + H2S that are detected using time-resolved Fourier-transform infrared emission spectroscopy. The excited state 1(nO, π*CO) has a radiative lifetime of 249 ± 11 ns long enough to allow for Ar collisions that induce internal conversion and enhance the fragment yields. The rate constant of collision-induced internal conversion is estimated to be 1.1 × 10-10 cm3 molecule-1 s-1. Among the primary dissociation products, a fraction of the CH2CO moiety may undergo further decomposition to CH2 + CO, of which CH2 is confirmed by reaction with O2 producing CO2, CO, OH, and H2CO. Such a secondary decomposition was not observed previously in the Ar matrix-isolated experiments. The high-resolution spectra of CO are analyzed to determine the ro-vibrational energy deposition of 8.7 ± 0.7 kcal/mol, while the remaining primary products with smaller rotational constants are recognized but cannot be spectrally resolved. The CO fragment detected is mainly ascribed to the primary production. A prior distribution method is applied to predict the vibrational distribution of CO that is consistent with the experimental findings.

  9. Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer.

    PubMed

    Knyazev, Vadim D; Stein, Stephen E

    2010-03-01

    Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes. PMID:20060316

  10. 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.

  11. Collision-induced absorption in the far infrared spectrum of Titan

    NASA Technical Reports Server (NTRS)

    Hunt, J. L.; Poll, J. D.; Goorvitch, D.; Tipping, R. H.

    1983-01-01

    The effects of collision-induced absorption on the far infrared spectrum of Titan have been investigated. After a review of the procedure for the theoretical calculation of the N2 translation-rotational spectrum, new results for the temperature range o 70 to 120 K are reported. These are used as input data for a simple atmospheric model in order to compute the far infrared radiance, brightness temperature, and specral limb function. This source of opacity alone is not capable of explaining the Voyager results. When the collision-induced methane is included, the results are in closer agreement in the range between 200 and 300/cm, suggesting that a more complete treatment of collision-induced absorption including particularly CH4-N2, N2-H2, and H2-H2 results, may provide sufficient opacity to reduce or obviate the need for opacities due to clouds or aerosols in order to explain the observed spectra.

  12. Collision-induced radio-frequency transitions in CH 3I

    NASA Astrophysics Data System (ADS)

    Tamassia, F.; Danieli, R.; Scappini, F.

    1999-02-01

    The highly sensitive method of radio-frequency-infrared double resonance inside a CO 2 laser is applied to study collision-induced transitions in CH 3I in a four-level double resonance scheme. Pure nuclear quadrupole resonances are observed as the result of collision population transfer between different rotational levels. The intensity ratios of the collision-induced dips to the corresponding three-level double resonance signals are measured for a number of transitions in the ground and excited vibrational states. Collision selection rules in the pure gas and in mixtures with polar and non-polar gases are discussed.

  13. Infilling of Vector Collision-Sequence Interference Dips in Collision-Induced Spectra

    NASA Astrophysics Data System (ADS)

    Courtenay Lewis, John

    2014-11-01

    The vector interference dip most clearly seen in the fundamental collision-induced band of H2 and H2 mixtures at densities upward of 20amagat, is well known to persist at densities down to 1 amagat. However, At lower densities it is not seen. Lewis and Herman gave a theory of this infilling. In this work we approach the problem from the simple statistical models for collision-induced absorption introduced by Lewis in 2000 and subsequently much elaborated. The statistical model shows infilling, but rather than a uniformly infilling dip the model shows a small central peak forming in the dip, then broadening with increasing amplitude.

  14. Identification of disulfide bonds in wheat gluten proteins by means of mass spectrometry/electron transfer dissociation.

    PubMed

    Lutz, Elena; Wieser, Herbert; Koehler, Peter

    2012-04-11

    Disulfide bonds within gluten proteins play a key role in the breadmaking performance of wheat flour. In the present study, disulfide bonds of wheat gluten proteins were identified by using a new liquid chromatography-mass spectrometry (LC-MS) technique with alternating electron transfer dissociation (ETD)/collision-induced dissociation (CID). Wheat flour was partially hydrolyzed with thermolysin (pH 6.5, 37 °C, 16 h), and the digest was subjected to LC-MS with alternating ETD/CID fragmentation. Whereas CID provided peptide fragments with intact disulfide bonds, cleavage of disulfide bonds was preferred over peptide backbone fragmentations in ETD. The simultaneous observation of disulfide-linked and disulfide-cleaved peptide ions in the mass spectra not only provided distinct interpretation with high confidence but also simplified the conventional approach for determination of disulfide bonds, which often requires two separate experiments with and without chemical reduction. By application of the new method 14 cystine peptides were identified. Eight peptides confirmed previously established disulfide bonds within gluten proteins, and the other six cystine peptides were identified for the first time. One of the newly identified cystine peptides represented a "head-to-tail" cross-link between high molecular weight glutenin subunits. This type of cross-link, which has been postulated as an integral part of glutenin models published previously, has now been proven experimentally for the first time. From the six remaining cystine peptides interchain disulfide bonds between α-gliadins, γ-gliadins, and low molecular weight glutenin subunits were established. PMID:22439977

  15. Fragmentation Pathways in the Uracil Radical Cation

    SciTech Connect

    Zhou, Congyi; Matsika, Spiridoula; Kotur, Marija; Weinacht, Thomas C.

    2012-08-24

    We investigate pathways for fragmentation in the uracil radical cation using ab initio electronic structure calculations. We focus on the main fragments produced in pump–probe dissociative ionization experiments. These are fragments with mass to charge ratios (m/z) of 69, 28, 41, and 42. Barriers to dissociation along the ground ionic surface are reported, which provide an estimate of the energetic requirements for the production of the main fragments. Finally, direct and sequential fragmentation mechanisms have been analyzed, and it is concluded that sequential fragmentation after production of fragment with m/z 69 is the dominant mechanism for the production of the smaller fragments.

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

    PubMed

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

    2016-08-16

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

  17. Spondylopelvic dissociation.

    PubMed

    Sullivan, Matthew P; Smith, Harvey E; Schuster, James M; Donegan, Derek; Mehta, Samir; Ahn, Jaimo

    2014-01-01

    Spondylopelvic dissociation is a complex injury pattern resulting in multiplanar instability of the lumbopelvis. These injuries have traditionally been known as "suicide jumper's fractures" and have recently increased in prevalence as a result of under-vehicle explosions seen in the past decade of military conflicts in the Middle East. The hallmarks of spondylopelvic dissociation are bilateral vertical sacral fractures with a horizontal component, resulting in lumbosacral instability in the sagittal and axial planes. Surgical treatment has evolved greatly and both percutaneous and open options are available, with triangular osteosynthesis being the most relied on method of fixation. PMID:24267208

  18. Gas-Phase Fragmentation Pathways of Mixed Addenda Keggin Anions: PMo12-nW nO 40 3- (n = 0-12).

    PubMed

    Gunaratne, K Don D; Prabhakaran, Venkateshkumar; Johnson, Grant E; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo(12-n)W(n)O(40)(3-) (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed addenda POMs examined in this study. CID of molybdenum-rich anions, PMo(12-n)W(n)O(40)(3-) (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and 22 oxygen atoms (M(7)O(22)(2-)) and its complementary singly charged PM(5)O(18)(-) ion. In comparison, the doubly charged Lindqvist anion, (M(6)O(19)(2-)) and its complementary singly charged PM(6)O(21)(-) ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo(12-n)W(n)O(40)(3-) (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms in the POM may be attributed to the higher barrier of tungsten-rich anions towards isomerization. We present evidence that the observed distribution of Mo and W atoms in the major M(6)O(19)(2-) and M(7)O(22)(2-) fragment ions is different from that predicted by a random distribution, indicating substantial segregation of the addenda metal atoms in the POMs. Charge reduction of the triply charged precursor anion resulting in formation of doubly charged anions is also observed. This is a dominant pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and charge loss pathways in CID of POM anions. PMID:25832027

  19. Gas-Phase Fragmentation Pathways of Mixed Addenda Keggin Anions: PMo12-nWnO40 3- (n = 0-12)

    NASA Astrophysics Data System (ADS)

    Gunaratne, K. Don D.; Prabhakaran, Venkateshkumar; Johnson, Grant E.; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo12-nWnO40 3- (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed addenda POMs examined in this study. CID of molybdenum-rich anions, PMo12-nWnO40 3- (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and 22 oxygen atoms (M7O22 2-) and its complementary singly charged PM5O18 - ion. In comparison, the doubly charged Lindqvist anion, (M6O19 2-) and its complementary singly charged PM6O21 - ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo12-nWnO40 3- (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms in the POM may be attributed to the higher barrier of tungsten-rich anions towards isomerization. We present evidence that the observed distribution of Mo and W atoms in the major M6O19 2- and M7O22 2- fragment ions is different from that predicted by a random distribution, indicating substantial segregation of the addenda metal atoms in the POMs. Charge reduction of the triply charged precursor anion resulting in formation of doubly charged anions is also observed. This is a dominant pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and charge loss pathways in CID of POM anions.

  20. First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

    NASA Astrophysics Data System (ADS)

    Varghese, Jithin J.; Mushrif, Samir H.

    2015-05-01

    Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cun where n = 2-12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barrier for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C-H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH3 and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CHx (x = 1-3) species and recombination of H with CHx have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.

  1. Renormalization screening and collision-induced quantum interference in dense plasmas

    SciTech Connect

    Jung, Young-Dae; Rasheed, A.; Jamil, M.

    2014-07-15

    The influence of renormalization screening and collision-induced quantum interference in electron-electron collisions is investigated in partially ionized dense hydrogen plasmas. The effective interaction potential with the total spin-states of the collision system is considered to obtain the differential electron-electron scattering cross section. The results show that the renormalization plasma screening effect suppresses the electron-electron scattering cross section, including the quantum interference effect, especially, except for the forward and backward scattering directions. It is also shown that the renormalization plasma screening effect on the scattering cross section decreases with increasing collision energy. However, the renormalization screening effect is found to be important for the forward directions in the scattering cross section neglecting the quantum interference effect. The variations of the renormalization screening and collision-induced quantum interference effects are also discussed.

  2. Theory of collision-induced translation-rotation spectra: H2-He

    NASA Technical Reports Server (NTRS)

    Birnbaum, G.; Chu, S.-I.; Dalgarno, A.; Frommhold, L.; Wright, E. L.

    1984-01-01

    An adiabatic quantal theory of spectral line shapes in collision-induced absorption and emission is presented which incorporates the induced translation-rotation and translation-vibration spectra. The generalization to account for the anisotropy of the scattering potential is given. Calculations are carried out of the collision-induced absorption spectra of He in collisions with H2 with ab initio electric dipole functions and realistic potentials. The anisotropy of the interaction potential is small and is not included in the calculations. The predicted spectra are in satisfactory agreement with experimental data though some deviations occur which may be significant. The rotational line shapes have exponential wings and are not Lorentzian. The connection between the quantal and classical theories is written out explicitly for the isotropic overlap induction.

  3. Collision-induced absorption of radiation in the atmospheres of late-type stars

    NASA Astrophysics Data System (ADS)

    Pavlenko, Ya. V.

    2016-05-01

    Problems associated with taking into account absorption induced by collisions between hydrogen and helium atoms, helium atoms and hydrogen molecules, and hydrogen molecules, resulting in the formation of short-lived, quasi-molecular complexes are discussed, together with opacity in the atmospheres of late-type stars due to such absorption. There is good agreement between such opacities computed using codes developed by the author and by R. Kurucz. To demonstrate the importance of including collision-induced opacity, theoretical fluxes are compared to the observed spectral energy distribution of the metal-poor L subdwarf SDSS J125637.13-022452.4. The spectral energy distribution of this object can be reproduced with an effective temperature of T eff = 2600 K only if collision-induced absorption is taken into account.

  4. Correlation diagram model for interpreting propensity rules in collision induced vibrational relaxation

    SciTech Connect

    McDonald, D.B.; Rice, S.A.

    1981-05-01

    Propensity rules for collision induced vibrational energy transfer are derived by a correlation diagram technique similar to that used by Woodward and Hoffman to treat symmetry restrictions in concerted reactions. A rough quantification is accomplished by an ad hoc generalization of the modified SSH breathing sphere model. Predicted relative transfer rates agree qualitatively and, in some cases, quantitatively with those observed for collisions of benzene, aniline, and pyrazine with inert atoms.

  5. Transition probability of the 5971-A line in neutral uranium from collision-induced fluorescence spectroscopy

    SciTech Connect

    Gagne, J.M.; Mongeau, B.; Demers, Y.; Pianarosa, P.

    1981-09-01

    From collision-induced fluorescence spectroscopy measurements, we have determined the transition probability Aof the 5971-A transition in neutral uranium. Our value, A/sub 5971/ = (5.9 +- 1.8) x 10/sup 5/ sec/sup -1/, is, within experimental error, in good agreement with the previous determination of Corliss, A/sub 5971/ = (7.3 +- 3.0) x 10/sup 5/ sec/sup -1/ (J. Res. Nat. Bur. Stand. Sect. A 80,1 (1976)).

  6. Multipolar polarizations of methane from isotropic and anisotropic collision-induced light scattering

    SciTech Connect

    Bancewicz, T.; Nowicka, K.; Godet, J.-L.; Le Duff, Y.

    2004-06-01

    The anisotropic and isotropic binary collision-induced spectra scattered by gaseous methane have been measured in absolute units up to 900 cm{sup -1} from the Rayleigh line. Corresponding theoretical intensities taking into account multipolar polarizabilities have been calculated using a semiclassical procedure. From the analysis of, mainly, our isotropic scattering data, values of the dipole-quadrupole and dipole-octopole polarizabilities are deduced. They are found to be in good agreement with recent ab initio calculations.

  7. Collision-induced Magnetic Reconnection and a Unified Interpretation of Polarization Properties of GRBs and Blazars

    NASA Astrophysics Data System (ADS)

    Deng, Wei; Zhang, Haocheng; Zhang, Bing; Li, Hui

    2016-04-01

    The jet composition and energy dissipation mechanism of gamma-ray bursts (GRBs) and blazars are fundamental questions that remain not fully understood. One plausible model is to interpret the γ-ray emission of GRBs and optical emission of blazars as synchrotron radiation of electrons accelerated from the collision-induced magnetic dissipation regions in Poynting-flux-dominated jets. The polarization observation is an important and independent information to test this model. Based on our recent 3D relativistic MHD simulations of collision-induced magnetic dissipation of magnetically dominated blobs, here we perform calculations of the polarization properties of the emission in the dissipation region and apply the results to model the polarization observational data of GRB prompt emission and blazar optical emission. We show that the same numerical model with different input parameters can reproduce well the observational data of both GRBs and blazars, especially the 90° polarization angle (PA) change in GRB 100826A and the 180° PA swing in blazar 3C279. This supports a unified model for GRB and blazar jets, suggesting that collision-induced magnetic reconnection is a common physical mechanism to power the relativistic jet emission from events with very different black hole masses.

  8. Electron capture induced dissociation of nucleotide anions in water nanodroplets.

    PubMed

    Liu, B; Haag, N; Johansson, H; Schmidt, H T; Cederquist, H; Brondsted Nielsen, S; Zettergren, H; Hvelplund, P; Manil, B; Huber, B A

    2008-02-21

    We have studied the outcome of collisions between the hydrated nucleotide anion adenosine 5'-monophosphate (AMP) and sodium. Electron capture leads to hydrogen loss as well as water evaporation regardless of the initial number m of water molecules attached to the parent ion (m< or =16). The yield of dianions with microsecond lifetimes increases strongly with m, which is explained from dielectric screening of the two charges by the water nanodroplet. For comparison, collision induced dissociation results in water losses with no or very little damage of the AMP molecule itself. PMID:18298174

  9. Computational study of collision-induced dipole moments and absorption spectra of H

    NASA Astrophysics Data System (ADS)

    Zheng, Chunguang

    1997-08-01

    H2-H2 collision-induced absorption (CIA) spectra are computed for the first over-tone band at temperatures from 20 to 500 K, and for the rototranslational band at temperatures from 600 to 7,000 K. The theoretical results are based on simple model line shapes. The parameters of the model functions are obtained from the three lowest translational spectral moments, which are computed from the H2-H2 collision-induced dipole moments of Meyer et al. (1) using the sum formulae (2, 3). Ab initio computations of H2-H2 collision- induced dipole moments are performed using the Gaussian 92 program (4). The computations extend the previous work of Meyer et al. (1). Four internuclear distances of H2 molecule 1.111, 1.449, 1.787 and 2.150 a.u., and eleven intermolecular distances of H2-H2 from 2.5 to 9.0 a.u. are included in the computations. The radial transition matrix elements of the collision- induced dipole components are obtained for vibrational transitions /Delta v = (v1' - v1) + (v2' - v2) = 0, 1, 2, 3 and v1,/ v2 = 0, 1, 2. where v1 and v2 are the vibrational quantum numbers of the two interacting H2 molecules, and primes denote final states. The dependences of these matrix elements on the rotational quantum numbers of the two H2 molecules j1j1'j2j2' are obtained for j1j1'j2j2' up to 10. These matrix elements are suitable for high temperature H2-H2 CIA computations. The second overtone band H2-H2 CIA spectra are computed for the first time at temperatures from 20 to 500 K employing the newly developed H2-H2 collision-induced dipole moments. The computations are based on the three lowest translational spectral moments and simple model line shapes.

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  11. Investigations of acidity and nucleophilicity of diphenyldithiophosphinate ligands using theory and gas-phase dissociation reactions

    SciTech Connect

    Christopher M. Leavitt; Garold L. Gresham; Michael T. Benson; Jean-Jaques Gaumet; Dean Peterman; John Klaehn; Megan Moser; Frederic Aubriet; Michael J. Van Stipdonk; Gary S. Groenewold

    2008-04-01

    Diphenyldithiophosphinate (DTP) ligands modified with electron-withdrawing trifluoromethyl (TFM) substitutents are of high interest because they have demonstrated potential for exceptional separation of Am3+ from lanthanide3+ cations. Specifically, the bis(ortho-TFM) (L1-) and (ortho-TFM)(meta-TFM) (L2-) derivatives have shown excellent separation selectivity, while the bis(meta-TFM) (L3)- and unmodified DTP (Lu-) did not. Factors responsible for selective coordination have been investigated using density functional theory (DFT) calculations in concert with competitive dissociation reactions in the gas phase. To evaluate the role of (DTP+H) acidity, density functional calculations were used to predict pKa values, which followed the trend of L3 < L2 < L1 < Lu. The order of the TFM-modified (DTP+H) acids was opposite of what would be expected based on the e--withdrawing effects of the TFM group, suggesting that secondary factors are influencing the pKa and nucleophilicity. The relative nucleophilicities of the DTP anions were evaluated by forming metal-mixed ligand complexes in a trapped ion mass spectrometer, and then fragmenting them using competitive collision induced dissociation. Relative to Na+, the unmodified Lu- anion was the strongest nucleophile. Comparing the TFM derivatives, the bis(ortho-TFM) derivative L1- was found to be the strongest nucleophile, while the bis(meta-TFM) L3- was the weakest, a trend consistent with the pKa calculations. DFT modeling of the Na+ complexes suggested that the elevated cation affinity of the L1- and L2- anions was due to donation of electron density from fluorine atoms to the metal center, which was occurring in rotational conformers where the TFM moiety was proximate to the Na+-dithiophosphinate group. Competitive dissociation experiments were performed with the dithiophosphinate anions complexed with europium nitrate species; ionic dissociation of these complexes always produced the TFM-modified dithiophosphinate anions

  12. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS

    NASA Astrophysics Data System (ADS)

    Hage, Christoph; Ihling, Christian H.; Götze, Michael; Schäfer, Mathias; Sinz, Andrea

    2016-07-01

    We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids.

  13. Dissociative disorders in DSM-5.

    PubMed

    Spiegel, David; Lewis-Fernández, Roberto; Lanius, Ruth; Vermetten, Eric; Simeon, Daphne; Friedman, Matthew

    2013-01-01

    The rationale, research literature, and proposed changes to the dissociative disorders and conversion disorder in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) are presented. Dissociative identity disorder will include reference to possession as well as identity fragmentation, to make the disorder more applicable to culturally diverse situations. Dissociative amnesia will include dissociative fugue as a subtype, since fugue is a rare disorder that always involves amnesia but does not always include confused wandering or loss of personality identity. Depersonalization disorder will include derealization as well, since the two often co-occur. A dissociative subtype of posttraumatic stress disorder (PTSD), defined by the presence of depersonalization or derealization in addition to other PTSD symptoms, is being recommended, based upon new epidemiological and neuroimaging evidence linking it to an early life history of adversity and a combination of frontal activation and limbic inhibition. Conversion disorder (functional neurological symptom disorder) will likely remain with the somatic symptom disorders, despite considerable dissociative comorbidity. PMID:23394228

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

    SciTech Connect

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

    2010-11-15

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

  15. 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.

  16. Identification of Anthropogenic Compounds in Urban Environments and Evaluation of Automated Methods for Reading Fragmentation-A Case of River Water.

    PubMed

    Yamamoto, Atsushi; Matsumoto, Naoko; Kawasaki, Hideya; Arakawa, Ryuichi

    2016-01-01

    A workflow based on liquid chromatography/high-resolution mass spectrometry (LC/HR-MS) was applied for the identification of compounds in urban environments. Substances extracted by solid-phase extraction from river water were wholly analyzed by LC/HR-MS without any purification. Fragmentation in collision-induced dissociation was manually studied for the 20 most intense ions in positive- and negative-ion electrospray ionization with accurate mass determination at a resolution of 100,000. Sixteen anthropogenic compounds in the extract were identified and confirmed using standard reference reagents. These compounds consisted of pharmaceuticals, surfactants, flame retardants, and industrial intermediates. The majority of the compounds are common in our daily life. In the identification process, two automated methods, MAGMa and MetFrag/MetFusion, for reading fragmentation were evaluated for the sixteen compounds. Although automated methods could be used to retrieve the correct molecular structures in most cases, they could not always be promoted to the top rank. Automated methods have yet to be a complete solution for identifying chemical compounds, but will considerably reduce the burden for humans in reading fragmentation. PMID:27313978

  17. Momentum mapping spectrometer for probing the fragmentation dynamics of molecules induced by keV electrons

    NASA Astrophysics Data System (ADS)

    Singh, Raj; Bhatt, Pragya; Yadav, Namita; Shanker, R.

    2011-05-01

    We describe a new experimental setup for studying the fragmentation dynamics of molecules induced by the impact of keV electrons using the well-known technique of recoil ion momentum spectroscopy. The apparatus consists of mainly a time- and position-sensitive multi-hit particle detector for ion analysis and a channel electron multiplier detector for detecting the ejected electrons. Different components of the setup and the relevant electronics for data acquisition are described in detail with their working principles. In order to verify the reliable performance of the setup, we have recorded the collision-induced ionic spectra of the CO2 molecule by the impact of keV electrons. Information about the ion pairs of CO+:O+, C+:O+ and O+:O+ resulting from dissociative ionizing collisions of 20 and 26 keV electrons with a dilute gaseous target of CO2 molecules has been obtained. Under conditions of the present experiment, the momentum resolutions of the spectrometer for the combined momenta of CO+ and O+ ions in the direction of the time-of-flight axis and perpendicular to the direction of an electron beam are found to be 10.0 ± 0.2 and 15.0 ± 0.3 au, respectively.

  18. Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.

    PubMed

    Tsugawa, Hiroshi; Kind, Tobias; Nakabayashi, Ryo; Yukihira, Daichi; Tanaka, Wataru; Cajka, Tomas; Saito, Kazuki; Fiehn, Oliver; Arita, Masanori

    2016-08-16

    Compound identification from accurate mass MS/MS spectra is a bottleneck for untargeted metabolomics. In this study, we propose nine rules of hydrogen rearrangement (HR) during bond cleavages in low-energy collision-induced dissociation (CID). These rules are based on the classic even-electron rule and cover heteroatoms and multistage fragmentation. We evaluated our HR rules by the statistics of MassBank MS/MS spectra in addition to enthalpy calculations, yielding three levels of computational MS/MS annotation: "resolved" (regular HR behavior following HR rules), "semiresolved" (irregular HR behavior), and "formula-assigned" (lacking structure assignment). With this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in the MassBank database and 84.8% of a total of 36370 MS/MS fragment ions in the GNPS database were (semi-) resolved by predicted bond cleavages. We also introduce the MS-FINDER software for structure elucidation. Molecular formulas of precursor ions are determined from accurate mass, isotope ratio, and product ion information. All isomer structures of the predicted formula are retrieved from metabolome databases, and MS/MS fragmentations are predicted in silico. The structures are ranked by a combined weighting score considering bond dissociation energies, mass accuracies, fragment linkages, and, most importantly, nine HR rules. The program was validated by its ability to correctly calculate molecular formulas with 98.0% accuracy for 5063 MassBank MS/MS records and to yield the correct structural isomer with 82.1% accuracy within the top-3 candidates. In a test with 936 manually identified spectra from an untargeted HILIC-QTOF MS data set of human plasma, formulas were correctly predicted in 90.4% of the cases, and the correct isomer structure was retrieved at 80.4% probability within the top-3 candidates, including for compounds that were absent in mass spectral libraries. The MS-FINDER software is freely available at http

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

    NASA Astrophysics Data System (ADS)

    Harrison, Alex G.; Wang, Jian-Yao

    1997-01-01

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

  20. Fusion reactions in collisions induced by Li isotopes on Sn targets

    SciTech Connect

    Fisichella, M.; Shotter, A. C.; Di Pietro, A.; Figuera, P.; Lattuada, M.; Marchetta, C.; Musumarra, A.; Pellegriti, M. G.; Ruiz, C.; Scuderi, V.; Strano, E.; Torresi, D.; Zadro, M.

    2012-10-20

    Fusion cross sections for the {sup 6}Li+{sup 120}Sn and {sup 7}Li+{sup 119}Sn systems have been measured. We aim to search for possible effects due to the different neutron transfer Q-values, by comparing the fusion cross sections for the two systems below the barrier. This experiment is the first step of a wider systematic aiming to study the above problems in collisions induced by stable and unstable Li isotopes on tin all forming the same compound nucleus.

  1. The temperature dependence of collision-induced absorption by oxygen near 6 microns

    NASA Technical Reports Server (NTRS)

    Orlando, John J.; Tyndall, Geoffrey S.; Nickerson, Karen E.; Calvert, Jack G.

    1991-01-01

    Coefficients for oxygen absorption in the infrared induced by collisions with O2 and N2 are reported over the range 1400-1800/cm and 225-356 K. These coefficients are used to calculate the absorption for O2 in air as a function of temperature and wavenumber, and comparisons are made with previous determinations. In addition, structured absorption features superimposed on the broad collision-induced absorption band, which were observed at all temperatures studied, are interpreted in terms of the presence of (O2)2 and O2-N2 van der Waals molecules.

  2. Restoring detailed balance in the Landau-Teller probabilities for collision-induced vibrational transitions.

    PubMed

    Nikitin, E E; Troe, J

    2006-05-01

    The general quasi-classical treatment for collision-induced vibrational transitions in diatomic molecules, under near-adiabatic conditions, is used to derive quantum corrections for probabilities, calculated in the external field approximation originally used by Landau and Teller. The quantum corrections are expressed through the Landau-Teller classical collision time. The first-order correction to the classical exponent restores detailed balance for up- and down-transitions and does not depend on the properties of the bath except for its temperature. The limits of applicability of the first-order correction are discussed. PMID:16633688

  3. Isotropic collision-induced light scattering by gaseous CF{sub 4}

    SciTech Connect

    Elliasmine, A.; Godet, J.L.; Le Duff, Y.,; Bancewicz, T.

    1997-06-01

    The binary isotropic collision-induced scattering spectra of the gaseous tetrafluoromethane has been measured in absolute units in the 50{endash}150cm{sup {minus}1} frequency range. Corresponding theoretical intensities taking into account multipolar polarizabilities have been calculated in a semiclassical way. From a comparison with experiment, the independent components of dipole-quadrupole and dipole-octupole polarizability tensors have been estimated. They have been compared with those previously deduced from depolarized spectrum and with recent theoretical {ital ab initio} calculations. {copyright} {ital 1997} {ital The American Physical Society}

  4. Negative-charge driven fragmentations for evidencing zwitterionic forms from doubly charged coppered peptides.

    PubMed

    Boutin, Michel; Bich, Claudia; Afonso, Carlos; Fournier, Françoise; Tabet, Jean-Claude

    2007-01-01

    In aqueous solution, amino acids (AA) and peptides are known to exist as zwitterions over a large pH range. However, in the gas phase, i.e. in electrospray (ESI), the zwitterionic form becomes unfavorable owing to the absence of stabilizing effects from intermolecular solvation. Nevertheless, during mass spectrometry experiments, the presence of a metallic cation can reinforce the zwitterionic character of the molecule and thus influence its fragmentation under low energy collision-induced dissociation (CID) conditions. The [M + Cu(II)](2+) complexes of six pentapeptides (YGGFL, YGGFL(NH(2)), YGGFK, YGGFQ, KYGGF and QYGGF) were analyzed by collision to highlight the presence of zwitterions. The experiments were performed on a 3D-ion trap equipped with an orthogonal ESI source. For each peptides studied, negative-charge driven fragmentations on globally positively charged ions were observed. These fragmentation mechanisms, generally observed in the negative mode, suggest the competitive deprotonation of the C-terminal carboxylic acid or of the tyrosine side-chain residue for each peptide studied and thus a zwitterionic form to preserve the charge balance. Moreover, the specific loss of (CH(3)--C(6)H(4)--O)(*) characterizes YGGFK compared to YGGFQ and the specific loss of styrene characterizes KYGGF compared to QYGGF. These results allow the differentiation of the two couples of isobaric pentapeptides. An unusual loss of NH(4) (+), which occurred from the N-terminus, was also observed for YGGFL, YGGFL(NH(2)), YGGFK and YGGFQ. Finally, the reduction of Cu(II) to Cu(I), concomitant with the (CH(3)--C(6)H(4)--O)(*) release, was pointed out for YGGFK. PMID:17149792

  5. Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

    SciTech Connect

    Chowdhury, Saiful M.; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2009-07-01

    Chemical cross-linking combined with mass spectrometric analysis is emerging as a powerful technique for protein-protein interaction and protein structure elucidation studies.1 Cross-linkers covalently link two interacting proteins, often with chemistries specific to certain amino acid side chains. After enzymatic digestion of the proteins, the resulting cross-linked peptides can be subjected to analysis by LC-MS(/MS) to identify cross-linked species.2,3 For studying protein interactions using chemical cross-linking towards global discovery-based applications, the critical needs are the development of cross-linkers that are highly specific, amenable to LC-MS/MS, and resulting spectra are interpretable by bioinformatics tools to automatically assign cross-linked peptides with high confidence.4-10 As recently mentioned by Aebersold and co-workers, due to the low relative abundances of cross-linking products compared to their unmodified counterparts, enrichment of cross-linked species is also highly desirable to improve the likelihood of unambiguous identification of cross-linked peptides.6 Most of the currently available enrichable cross-linkers are bulky and are not amenable to studying protein-protein interactions in vivo. To discover protein-protein interactions with high confidence, there is a need for chemical cross-linkers that can effectively label protein complexes, utilize mass spectrometry based bottom-up proteomics analysis pipelines and also contains enrichment functionality.

  6. Infrared Multiple Photon Dissociation Spectroscopy of a Gas-Phase Oxo-Molybdenum Complex with 1,2-Dithiolene Ligands

    PubMed Central

    2015-01-01

    Electrospray ionization (ESI) in the negative ion mode was used to create anionic, gas-phase oxo-molybdenum complexes with dithiolene ligands. By varying ESI and ion transfer conditions, both doubly and singly charged forms of the complex, with identical formulas, could be observed. Collision-induced dissociation (CID) of the dianion generated exclusively the monoanion, while fragmentation of the monoanion involved decomposition of the dithiolene ligands. The intrinsic structure of the monoanion and the dianion were determined by using wavelength-selective infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory calculations. The IRMPD spectrum for the dianion exhibits absorptions that can be assigned to (ligand) C=C, C–S, C—C≡N, and Mo=O stretches. Comparison of the IRMPD spectrum to spectra predicted for various possible conformations allows assignment of a pseudo square pyramidal structure with C2v symmetry, equatorial coordination of MoO2+ by the S atoms of the dithiolene ligands, and a singlet spin state. A single absorption was observed for the oxidized complex. When the same scaling factor employed for the dianion is used for the oxidized version, theoretical spectra suggest that the absorption is the Mo=O stretch for a distorted square pyramidal structure and doublet spin state. A predicted change in conformation upon oxidation of the dianion is consistent with a proposed bonding scheme for the bent-metallocene dithiolene compounds [Lauher, J. W.; Hoffmann, R. J. Am. Chem. Soc.1976, 98, 1729−1742], where a large folding of the dithiolene moiety along the S···S vector is dependent on the occupancy of the in-plane metal d-orbital. PMID:24988369

  7. Photodissociation of gaseous CH{sub 3}COSH at 248 nm by time-resolved Fourier-transform infrared emission spectroscopy: Observation of three dissociation channels

    SciTech Connect

    Hu, En-Lan; Tsai, Po-Yu; Fan, He; Lin, King-Chuen

    2013-01-07

    Upon one-photon excitation at 248 nm, gaseous CH{sub 3}C(O)SH is dissociated following three pathways with the products of (1) OCS + CH{sub 4}, (2) CH{sub 3}SH + CO, and (3) CH{sub 2}CO + H{sub 2}S that are detected using time-resolved Fourier-transform infrared emission spectroscopy. The excited state {sup 1}(n{sub O}, {pi}{sup *}{sub CO}) has a radiative lifetime of 249 {+-} 11 ns long enough to allow for Ar collisions that induce internal conversion and enhance the fragment yields. The rate constant of collision-induced internal conversion is estimated to be 1.1 Multiplication-Sign 10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}. Among the primary dissociation products, a fraction of the CH{sub 2}CO moiety may undergo further decomposition to CH{sub 2}+ CO, of which CH{sub 2} is confirmed by reaction with O{sub 2} producing CO{sub 2}, CO, OH, and H{sub 2}CO. Such a secondary decomposition was not observed previously in the Ar matrix-isolated experiments. The high-resolution spectra of CO are analyzed to determine the ro-vibrational energy deposition of 8.7 {+-} 0.7 kcal/mol, while the remaining primary products with smaller rotational constants are recognized but cannot be spectrally resolved. The CO fragment detected is mainly ascribed to the primary production. A prior distribution method is applied to predict the vibrational distribution of CO that is consistent with the experimental findings.

  8. A tandem mass spectrometric study of bile acids: interpretation of fragmentation pathways and differentiation of steroid isomers.

    PubMed

    Qiao, Xue; Ye, Min; Liu, Chun-fang; Yang, Wen-zhi; Miao, Wen-juan; Dong, Jing; Guo, De-an

    2012-02-01

    Bile acids are steroids with a pentanoic acid substituent at C-17. They are the terminal products of cholesterol excretion, and play critical physiological roles in human and animals. Bile acids are easy to detect but difficult to identify by using mass spectrometry due to their poly-ring structure and various hydroxylation patterns. In this study, fragmentation pathways of 18 free and conjugated bile acids were interpreted by using tandem mass spectrometry. The analyses were conducted on ion trap and triple quadrupole mass spectrometers. Upon collision-induced dissociation, the conjugated bile acids could cleave into glycine or taurine related fragments, together with the steroid skeleton. Fragmentations of free bile acids were further elucidated, especially by atmospheric pressure chemical ionization mass spectrometry in positive ion mode. Aside from universally observed neutral losses, eliminations occurred on bile acid carbon rings were proposed for the first time. Moreover, four isomeric 5β-cholanic acid hydroxyl derivatives (3α,6α-, 3α,7β-, 3α,7α-, and 3α,12α-) were differentiated using electrospray ionization in negative ion mode: 3α,7β-OH substituent inclined to eliminate H(2)O and CH(2)O(2) groups; 3α,6α-OH substituent preferred neutral loss of two H(2)O molecules; 3α,12α-OH substituent apt to lose the carboxyl in the form of CO(2) molecule; and 3α,7α-OH substituent exhibited no further fragmentation after dehydration. This study provided specific interpretation for mass spectra of bile acids. The results could contribute to bile acid analyses, especially in clinical assays and metabonomic studies. PMID:22133544

  9. Collision-induced rotovibrational spectra of H/sub 2/-He pairs from first principles

    SciTech Connect

    Frommhold, L.; Meyer, W.

    1987-01-15

    A previous study of the collision-induced dipole moment has treated the H/sub 2/-He complex as a molecule in self-consistent-field and size-consistent coupled-electron-pair approximation (Meyer and Frommhold, Phys. Rev. A 34, 2771 (1986)). Based on that work, the vibrational dipole transition elements associated with the fundamental band (v = 0..-->..v' = 1) are obtained as functions of separation R of the collisional pair for the isotropic and anisotropic overlap induction components (lambdaL = 01 and 21), and the quadrupole- and hexadecapole-induced parts (lambdaL = 23 and 45). From these induced dipole components and Meyer, Hariharan, and Kutzelnigg's isotropic part of the ab initio potential surface, we compute in the (forbidden) fundamental band of hydrogen the collision-induced absorption spectra of the collisional complex of hydrogen (H/sub 2/) and helium from an exact quantum formalism. Both the shape of the computed spectral profiles and the theoretical absolute intensity agree closely with existing measurements at temperatures from 18 to 300 K. The fact that these spectra, and presumably the analogous overtone and ''hot'' (v>0) bands of the H/sub 2/-He complex which are not known from measurements, can be accurately obtained from basic principles is significant for research related to the atmospheres of the giant planets and late-type stars.

  10. Collision-induced hyper-Rayleigh light scattering in gaseous dihydrogen-neon mixtures

    SciTech Connect

    Glaz, W.; Bancewicz, T.; Godet, J.-L.; Haskopoulos, A.; Maroulis, G.

    2011-07-15

    Cartesian components of the collision-induced (CI) hyperpolarizability {Delta}{beta} tensor are computed for the linear, T-shaped, and 45 deg. configurations of the H{sub 2}-Ne pair in the intermolecular range 3 to 14 bohr. Symmetry-adapted components {Delta}{beta}{sub {lambda}L}{sup (K)}(R) of the vector (K=1) part, as well as the septor (K=3) part, of the H{sub 2}-Ne CI hyperpolarizability are calculated starting from the ab initio Cartesian hyperpolarizability tensor values transformed into their spherical counterparts. By applying these quantities, the vector together with the septor collision-induced hyper-Rayleigh (CIHR) spectra for the H{sub 2}-Ne binary gas mixture are determined in the frequency range from -1250 to 2500 cm{sup -1}. The profiles are partially employed as a benchmarking device to estimate the importance of the short intermolecular distance part of the {Delta}{beta}(R) dependence. The depolarization ratio of the CIHR spectra in the whole frequency range is also calculated. The nature of the CIHR signal and the feasibility of the related experiments are discussed and analyzed.

  11. Fragmentation pathways of polymer ions.

    PubMed

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

    2011-01-01

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

  12. Middle-down fragmentation for the identification and quantitation of site-specific methionine oxidation in an IgG1 molecule.

    PubMed

    Pipes, Gary D; Campbell, Phillip; Bondarenko, Pavel V; Kerwin, Bruce A; Treuheit, Michael J; Gadgil, Himanshu S

    2010-11-01

    A middle-down LC/MS approach, for the rapid quantitation and characterization of site-specific methionine oxidation in a recombinant monoclonal IgG1 molecule, is described. An IgG1 antibody was digested with endoprotease LysC under limited proteolytic conditions to produce two major components; an antigen binding fragment (Fab) and a crystallizable fraction (Fc). These fractions were then reduced to produce three major species; light chain (LC), Fc/2 which is the C terminal region of the heavy chain (HC) and the N-terminal heavy chain region (Fd). These three fragments were separated by reversed-phase HPLC using a diphenyl column. The diphenyl column resolved site-specific methionine oxidation in all three subunits. Middle-down N-terminal sequencing with a LCT premier mass spectrometer was used to identify the sites of oxidation in the LC. Sites of oxidation in the Fc/2 were identified using middle-down collision-induced dissociation (CID) on a Qtof premier. This method allowed for the rapid quantitation and identification of oxidation on each methionine residue in an IgG1 molecule. PMID:20845446

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

    PubMed

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

    2014-01-01

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

  14. Dynamics of dissociative electron attachment to ammonia

    NASA Astrophysics Data System (ADS)

    Rescigno, T. N.; Trevisan, C. S.; Orel, A. E.; Slaughter, D. S.; Adaniya, H.; Belkacem, A.; Weyland, Marvin; Dorn, Alexander; McCurdy, C. W.

    2016-05-01

    Ab initio theoretical studies and momentum-imaging experiments are combined to provide a consistent picture of the dynamics of dissociative electron attachment to ammonia through its 5.5- and 10.5-eV resonance channels. The present study clarifies the character and symmetry of the anion states involved and the dynamics that leads to the observed fragment-ion channels, their branching ratios, and angular distributions.

  15. 2D laser-collision induced fluorescence in low-pressure argon discharges

    SciTech Connect

    Barnat, E. V.; Weatherford, B. R.

    2015-09-25

    Development and application of laser-collision induced fluorescence (LCIF) diagnostic technique is presented for the use of interrogating argon plasma discharges. Key atomic states of argon utilized for the LCIF method are identified. A simplified two-state collisional radiative model is then used to establish scaling relations between the LCIF, electron density, and reduced electric fields (E/N). The procedure used to generate, detect and calibrate the LCIF in controlled plasma environments is discussed in detail. LCIF emanating from an argon discharge is then presented for electron densities spanning 109 e cm–3 to 1012 e cm–3 and reduced electric fields spanning 0.1 Td to 40 Td. Lastly, application of the LCIF technique for measuring the spatial distribution of both electron densities and reduced electric field is demonstrated.

  16. 2D laser-collision induced fluorescence in low-pressure argon discharges

    DOE PAGESBeta

    Barnat, E. V.; Weatherford, B. R.

    2015-09-25

    Development and application of laser-collision induced fluorescence (LCIF) diagnostic technique is presented for the use of interrogating argon plasma discharges. Key atomic states of argon utilized for the LCIF method are identified. A simplified two-state collisional radiative model is then used to establish scaling relations between the LCIF, electron density, and reduced electric fields (E/N). The procedure used to generate, detect and calibrate the LCIF in controlled plasma environments is discussed in detail. LCIF emanating from an argon discharge is then presented for electron densities spanning 109 e cm–3 to 1012 e cm–3 and reduced electric fields spanning 0.1 Tdmore » to 40 Td. Lastly, application of the LCIF technique for measuring the spatial distribution of both electron densities and reduced electric field is demonstrated.« less

  17. New section of the HITRAN database: Collision-induced absorption (CIA)

    NASA Astrophysics Data System (ADS)

    Richard, C.; Gordon, I. E.; Rothman, L. S.; Abel, M.; Frommhold, L.; Gustafsson, M.; Hartmann, J.-M.; Hermans, C.; Lafferty, W. J.; Orton, G. S.; Smith, K. M.; Tran, H.

    2012-07-01

    This paper describes the addition of Collision-Induced Absorption (CIA) into the HITRAN compilation. The data from different experimental and theoretical sources have been cast into a consistent format and formalism. The implementation of these new spectral data into the HITRAN database is invaluable for modeling and interpreting spectra of telluric and other planetary atmospheres as well as stellar atmospheres. In this implementation for HITRAN, CIAs of N2, H2, O2, CO2, and CH4 due to various collisionally interacting atoms or molecules are presented. Some CIA spectra are given over an extended range of frequencies, including several H2 overtone bands that are dipole-forbidden in the non-interacting molecules. Temperatures from tens to thousands of Kelvin are considered, as required, for example, in astrophysical analyses of objects, including cool white dwarfs, brown dwarfs, M dwarfs, cool main sequence stars, solar and extra-solar planets, and the formation of so-called first stars.

  18. Structure Effects in Collisions Induced by Halo and Weakly Bound Nuclei around the Coulomb Barrier

    NASA Astrophysics Data System (ADS)

    Scuderi, V.; di Pietro, A.; Acosta, L.; Amorini, F.; Borge, M. J. G.; Figuera, P.; Fisichella, M.; Fraile, L. M.; Gomez-Camacho, J.; Jeppesen, H.; Lattuada, M.; Martel, I.; Milin, M.; Musumarra, A.; Papa, M.; Pellegriti, M. G.; Raabe, R.; Randisi, G.; Rizzo, F.; Santonocito, D.; Sanchez, E. M. R.; Scalia, G.; Tengblad, O.; Torresi, D.; Vidal, A. M.; Zadro, M.

    In this contribution, results concerning different reaction channels for the collisions induced by the three Be isotopes, 9,10,11Be, on a 64Zn target at energies around the Coulomb barrier will be presented. The experiments with the radioactive 10,11Be beams were performed at REX-ISOLDE (CERN) whereas the experiment with the stable weakly bound 9Be beam was performed at LNS Catania. Elastic scattering angular distributions have been measured for the three systems 9,10,11Be + 64Zn at the same center of mass energy. The angular distributions were analyzed with optical potentials and reaction cross sections were obtained from optical model calculations, performed with the code PTOLEMY. For the 11Be + 64Zn reaction, the break-up angular distribution was also measured.

  19. Collision-induced desorption of CO from Ru(0001) by hyperthermal argon and nitrogen

    NASA Astrophysics Data System (ADS)

    Huang, Qiang; Lou, Yuanfu; Kleyn, Aart W.; Zaharia, Teodor; Gleeson, Michael A.

    2016-08-01

    Collision-induced desorption of CO from Ru(0001) by hyperthermal (5-9 eV) effusive beams of Ar and N + N2 has been studied at a sample temperature of 400 K. Prompt desorption occurs with cross sections on the order of 4 Å2. Based on post-exposure thermal desorption measurements, ~ 1/3 of the initial CO coverage cannot be desorbed by Ar on the time scale of the current experiments. In contrast, exposure to the mixed N + N2 beam appears to remove all CO from the irradiated region. This is attributed to a lowering of the CO binding energy by adsorbed N-atoms. While there is no evidence of a large influence of surface diffusion on the time scale of these exposure, desorption simulations suggest that local diffusion in the periphery of the exposed region influences the measured decay.

  20. Studies of collision-induced emission in the fundamental vibration-rotation band of H2

    NASA Astrophysics Data System (ADS)

    Caledonia, G. E.; Krech, R. H.; Wilkerson, T.; Taylor, R. L.; Birnbaum, G.

    Measurements are presented of the collision induced emission (CIE) from the fundamental vibration-rotation band of H2 taken over the temperature range of 900-3000 K. The spectral shape and strength of this IR band centered about 2.4 microns has been measured behind reflected shocks in mixtures of H2/Ar. The observed radiation at elevated temperatures is found to be dominantly in the Q branch. The results, compared with theory, show that radiation at elevated temperatures is primarily the result of an induced dipole moment in H2 induced by the overlap between the H2 and Ar electron clouds during collision. The strength of this interaction has been evaluated by an analysis of the measured temperature dependence of the absolute bandstrengths.

  1. Collision-induced frequency shifts in bright matter-wave solitons and soliton molecules

    NASA Astrophysics Data System (ADS)

    Martin, A. D.

    2016-02-01

    A recent experiment has detected collision-induced frequency shifts in bright matter-wave solitons [J. H. V. Nguyen et al., Nat. Phys. 10, 918 (2014), 10.1038/nphys3135]. Using a particle model, we derive the frequency shift for two solitons in a harmonic trap, and compare it to the recent experimental results and reported theoretical approximation. We find regimes where the frequency shift is much smaller than previously predicted, and propose experiments to test these findings. We also predict that reducing the experimental trap frequency will reveal soliton molecules or soliton bound states in a cold-atom system. The bound-state dynamics are found to be both highly phase dependent and sensitive to the residual 3D nature of the experiment.

  2. Quantum mechanical calculation of the collision-induced absorption spectra of N2-N2 with anisotropic interactions.

    PubMed

    Karman, Tijs; Miliordos, Evangelos; Hunt, Katharine L C; Groenenboom, Gerrit C; van der Avoird, Ad

    2015-02-28

    We present quantum mechanical calculations of the collision-induced absorption spectra of nitrogen molecules, using ab initio dipole moment and potential energy surfaces. Collision-induced spectra are first calculated using the isotropic interaction approximation. Then, we improve upon these results by considering the full anisotropic interaction potential. We also develop the computationally less expensive coupled-states approximation for calculating collision-induced spectra and validate this approximation by comparing the results to numerically exact close-coupling calculations for low energies. Angular localization of the scattering wave functions due to anisotropic interactions affects the line strength at low energies by two orders of magnitude. The effect of anisotropy decreases at higher energy, which validates the isotropic interaction approximation as a high-temperature approximation for calculating collision-induced spectra. Agreement with experimental data is reasonable in the isotropic interaction approximation, and improves when the full anisotropic potential is considered. Calculated absorption coefficients are tabulated for application in atmospheric modeling. PMID:25725730

  3. Ion-induced dissociation dynamics of acetylene

    SciTech Connect

    De, Sankar; Rajput, Jyoti; Roy, A.; Safvan, C. P.; Ghosh, P. N.

    2008-02-15

    We report on the results of dissociation dynamics of multiple charged acetylene molecules formed in collision with 1.2 MeV Ar{sup 8+} projectiles. Using the coincidence map, we can separate out the different dissociation pathways between carbon and hydrogen ionic fragments as well as complete two-body breakup events. From the measured slopes of the coincidence islands for carbon atomic fragments and theoretical values determined from the charge and momentum distribution of the correlated particles, we observe a diatom like behavior of the C-C charged complex during dissociation of multiply charged C{sub 2}H{sub 2}. We conclude that this behavior in breakup dynamics is a signature of sequentiality in dissociation of this multiply charged molecular species. The shape and orientation of the islands give further information about the momentum balance in the fragmentation process of two- or many-body dissociation pathways. Kinetic energy release of different breakup channels are reported here and compared with values calculated from the pure Coulomb explosion model.

  4. Electron Transfer Dissociation of Oligonucleotide Cations.

    PubMed

    Smith, Suncerae I; Brodbelt, Jennifer S

    2009-06-01

    Electron transfer dissociation (ETD) of multi-protonated 6 - 20-mer oligonucleotides and 12- and 14-mer duplexes is compared to collision activated dissociation (CAD). ETD causes efficient charge reduction of the multi-protonated oligonucleotides in addition to limited backbone cleavages to yield sequence ions of low abundance. Subsequent CAD of the charge-reduced oligonucleotides formed upon electron transfer, in a net process termed electron transfer collision activated dissociation (ETcaD), results in rich fragmentation in terms of w, a, z, and d products, with a marked decrease in the abundance of base loss ions and internal fragments. Complete sequencing was possible for nearly all oligonucleotides studied. ETcaD of an oligonucleotide duplex resulted in specific backbone cleavages, with conservation of weaker non-covalent bonds. PMID:20161288

  5. Dissociation of acetaldehyde in intense laser field: Coulomb explosion or field-assisted dissociation?

    NASA Astrophysics Data System (ADS)

    Elshakre, Mohamed E.; Gao, Lirong; Tang, Xiaoping; Wang, Sufan; Shu, Yafei; Kong, Fanao

    2003-09-01

    Dissociation of acetaldehyde in moderate strong laser field of 1013-1014W/cm2 was investigated. Singly charged parent ion CH3CHO+ and fragmental ions CH3+, CHO+, C2H4+, O+, CH2CHO+, and H+ were produced by 800 nm laser of 100 fs pulse duration and recorded by time-of-flight mass spectrometer. The CH3+ fragment further dissociated to CH2+, CH+, and C+ ions at higher intensity. Ab initio calculated results show that the singly-, doubly-, and triply charged parent ions are stable. So, the dissociation mechanism was not due to Coulomb explosion of multicharged ion. A field-assisted dissociation (FAD) theory, which assumes that only one bond undergoes dissociation while the rest of the molecular geometry stays unchanged, was employed to treat the dissociation dynamics. Accordingly, the dressed potential energy surfaces of the ground state for the parent and the fragment ions were calculated. Corresponding quasiclassical trajectory calculations show that the bond ruptures take place in the order of C-C, C-O, and C-H, agreeing with the observation. The observed angular dependence and charge distribution of the product ions can also be interpreted by the FAD theory.

  6. Structures, Unimolecular Fragmentations, and Reactivities of the Self-Assembled Multimetallic/Peptide Complexes [Mnn (GlyGly-H)2n-1 ](+) and [Mnn+1 (GlyGly-H)2n ](2.).

    PubMed

    Moghaddam, Maryam B; Fridgen, Travis D

    2016-07-18

    Complexes of Mn(2+) with deprotonated GlyGly are investigated by sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiple-photon dissociation spectroscopy, ion-molecule reactions, and computational methods. Singly [Mnn (GlyGly-H)2n-1 ](+) and doubly [Mnn+1 (GlyGly-H)2n ](2+) charged clusters are formed from aqueous solutions of MnCl2 and GlyGly by electrospray ionization. The most intense ion produced was the singly charged [M2 (GlyGly-H)3 ](+) cluster. Singly charged clusters show extensive fragmentations of small neutral molecules such as water and carbon dioxide as well as dissociation pathways related to the loss of NH2 CHCO and GlyGly. For the doubly charged clusters, however, loss of GlyGly is observed as the main dissociation pathway. Structure elucidation of [Mn3 (GlyGly-H)4 ](2+) clusters has also been done by IRMPD spectroscopy as well as DFT calculations. It is shown that the lowest energy structure of the [Mn3 (GlyGly-H)4 ](2+) cluster is deprotonated at all carboxylic acid groups and metal ions are coordinated with carbonyl oxygen atoms, and that all amine nitrogen atoms are hydrogen bonded to the amide hydrogen. A comparison of the calculated high-spin (sextet) and low-spin (quartet) state structures of [Mn3 (GlyGly-H)4 ](2+) is provided. IRMPD spectroscopic results are in agreement with the lowest energy high-spin structure computed. Also, the gas-phase reactivity of these complexes towards neutral CO and water was investigated. The parent complexes did not add any water or CO, presumably due to saturation at the metal cation. However, once some of the ligand was removed via CO2 laser IRMPD, water was seen to add to the complex. These results are consistent with high-spin Mn(2+) complexes. PMID:27037623

  7. Resolvin D1, Protectin D1, and Related Docosahexaenoic Acid-Derived Products: Analysis via Electrospray/Low Energy Tandem Mass Spectrometry based on Spectra and Fragmentation Mechanisms

    PubMed Central

    Hong, Song; Lu, Yan; Yang, Rong; Gotlinger, Katherine H.; Petasis, Nicos P.; Serhan, Charles N.

    2009-01-01

    Resolvin D1 (RvD1) and Protectin D1 (Neuroprotectin D1, PD1/NPD1) are newly identified anti-inflammatory lipid mediators biosynthesized from docosahexaenoic acid (DHA). In this report, the spectra-structure correlations and fragmentation mechanisms were studied using electrospray low-energy collision-induced dissociation tandem mass spectrometry (MS/MS) for biogenic RvD1 and PD1, as well as mono-hydroxy-DHA and related hydroperoxy-DHA. The loss of H2O and CO2 in the spectra indicates the number of functional group(s). Chain-cut ions are the signature of the positions and numbers of functional groups and double-bonds. The observed chain-cut ion is equivalent to a hypothetical homolytic-segment (cc, cm, mc, or mm) with addition or extraction of up to 2 protons (H). The α-cleavage ions are equivalent to: [cc + H], with H from the hydroxyl through a β-ene or γ-ene rearrangement; [cm - 2H], with 2H from hydroxyls of PD1 through a γ-ene rearrangement, or one H from the hydroxyl and the other H from the α-carbon of mono-HDHA through an α-H-β-ene rearrangement; [mc – H], with H from hydroxyl through a β-ene or γ-ene rearrangement, or from the α-carbon through an α-H-β-ene rearrangement; or [mm] through charge-direct fragmentations. The β-ene or γ-ene facilitates the H shift to γ position and α-cleavage. Deuterium labeling confirmed the assignment of MS/MS ions and the fragmentation mechanisms. Based on the MS/MS spectra and fragmentation mechanisms, we identified RvD1, PD1, and mono-hydroxy-DHA products in human neutrophils and blood, trout head-kidney, and stroke-injury murine brain-tissues. PMID:17055291

  8. Dissociated Vertical Deviation

    MedlinePlus

    ... Eye Terms Conditions Frequently Asked Questions Español Condiciones Chinese Conditions Dissociated Vertical Deviation En Español Read in Chinese What is Dissociated Vertical Deviation (DVD)? DVD is ...

  9. 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

  10. Fragmentation behavior of Amadori-peptides obtained by non-enzymatic glycosylation of lysine residues with ADP-ribose in tandem mass spectrometry.

    PubMed

    Fedorova, Maria; Frolov, Andrej; Hoffmann, Ralf

    2010-06-01

    Mono- and poly-adenosine diphosphate (ADP)-ribosylation are common post-translational modifications incorporated by sequence-specific enzymes at, predominantly, arginine, asparagine, glutamic acid or aspartic acid residues, whereas non-enzymatic ADP-ribosylation (glycation) modifies lysine and cysteine residues. These glycated proteins and peptides (Amadori-compounds) are commonly found in organisms, but have so far not been investigated to any great degree. In this study, we have analyzed their fragmentation characteristics using different mass spectrometry (MS) techniques. In matrix-assisted laser desorption/ionization (MALDI)-MS, the ADP-ribosyl group was cleaved, almost completely, at the pyrophosphate bond by in-source decay. In contrast, this cleavage was very weak in electrospray ionization (ESI)-MS. The same fragmentation site also dominated the MALDI-PSD (post-source decay) and ESI-CID (collision-induced dissociation) mass spectra. The remaining phospho-ribosyl group (formed by the loss of adenosine monophosphate) was stable, providing a direct and reliable identification of the modification site via the b- and y-ion series. Cleavage of the ADP-ribose pyrophosphate bond under CID conditions gives access to both neutral loss (347.10 u) and precursor-ion scans (m/z 348.08), and thereby permits the identification of ADP-ribosylated peptides in complex mixtures with high sensitivity and specificity. With electron transfer dissociation (ETD), the ADP-ribosyl group was stable, providing ADP-ribosylated c- and z-ions, and thus allowing reliable sequence analyses. PMID:20527035

  11. On the dissociation pathways of nitrobenzene

    NASA Astrophysics Data System (ADS)

    Kosmidis, C.; Ledingham, K. W. D.; Clark, A.; Marshall, A.; Jennings, R.; Sander, J.; Singhal, R. P.

    1994-08-01

    The fragmentation of nitrobenzene has been studied in the wavelength range 225-275 nm using a single dye laser, frequency doubled, in conjunction with a time-of-flight (TOF) mass spectrometer. The parent (C6H5NO2+), nitrosobenzene (C6H5NO+), phenoxy (C6H5O+) and phenyl (C6H5+) ions were all observed in addition to many other lighter daughter fragments. The formation of the nitrobenzene, phenoxy and phenyl ions are all explained invoking pathways where dissociation of the parent molecule from an excited state takes place first, followed by ionization after the absorption of further photons (DI) by the fragmented neutrals. Ionization of the parent molecule to states which are dissociative (ID) can explain the increase in the production of phenyl ions at wavelengths shorter than 230 nm.

  12. First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

    SciTech Connect

    Varghese, Jithin J.; Mushrif, Samir H.

    2015-05-14

    Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cu{sub n} where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barrier for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH{sub 3} and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CH{sub x} (x = 1–3) species and recombination of H with CH{sub x} have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.

  13. Novel 2-alkyl-1-ethylpyridinium ionic liquids: synthesis, dissociation energies and volatility.

    PubMed

    Vilas, Miguel; Rocha, Marisa A A; Fernandes, Ana M; Tojo, Emilia; Santos, Luís M N B F

    2015-01-28

    This work presents the synthesis, volatility study and electrospray ionization mass spectrometry with energy-variable collision induced dissociation of the isolated [(cation)2(anion)](+) of a novel series of 2-alkyl-1-ethyl pyridinium based ionic liquids, [(2)CN-2(1)C2Py][NTf2]. Compared to the imidazolium based ionic liquids, the new ionic liquid series presents a higher thermal stability and lower volatility. The [(cation)2(anion)](+) collision induced dissociation energies of both [(2)CN-2(1)C2Py][NTf2] and [CNPy][NTf2] pyridinium series show an identical trend with a pronounced decrease of the relative cation-anion interaction energy towards an almost constant value for N = 6. It was found that the lower volatility of [(2)CN-2(1)C2Py][NTf2] with a shorter alkyl chain length is due to its higher enthalpy of vaporization. Starting from [(2)C3(1)C2Py][NTf2], the lower volatility is governed by the combination of slightly lower entropies and higher enthalpies of vaporization, an indication of a higher structural disorder of the pyridinium based ionic liquids than the imidazolium based ionic liquids. Dissociation energies and volatility trends support the cohesive energy interpretation model based on the overlapping of the electrostatic and van der Waals functional interaction potentials. PMID:25493639

  14. Dissociation curves of diatomic molecules: A DC-DFT study

    SciTech Connect

    Sim, Eunji; Kim, Min-Cheol; Burke, Kieron

    2015-12-31

    We investigate dissociation of diatomic molecules using standard density functional theory (DFT) and density-corrected density functional theory (DC-DFT) compared with CCSD(T) results as reference. The results show the difference between the HOMO values of dissociated atomic species often can be used as an indicator whether DFT would predict the correct dissociation limit. DFT predicts incorrect dissociation limits and charge distribution in molecules or molecular ions when the fragments have large HOMO differences, while DC-DFT and CCSD(T) do not. The criteria for large HOMO difference is about 2 ∼ 4 eV.

  15. Kinetic ion thermometers for electron transfer dissociation.

    PubMed

    Pepin, Robert; Tureček, František

    2015-02-19

    Peptide fragment ions of the z-type were used as kinetic ion thermometers to gauge the internal energy of peptide cation-radicals produced by electron transfer in the gas-phase. Electron transfer dissociation (ETD)-produced z2 ions containing the leucine residue, z2(Leu-Lys) and z2(Leu-Arg), were found to undergo spontaneous dissociation by loss of C3H7 that was monitored by time-resolved kinetic measurements on the time scale of the linear ion trap mass spectrometer. Kinetic modeling of the dissociations, including collisional cooling and product loss by neutralization, provided unimolecular rate constants for dissociation that were converted to the z ion internal energies using RRKM theory. The internal energy of z2(Leu-Lys) and z2(Leu-Arg) fragment ions was found to decrease with the increasing size of the precursor peptide ion, indicating vibrational energy partitioning between the ion and neutral fragments and ergodic behavior. The experimentally determined excitation in the peptide cation-radicals upon electron transfer (285-327 kJ mol(-1)) was found to be lower than that theoretically calculated from the reaction exothermicity. The reasons for this missing energy are discussed. PMID:25594857

  16. Collision Induced Unfolding of Intact Antibodies: Rapid Characterization of Disulfide Bonding Patterns, Glycosylation, and Structures.

    PubMed

    Tian, Yuwei; Han, Linjie; Buckner, Adam C; Ruotolo, Brandon T

    2015-11-17

    Monoclonal antibodies (mAbs) are among the fastest growing class of therapeutics due to their high specificity and low incidence of side effects. Unlike most drugs, mAbs are complex macromolecules (∼150 kDa), leading to a host of quality control and characterization challenges inherent in their development. Recently, we introduced a new approach for the analysis of the intact proteins based on ion mobility-mass spectrometry (IM-MS). Our protocol involves the collision induced unfolding (CIU) of intact antibodies, where collisional heating in the gas-phase is used to generate unfolded antibody forms, which are subsequently separated by IM and then analyzed by MS. Collisional energy is added to the antibody ions in a stepwise fashion, and "fingerprint plots" are created that track the amount of unfolding undergone as a function of the energy imparted to the ions prior to IM separation. In this report, we have used these fingerprints to rapidly distinguish between antibody isoforms, possessing different numbers and/or patterns of disulfide bonding and general levels of glycosylation. In addition, we validate our CIU protocols through control experiments and systematic statistical evaluations of CIU reproducibility. We conclude by projecting the impact of our approach for antibody-related drug discovery and development applications. PMID:26471104

  17. Collision-induced Absorption in the Infrared: A Data Base for Modelling Planetary and Stellar Atmospheres

    NASA Technical Reports Server (NTRS)

    Borysow, Aleksandra

    1998-01-01

    Accurate knowledge of certain collision-induced absorption continua of molecular pairs such as H2-H2, H2-He, H2-CH4, CO2-CO2, etc., is a prerequisite for most spectral analyses and modelling attempts of atmospheres of planets and cold stars. We collect and regularly update simple, state of the art computer programs for the calculation of the absorption coefficient of such molecular pairs over a broad range of temperatures and frequencies, for the various rotovibrational bands. The computational results are in agreement with the existing laboratory measurements of such absorption continua, recorded with a spectral resolution of a few wavenumbers, but reliable computational results may be expected even in the far wings, and at temperatures for which laboratory measurements do not exist. Detailed information is given concerning the systems thus studied, the temperature and frequency ranges considered, the rotovibrational bands thus modelled, and how one may obtain copies of the FORTRAN77 computer programs by e-mail.

  18. High-energy limit of collision-induced false vacuum decay

    NASA Astrophysics Data System (ADS)

    Demidov, Sergei; Levkov, Dmitry

    2015-06-01

    We develop a consistent semiclassical description of field-theoretic collision-induced tunneling at arbitrary high collision energies. As a playground we consider a (1 + 1)-dimensional false vacuum decay initiated by a collision of N particles at energy E, paying special attention to the realistic case of N = 2 particles. We demonstrate that the cross section of this process is exponentially suppressed at all energies. Moreover, the respective suppressesion exponent F N ( E) exhibits a specific behavior which is significant for our semiclassical method and assumed to be general: it decreases with energy, reaches absolute minimum F = F min( N ) at a certain threshold energy E = E rt( N ), and stays constant at higher energies. We show that the minimal suppression F min( N ) and threshold energy can be evaluated using a special class of semiclassical solutions which describe exponentially suppressed transitions but nevertheless evolve in real time. Importantly, we argue that the cross section at energies above E rt( N ) is computed perturbatively in the background of the latter solutions, and the terms of this perturbative expansion stay bounded in the infinite-energy limit. Transitions in the high-energy regime proceed via emission of many soft quanta with total energy E rt; the energy excess E - E rt remains in the colliding particles till the end of the process.

  19. Concentration studies of collision-induced fundamental absorption of hydrogen dissolved in liquid neon.

    PubMed

    Herrebout, W A; van der Veken, B J; Kouzov, A P

    2012-08-28

    We report further and more detailed results of our recent investigation [W. A. Herrebout, B. J. van der Veken, and A. P. Kouzov, Phys. Rev. Lett. 101, 093001 (2008)] on the collision-induced fundamental absorption by hydrogen dissolved in liquid neon (T ≈ 25 K). The band shapes were studied in a wide range of concentrations (0.003-0.05 mole fractions) as well as for different ortho/para ratios and at much higher level of accuracy and resolution than before. Due to almost unhindered rotation of the hydrogen molecule and low temperature, an unprecedently rich frequency-domain picture produced by different terms of the interaction-induced polarization was observed. While some of them are conspicuous via fast intracell motion of a light guest (H(2)), others--induced by the electrostatic field of the guest--give rise to lines whose shapes are imprinted by fluctuations of the nearest surrounding. Strong motional narrowing observed on the guest-guest induced lines shows up in their Lorentzian shapes which are signatures of microscopic-scale diffusion. Near-Lorentzian peaks were also detected at the tops of the diffuse lines induced by isolated guests. Their formation may be associated with a long-living defect (vacancy) emerging in the vicinity of the polarization inductor. Altogether, our results give the first unambiguous spectroscopic evidence on the diffusional evolution of isolated binary interactions that emerge in dense chaotic media. PMID:22938252

  20. Ab initio calculations for the far infrared collision induced absorption by N2 gas

    NASA Astrophysics Data System (ADS)

    Bussery-Honvault, Béatrice; Hartmann, Jean-Michel

    2014-02-01

    We present (far-infrared) Collision Induced Absorption (CIA) spectra calculations for pure gaseous N2 made for the first time, from first-principles. They were carried out using classical molecular dynamics simulations based on ab initio predictions of both the intermolecular potential and the induced-dipole moment. These calculations reproduce satisfactory well the experimental values (intensity and band profile) with agreement within 3% at 149 K. With respect to results obtained with only the long range (asymptotic) dipole moment (DM), including the short range overlap contribution improves the band intensity and profile at 149 K, but it deteriorates them at 296 K. The results show that the relative contribution of the short range DM to the band intensity is typically around 10%. We have also examined the sensitivity of the calculated CIA to the intermolecular potential anisotropy, providing a test of the so-called isotropic approximation used up to now in all N2 CIA calculations. As all these effects interfere simultaneously with quantitatively similar influences (around 10%), it is rather difficult to assert which one could explain remaining deviations with the experimental results. Furthermore, the rather large uncertainties and sometimes inconsistencies of the available measurements forbid any definitive conclusion, stressing the need for new experiments.

  1. The Binary Collision-Induced Second Overtone Band of Gaseous Hydrogen: Modelling and Laboratory Measurements

    NASA Technical Reports Server (NTRS)

    Brodbeck, C.; Bouanich, J.-P.; Nguyen, Van Thanh; Borysow, Aleksandra

    1999-01-01

    Collision-induced absorption (CIA) is the major source of the infrared opacity of dense planetary atmospheres which are composed of nonpolar molecules. Knowledge of CIA absorption spectra of H2-H2 pairs is important for modelling the atmospheres of planets and cold stars that are mainly composed of hydrogen. The spectra of hydrogen in the region of the second overtone at 0.8 microns have been recorded at temperatures of 298 and 77.5 K for gas densities ranging from 100 to 800 amagats. By extrapolation to zero density of the absorption coefficient measured every 10 cm(exp -1) in the spectral range from 11100 to 13800 cm(exp -1), we have determined the binary absorption coefficient. These extrapolated measurements are compared with calculations based on a model that was obtained by using simple computer codes and lineshape profiles. In view of the very weak absorption of the second overtone band, we find the agreement between results of the model and experiment to be reasonable.

  2. Ab initio calculations for the far infrared collision induced absorption by N2 gas.

    PubMed

    Bussery-Honvault, Béatrice; Hartmann, Jean-Michel

    2014-02-01

    We present (far-infrared) Collision Induced Absorption (CIA) spectra calculations for pure gaseous N2 made for the first time, from first-principles. They were carried out using classical molecular dynamics simulations based on ab initio predictions of both the intermolecular potential and the induced-dipole moment. These calculations reproduce satisfactory well the experimental values (intensity and band profile) with agreement within 3% at 149 K. With respect to results obtained with only the long range (asymptotic) dipole moment (DM), including the short range overlap contribution improves the band intensity and profile at 149 K, but it deteriorates them at 296 K. The results show that the relative contribution of the short range DM to the band intensity is typically around 10%. We have also examined the sensitivity of the calculated CIA to the intermolecular potential anisotropy, providing a test of the so-called isotropic approximation used up to now in all N2 CIA calculations. As all these effects interfere simultaneously with quantitatively similar influences (around 10%), it is rather difficult to assert which one could explain remaining deviations with the experimental results. Furthermore, the rather large uncertainties and sometimes inconsistencies of the available measurements forbid any definitive conclusion, stressing the need for new experiments. PMID:24511942

  3. CIUSuite: A Quantitative Analysis Package for Collision Induced Unfolding Measurements of Gas-Phase Protein Ions.

    PubMed

    Eschweiler, Joseph D; Rabuck-Gibbons, Jessica N; Tian, Yuwei; Ruotolo, Brandon T

    2015-11-17

    Ion mobility-mass spectrometry (IM-MS) is a technology of growing importance for structural biology, providing complementary 3D structure information for biomolecules within samples that are difficult to analyze using conventional analytical tools through the near-simultaneous acquisition of ion collision cross sections (CCSs) and masses. Despite recent advances in IM-MS instrumentation, the resolution of closely related protein conformations remains challenging. Collision induced unfolding (CIU) has been demonstrated as a useful tool for resolving isocrossectional protein ions, as they often follow distinct unfolding pathways when subjected to collisional heating in the gas phase. CIU has been used for a variety of applications, from differentiating binding modes of activation state-selective kinase inhibitors to characterizing the domain structure of multidomain proteins. With the growing utilization of CIU as a tool for structural biology, significant challenges have emerged in data analysis and interpretation, specifically the normalization and comparison of CIU data sets. Here, we present CIUSuite, a suite of software modules designed for the rapid processing, analysis, comparison, and classification of CIU data. We demonstrate these tools as part of a series of workflows for applications in comparative structural biology, biotherapeutic analysis, and high throughput screening of kinase inhibitors. These examples illustrate both the potential for CIU in general protein analysis as well as a demonstration of best practices in the interpretation of CIU data. PMID:26489593

  4. Interacting He and Ar atoms: Revised theoretical interaction potential, dipole moment, and collision-induced absorption spectra

    SciTech Connect

    Meyer, Wilfried; Frommhold, Lothar

    2015-09-21

    Coupled cluster quantum chemical calculations of the potential energy surface and the induced dipole surface are reported for the He–Ar van der Waals collisional complex. Spectroscopic parameters are derived from global analytical fits while an accurate value for the long-range dipole coefficient D{sub 7} is obtained by perturbation methods. Collision-induced absorption spectra are computed quantum mechanically and compared with existing measurements.

  5. Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations

    SciTech Connect

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K.; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  6. Quantum mechanical calculation of the collision-induced absorption spectra of N{sub 2}–N{sub 2} with anisotropic interactions

    SciTech Connect

    Karman, Tijs; Groenenboom, Gerrit C.; Avoird, Ad van der; Miliordos, Evangelos; Hunt, Katharine L. C.

    2015-02-28

    We present quantum mechanical calculations of the collision-induced absorption spectra of nitrogen molecules, using ab initio dipole moment and potential energy surfaces. Collision-induced spectra are first calculated using the isotropic interaction approximation. Then, we improve upon these results by considering the full anisotropic interaction potential. We also develop the computationally less expensive coupled-states approximation for calculating collision-induced spectra and validate this approximation by comparing the results to numerically exact close-coupling calculations for low energies. Angular localization of the scattering wave functions due to anisotropic interactions affects the line strength at low energies by two orders of magnitude. The effect of anisotropy decreases at higher energy, which validates the isotropic interaction approximation as a high-temperature approximation for calculating collision-induced spectra. Agreement with experimental data is reasonable in the isotropic interaction approximation, and improves when the full anisotropic potential is considered. Calculated absorption coefficients are tabulated for application in atmospheric modeling.

  7. Unimolecular dissociation of cyclopentadiene and indene

    SciTech Connect

    Yi, W.; Chattopadhyay, A.; Bersohn, R. )

    1991-05-01

    The dissociation of hydrogen atoms from the methylene group of cyclopentadiene (CP) and indene (ID) excited with a 193 nm photon has been studied by hydrogen atom laser induced fluorescence. The rate of dissociation of IND was 7.4{times}10{sup 6} s{sup {minus}1} but that of CP was too fast to measure. The ratio of H atoms to D atoms generated from 5-deuteriocyclopentadiene (5-dCP) was 3.91{plus minus}0.46. Rice--Ramsberger--Kassel--Marcus theory was used to calculate the rates of dissociation of CP and 5-dCP. The quantum yield for dissociating H atoms from CP was 0.85{plus minus}0.07. The ejected H atoms have a Maxwell velocity distribution with temperatures which are equal to the vibrational temperatures, 3690 and 2479 K for CP and IND, respectively. The most important result of the work is this confirmation of an earlier finding on a different set of molecules that the translational temperature of the fragments {ital after} the dissociation is equal to the vibrational temperature {ital before} the dissociation. This is explained by the assumption that the motion of the fast, light hydrogen atom is partly decoupled from that of the heavier, slower atoms.

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

    PubMed

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

    2016-01-21

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

  9. Structural Identification of O-Linked Oligosaccharides Using Exoglycosidases and MSn Together with UniCarb-DB Fragment Spectra Comparison

    PubMed Central

    Ali, Liaqat; Kenny, Diarmuid T.; Hayes, Catherine A.; Karlsson, Niclas G.

    2012-01-01

    The availability of specific exoglycosidases alongside a spectral library of O-linked oligosaccharide collision induced dissociation (CID) MS fragments, UniCarb-DB, provides a pathway to make the elucidation of O-linked oligosaccharides more efficient. Here, we advise an approach of exoglycosidase-digestion of O-linked oligosaccharide mixtures, for structures that do not provide confirmative spectra. The combination of specific exoglycosidase digestion and MS2 matching of the exoglycosidase products with structures from UniCarb-DB, allowed the assignment of unknown structures. This approach was illustrated by treating sialylated core 2 O-linked oligosaccharides, released from the human synovial glycoprotein (lubricin), with a α2–3 specific sialidase. This methodology demonstrated the exclusive 3 linked nature of the sialylation of core 2 oligosaccharides on lubricin. When specific exoglycosidases were not available, MS3 spectral matching using standards was used. This allowed the unusual 4-linked terminal GlcNAc epitope in a porcine stomach to be identified in the GlcNAc1-4Galβ1–3(GlcNAcβ1-6)GalNAcol structure, indicating the antibacterial epitope GlcNAcα1–4. In total, 13 structures were identified using exoglycosidase and MSn, alongside UniCarb-DB fragment spectra comparison. UniCarb-DB could also be used to identify the specificity of unknown exoglycosidases in human saliva. Endogenous salivary exoglycosidase activity on mucin oligosaccharides could be monitored by comparing the generated tandem MS spectra with those present in UniCarb-DB, showing that oral exoglycosidases were dominated by sialidases with a higher activity towards 3-linked sialic acid rather than 6-linked sialic acid. PMID:24957756

  10. 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.

  11. Tandem Mass Spectrometric Characterization of Thiol Peptides Modified by the Chemoselective Cationic Sulfhydryl Reagent (4-Iodobutyl)Triphenylphosphonium—. Effects of a Cationic Thiol Derivatization on Peptide Fragmentation

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Zhang, Jie; Arbogast, Brian; Maier, Claudia S.

    2011-10-01

    Fixed charge chemical modifications on peptides and proteins can impact fragmentation behaviors in tandem mass spectrometry (MS/MS). In this study, we employed a thiol-specific cationic alkylation reagent, (4-iodobutyl)triphenylphosphonium (IBTP), to selectively modify cysteine thiol groups in mitochondrial proteome samples. Tandem mass spectrometric characteristics of butyltriphenylphosphonium (BTP)-modified peptides were evaluated by comparison to their carbamidomethylated (CAM) analogues using a quadrupole time-of-flight (Q-TOF) instrument under low energy collision-induced dissociation (CID) conditions. Introduction of the fixed charge modification resulted in the observation of peptide and fragment (bn and yn) ions with higher charge states than those observed for CAM-modified analogues. The charged BTP moiety had a significant effect on the neighboring amide bond fragmentation products. A decrease in relative abundances of the product ions at the corresponding cleavage sites was observed compared with those from the CAM-modified derivatives. This effect was particularly noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. We hypothesized that the presence of a phosphonium moiety will reduce the tendency for protonation of the proximal amide bonds in the peptide backbone. Indeed, calculations indicated that proton affinities of backbone amide bonds close to the modified cysteine residues were generally 20-50 kcal/mol lower for BTP-modified peptides than for the unmodified or CAM-modified analogues with the sequence motif -Ala-Cys-Alan-Ala2-, -Ala-Cys-Alan-Pro-Ala-, and -Ala-Pro-Alan-Cys-Ala-, n = 0-3.

  12. A Phosphohistidine Proteomics Strategy Based on Elucidation of a Unique Gas-Phase Phosphopeptide Fragmentation Mechanism

    PubMed Central

    2015-01-01

    Protein histidine phosphorylation is increasingly recognized as a critical posttranslational modification (PTM) in central metabolism and cell signaling. Still, the detection of phosphohistidine (pHis) in the proteome has remained difficult due to the scarcity of tools to enrich and identify this labile PTM. To address this, we report the first global proteomic analysis of pHis proteins, combining selective immunoenrichment of pHis peptides and a bioinformatic strategy based on mechanistic insight into pHis peptide gas-phase fragmentation during LC–MS/MS. We show that collision-induced dissociation (CID) of pHis peptides produces prominent characteristic neutral losses of 98, 80, and 116 Da. Using isotopic labeling studies, we also demonstrate that the 98 Da neutral loss occurs via gas-phase phosphoryl transfer from pHis to the peptide C-terminal α-carboxylate or to Glu/Asp side chain residues if present. To exploit this property, we developed a software tool that screens LC–MS/MS spectra for potential matches to pHis-containing peptides based on their neutral loss pattern. This tool was integrated into a proteomics workflow for the identification of endogenous pHis-containing proteins in cellular lysates. As an illustration of this strategy, we analyzed pHis peptides from glycerol-fed and mannitol-fed Escherichia coli cells. We identified known and a number of previously speculative pHis sites inferred by homology, predominantly in the phosphoenolpyruvate:sugar transferase system (PTS). Furthermore, we identified two new sites of histidine phosphorylation on aldehyde-alcohol dehydrogenase (AdhE) and pyruvate kinase (PykF) enzymes, previously not known to bear this modification. This study lays the groundwork for future pHis proteomics studies in bacteria and other organisms. PMID:25156620

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

    PubMed Central

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

    2008-01-01

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

  14. Dissociative electron attachment studies on acetone

    SciTech Connect

    Prabhudesai, Vaibhav S. Tadsare, Vishvesh; Ghosh, Sanat; Gope, Krishnendu; Davis, Daly; Krishnakumar, E.

    2014-10-28

    Dissociative electron attachment (DEA) to acetone is studied in terms of the absolute cross section for various fragment channels in the electron energy range of 0–20 eV. H{sup −} is found to be the most dominant fragment followed by O{sup −} and OH{sup −} with only one resonance peak between 8 and 9 eV. The DEA dynamics is studied by measuring the angular distribution and kinetic energy distribution of fragment anions using Velocity Slice Imaging technique. The kinetic energy and angular distribution of H{sup −} and O{sup −} fragments suggest a many body break-up for the lone resonance observed. The ab initio calculations show that electron is captured in the multi-centered anti-bonding molecular orbital which would lead to a many body break-up of the resonance.

  15. Orientation-dependent dissociative charge transfer

    SciTech Connect

    Wu, W.; Prior, M.H.; Braeuning, H.

    1998-01-01

    Recoil-ion momentum spectroscopy and molecular fragment imaging techniques are combined to study dissociative electron capture from He by HeH{sup +} at 0.20-a.u. collision velocity. Groups of final HeH states which dissociate to ground or excited H and He atoms are separated. For each group, the experiment provides two-dimensional H fragment distributions with respect to the collision plane and for fixed transverse momentum transfer. These patterns show that the capture probability is highest for HeH{sup +} ions with their axis oriented normal to the scattering plane for two of the three groups populated. {copyright} {ital 1998} {ital The American Physical Society}

  16. Dissociative electron attachment to the radiosensitizing chemotherapeutic agent hydroxyurea.

    PubMed

    Huber, S E; Śmiałek, M A; Tanzer, K; Denifl, S

    2016-06-14

    Dissociative electron attachment to hydroxyurea was studied in the gas phase for electron energies ranging from zero to 9 eV in order to probe its radiosensitizing capabilities. The experiments were carried out using a hemispherical electron monochromator coupled with a quadrupole mass spectrometer. Diversified fragmentation of hydroxyurea was observed upon low energy electron attachment and here we highlight the major dissociation channels. Moreover, thermodynamic thresholds for various fragmentation reactions are reported to support the discussion of the experimental findings. The dominant dissociation channel, which was observed over a broad range of energies, is associated with formation of NCO(-), water, and the amidogen (NH2) radical. The second and third most dominant dissociation channels are associated with formation of NCNH(-) and NHCONH2 (-), respectively, which are both directly related to formation of the highly reactive hydroxyl radical. Other ions observed with significant abundance in the mass spectra were NH2 (-)/O(-), OH(-), CN(-), HNOH(-), NCONH2 (-), and ONHCONH2 (-). PMID:27306009

  17. Dissociative electron attachment to the radiosensitizing chemotherapeutic agent hydroxyurea

    NASA Astrophysics Data System (ADS)

    Huber, S. E.; Śmiałek, M. A.; Tanzer, K.; Denifl, S.

    2016-06-01

    Dissociative electron attachment to hydroxyurea was studied in the gas phase for electron energies ranging from zero to 9 eV in order to probe its radiosensitizing capabilities. The experiments were carried out using a hemispherical electron monochromator coupled with a quadrupole mass spectrometer. Diversified fragmentation of hydroxyurea was observed upon low energy electron attachment and here we highlight the major dissociation channels. Moreover, thermodynamic thresholds for various fragmentation reactions are reported to support the discussion of the experimental findings. The dominant dissociation channel, which was observed over a broad range of energies, is associated with formation of NCO-, water, and the amidogen (NH2) radical. The second and third most dominant dissociation channels are associated with formation of NCNH- and NHCONH2-, respectively, which are both directly related to formation of the highly reactive hydroxyl radical. Other ions observed with significant abundance in the mass spectra were NH2-/O-, OH-, CN-, HNOH-, NCONH2-, and ONHCONH2-.

  18. Sequential Collision- and Ozone-Induced Dissociation Enables Assignment of Relative Acyl Chain Position in Triacylglycerols.

    PubMed

    Marshall, David L; Pham, Huong T; Bhujel, Mahendra; Chin, Jacqueline S R; Yew, Joanne Y; Mori, Kenji; Mitchell, Todd W; Blanksby, Stephen J

    2016-03-01

    Unambiguous identification of isomeric lipids by mass spectrometry represents a significant analytical challenge in contemporary lipidomics. Herein, the combination of collision-induced dissociation (CID) with ozone-induced dissociation (OzID) on an ion-trap mass spectrometer is applied to the identification of triacylglycerol (TG) isomers that vary only by the substitution pattern of fatty acyl (FA) chains esterified to the glycerol backbone. Isolated product ions attributed to loss of a single FA arising from CID of [TG + Na](+) ions react rapidly with ozone within the ion trap. The resulting CID/OzID spectra exhibit abundant ions that unequivocally reveal the relative position of FAs along the backbone. Isomeric TGs containing two or three different FA substituents are readily differentiated by diagnostic ions present in their CID/OzID spectra. Compatibility of this method with chromatographic separations enables the characterization of unusual TGs containing multiple short-chain FAs present in Drosophila. PMID:26799085

  19. Collision-Induced Infrared Absorption by Collisional Complexes in Dense Hydrogen-Helium Gas Mixtures at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Frommhold, Lothar; Li, Xiaoping; Hunt, Katharine L. C.

    2011-06-01

    The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of the outer planets and cool stars. The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H{_2}-H{_2}, H{_2}-He, and H{_2}-H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H{_2} pairs exist only at room temperature and below. We show that our results reproduce these measurements closely, so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 Xiaoping Li, Katharine L. C. Hunt, Fei Wang, Martin Abel, and Lothar Frommhold, "Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin", International Journal of Spectroscopy, vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, "Collision-induced absorption by H{_2} pairs: From hundreds to thousands of Kelvin," J. Phys. Chem. A, published online, DOI: 10.1021/jp109441f L. Frommhold, M. Abel, F. Wang, M. Gustafsson, X. Li, and K. L. C. Hunt, "Infrared atmospheric emission and absorption by simple molecular complexes, from first principles", Mol. Phys. 108, 2265, 2010

  20. Dissociative recombination in planetary ionospheres

    NASA Technical Reports Server (NTRS)

    Fox, J. L.

    1993-01-01

    Ionization in planetary atmospheres can be produced by solar photoionization, photoelectron impact ionization, and, in auroral regions, by impact of precipitating particles. This ionization is lost mainly in dissociative recombination (DR) of molecular ions. Although atomic ions cannot undergo DR, they can be transformed locally through ion-molecule reactions into molecular ions, or they may be transported vertically or horizontally to regions of the atmosphere where such transformations are possible. Because DR reactions tend to be very exothermic, they can be an important source of kinetically or internally excited fragments. In interplanetary thermospheres, the neutral densities decrease exponentially with altitude. Below the homopause (or turbopause), the atmosphere is assumed to be throughly mixed by convection and/or turbulence. Above the homopause, diffusion is the major transport mechanism, and each species is distributed according to its mass, with the logarithmic derivative of the density with repect to altitude given approximately by -1/H, where H = kT/mg is the scale height. In this expression, T is the neutral temperature, g is the local acceleratiion of gravity, and m is the mass of the species. Thus lighter species become relatively more abundant, and heavier species less abundant, as the altitude increases. This variation of the neutral composition can lead to changes in the ion composition; furthermore, as the neutral densities decrease, dissociative recombination becomes more important relative to ion-neutral reactions as a loss mechanism for molecular ions.

  1. The dissociative bond.

    PubMed

    Gordon, Nirit

    2013-01-01

    Dissociation leaves a psychic void and a lingering sense of psychic absence. How do 2 people bond while they are both suffering from dissociation? The author explores the notion of a dissociative bond that occurs in the aftermath of trauma--a bond that holds at its core an understanding and shared detachment from the self. Such a bond is confined to unspoken terms that are established in the relational unconscious. The author proposes understanding the dissociative bond as a transitional space that may not lead to full integration of dissociated knowledge yet offers some healing. This is exemplified by R. Prince's (2009) clinical case study. A relational perspective is adopted, focusing on the intersubjective aspects of a dyadic relationship. In the dissociative bond, recognition of the need to experience mutual dissociation can accommodate a psychic state that yearns for relationship when the psyche cannot fully confront past wounds. Such a bond speaks to the need to reestablish a sense of human relatedness and connection when both parties in the relationship suffer from disconnection. This bond is bound to a silence that becomes both a means of protection against the horror of traumatic memory and a way to convey unspoken gestures toward the other. PMID:23282044

  2. Electron transfer dissociation of dipositive uranyl and plutonyl coordination complexes.

    PubMed

    Rios, Daniel; Rutkowski, Philip X; Shuh, David K; Bray, Travis H; Gibson, John K; Van Stipdonk, Michael J

    2011-12-01

    Reported here is a comparison of electron transfer dissociation (ETD) and collision-induced dissociation (CID) of solvent-coordinated dipositive uranyl and plutonyl ions generated by electrospray ionization. Fundamental differences between the ETD and CID processes are apparent, as are differences between the intrinsic chemistries of uranyl and plutonyl. Reduction of both charge and oxidation state, which is inherent in ETD activation of [An(VI) O(2) (CH(3) COCH(3) )(4) ](2+) , [An(VI) O(2) (CH(3) CN)(4) ](2) , [U(VI) O(2) (CH(3) COCH(3) )(5) ](2+) and [U(VI) O(2) (CH(3) CN)(5) ](2+) (An = U or Pu), is accompanied by ligand loss. Resulting low-coordinate uranyl(V) complexes add O(2) , whereas plutonyl(V) complexes do not. In contrast, CID of the same complexes generates predominantly doubly-charged products through loss of coordinating ligands. Singly-charged CID products of [U(VI) O(2) (CH(3) COCH(3) )(4,5) ](2+) , [U(VI) O(2) (CH(3) CN)(4,5) ](2+) and [Pu(VI) O(2) (CH(3) CN)(4) ](2+) retain the hexavalent metal oxidation state with the addition of hydroxide or acetone enolate anion ligands. However, CID of [Pu(VI) O(2) (CH(3) COCH(3) )(4) ](2+) generates monopositive plutonyl(V) complexes, reflecting relatively more facile reduction of Pu(VI) to Pu(V). PMID:22223415

  3. Relativistic MHD simulations of collision-induced magnetic dissipation in poynting-flux-dominated jets/outflows

    DOE PAGESBeta

    Deng, Wei; Li, Hui; Zhang, Bing; Li, Shengtai

    2015-05-29

    We perform 3D relativistic ideal MHD simulations to study the collisions between high-σ (Poynting- ux-dominated) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable Poynting- ux-dominated jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvenic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in themore » relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini-jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. In conclusion, our results give support to the proposed astrophysical models that invoke signi cant magnetic energy dissipation in Poynting- ux-dominated jets, such as the internal collision-induced magnetic reconnection and turbulence (ICMART) model for GRBs, and reconnection triggered mini-jets model for AGNs.« less

  4. Relativistic MHD simulations of collision-induced magnetic dissipation in poynting-flux-dominated jets/outflows

    SciTech Connect

    Deng, Wei; Li, Hui; Zhang, Bing; Li, Shengtai

    2015-05-29

    We perform 3D relativistic ideal MHD simulations to study the collisions between high-σ (Poynting- ux-dominated) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable Poynting- ux-dominated jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvenic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in the relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini-jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. In conclusion, our results give support to the proposed astrophysical models that invoke signi cant magnetic energy dissipation in Poynting- ux-dominated jets, such as the internal collision-induced magnetic reconnection and turbulence (ICMART) model for GRBs, and reconnection triggered mini-jets model for AGNs.

  5. Relativistic MHD Simulations of Collision-induced Magnetic Dissipation in Poynting-flux-dominated Jets/outflows

    NASA Astrophysics Data System (ADS)

    Deng, Wei; Li, Hui; Zhang, Bing; Li, Shengtai

    2015-06-01

    We perform 3D relativistic ideal magnetohydrodynamics (MHD) simulations to study the collisions between high-σ (Poynting-flux-dominated (PFD)) blobs which contain both poloidal and toroidal magnetic field components. This is meant to mimic the interactions inside a highly variable PFD jet. We discover a significant electromagnetic field (EMF) energy dissipation with an Alfvénic rate with the efficiency around 35%. Detailed analyses show that this dissipation is mostly facilitated by the collision-induced magnetic reconnection. Additional resolution and parameter studies show a robust result that the relative EMF energy dissipation efficiency is nearly independent of the numerical resolution or most physical parameters in the relevant parameter range. The reconnection outflows in our simulation can potentially form the multi-orientation relativistic mini jets as needed for several analytical models. We also find a linear relationship between the σ values before and after the major EMF energy dissipation process. Our results give support to the proposed astrophysical models that invoke significant magnetic energy dissipation in PFD jets, such as the internal collision-induced magnetic reconnection and turbulence model for gamma-ray bursts, and reconnection triggered mini jets model for active galactic nuclei. The simulation movies are shown in http://www.physics.unlv.edu/∼deng/simulation1.html.

  6. Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics.

    PubMed

    Zhao, Yimeng; Riley, Nicholas M; Sun, Liangliang; Hebert, Alexander S; Yan, Xiaojing; Westphall, Michael S; Rush, Matthew J P; Zhu, Guijie; Champion, Matthew M; Mba Medie, Felix; Champion, Patricia A DiGiuseppe; Coon, Joshua J; Dovichi, Norman J

    2015-01-01

    Top-down proteomics offers the potential for full protein characterization, but many challenges remain for this approach, including efficient protein separations and effective fragmentation of intact proteins. Capillary zone electrophoresis (CZE) has shown great potential for separation of intact proteins, especially for differentially modified proteoforms of the same gene product. To date, however, CZE has been used only with collision-based fragmentation methods. Here we report the first implementation of electron transfer dissociation (ETD) with online CZE separations for top-down proteomics, analyzing a mixture of four standard proteins and a complex protein mixture from the Mycobacterium marinum bacterial secretome. Using a multipurpose dissociation cell on an Orbitrap Elite system, we demonstrate that CZE is fully compatible with ETD as well as higher energy collisional dissociation (HCD), and that the two complementary fragmentation methods can be used in tandem on the electrophoretic time scale for improved protein characterization. Furthermore, we show that activated ion electron transfer dissociation (AI-ETD), a recently introduced method for enhanced ETD fragmentation, provides useful performance with CZE separations to greatly increase protein characterization. When combined with HCD, AI-ETD improved the protein sequence coverage by more than 200% for proteins from both standard and complex mixtures, highlighting the benefits electron-driven dissociation methods can add to CZE separations. PMID:25893372

  7. Dissociation rates of diatomic molecules. Final report, 15 September 1985-15 May 1992

    SciTech Connect

    Cosby, P.C.; Helm, H.

    1992-12-01

    Absolute cross sections were measured for the electron-impact dissociation of simple molecules using a novel fast beam technique with multicoincident detection of the dissociation fragments. Translational energy released in the dissociation and product mass ratios were explicitly measured, allowing a detailed understanding of the dissociation mechanisms. The technique was applied to the molecules of nitrogen, oxygen, carbon monoxide, carbon dioxide, nitrogen dioxide, chlorine, and other molecules. A detailed description of the measurement technique is presented together with the measured data.... Dissociation, electron impact, cross sections, nitrogen, oxygen, carbon monoxide, carbon dioxide, nitrogen dioxide, chlorine.

  8. Fragmentation pathwaysfor selected electronic states of theacetylene dication

    SciTech Connect

    Osipov, Timur; Rescigno, Thomas N.; Weber, Thorsten; Miyabe,Shungo; Jahnke, T.; Alnaser, A.; Hertlein, Markus P.; Jagutzki, O.; Schmidt, L.Ph.H.; Schoffler, M.; Foucar, L.; Schossler, S.; Havermeier,T.; Odenweller,M.; Voss, S.; Feinberg, Ben; Landers, Alan; Prior, MichaelH.; Dorner, Reinhart; Cocke, C.L.; Belkacem, Ali

    2007-12-18

    Coincident measurement of the Auger electron and fragmention momenta emitted after carbon core-level photoionization of acetylenehas yielded new understanding of how the dication fragments. Ab initiocalculations and experimental data, including body-frame Auger angulardistributions, are used to identify the parent electronic states andtogether yield a comprehensive map of the dissociation pathways whichinclude surface crossings and barriers to direct dissociation. The Augerangular distributions show evidence of core-holelocalization.

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

    PubMed

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

    2014-07-15

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

  10. Collision-induced absorption with exchange effects and anisotropic interactions: Theory and application to H{sub 2} − H{sub 2}

    SciTech Connect

    Karman, Tijs; Avoird, Ad van der; Groenenboom, Gerrit C.

    2015-02-28

    We discuss three quantum mechanical formalisms for calculating collision-induced absorption spectra. First, we revisit the established theory of collision-induced absorption, assuming distinguishable molecules which interact isotropically. Then, the theory is rederived incorporating exchange effects between indistinguishable molecules. It is shown that the spectrum can no longer be written as an incoherent sum of the contributions of the different spherical components of the dipole moment. Finally, we derive an efficient method to include the effects of anisotropic interactions in the computation of the absorption spectrum. This method calculates the dipole coupling on-the-fly, which allows for the uncoupled treatment of the initial and final states without the explicit reconstruction of the many-component wave functions. The three formalisms are applied to the collision-induced rotation-translation spectra of hydrogen molecules in the far-infrared. Good agreement with experimental data is obtained. Significant effects of anisotropic interactions are observed in the far wing.

  11. Isospin effects on fragmentation in the asymmetric reactions induced by neutron-rich targets

    NASA Astrophysics Data System (ADS)

    Sharma, Arun

    2016-05-01

    To understand the isospin effects in terms of fragment's yield in the asymmetric reactions induced by neutron-rich targets, we perform a theoretical study using isospin-dependent quantum molecular dynamics (IQMD) model. Simulations are carried out for reactions of 16O+Br80,84,92 and 16O+Ag108,113,122. We envision that fragments's yield in the asymmetric collisions induced by neutron-rich targets is better candidate to study isospin effects via symmetry energy and nucleon-nucleon (nn) cross-sections. Also, pronounced effects of symmetry energy and cross-sections can be found at lower and higher beam energies, respectively.

  12. Identification of Foodborne Bacteria by High Energy Collision-Induced Dissociation of Their Protein Biomarkers by MALDI Tandem-Time-of-Flight Mass Spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of methods for rapid identification of foodborne bacteria is an important area of analytical science and food safety. MALDI-TOF-MS has been utilized to rapidly identify pathogens including foodborne bacteria. Identification typically involves detection of high copy cytosolic proteins i...

  13. An unusual family of glycosylated peptides isolated from Dendroaspis angusticeps venom and characterized by combination of collision induced and electron transfer dissociation.

    PubMed

    Quinton, Loïc; Gilles, Nicolas; Smargiasso, Nicolas; Kiehne, Andrea; De Pauw, Edwin

    2011-11-01

    This study describes the structural characterization of a totally new family of peptides from the venom of the snake green mamba (Dendroaspis angusticeps). Interestingly, these peptides differ in several points from other already known mamba toxins. First of all, they exhibit very small molecular masses, ranging from 1.3 to 2.4 kDa. The molecular mass of classical mamba toxins is in the range of 7 to 25 kDa. Second, the new peptides do not contain disulfide bonds, a post-translational modification commonly encountered in animal toxins. The third difference is the very high proportion of proline residues in the sequence accounting for about one-third of the sequence. Finally, these new peptides reveal a carbohydrate moiety, indicating a glycosylation in the sequence. The last two features have made the structural characterization of the new peptides by mass spectrometry a real analytical challenge. Peptides were characterized by a combined use of MALDI- TOF/TOF and nanoESI-IT-ETD experiments to determine not only the peptide sequence but also the composition and the position of the carbohydrate moiety. Anyway, such small glycosylated and proline-rich toxins are totally different from any other known snake peptide and form, as a consequence, a new family of peptides. PMID:21952754

  14. Collision-induced absorption by CO{sub 2} in the far infrared: Analysis of leading-order moments and interpretation of the experiment

    SciTech Connect

    Kouzov, A. P.; Chrysos, M.

    2009-10-15

    The diagrammatic theory, developed recently by the authors [Phys. Rev. A 74, 012732 (2006)], is applied to binary collision-induced properties, with emphasis on induced dipole moments. Assuming rototranslational dynamics to be classical and using irreducible spherical tensor formalism, exact analytical formulas are worked out for the two leading order spectral moments of a collision-induced band by two interacting linear molecules. The formulas are applied to the far infrared absorption by CO{sub 2}-CO{sub 2}, and permit interpretation of the experiment. This study provides evidence of the adequacy of the electrostatic induction mechanism, provided that hitherto missing vibrational terms of static polarizability are considered.

  15. Tandem mass spectrometry-based detection of c4'-oxidized abasic sites at specific positions in DNA fragments.

    PubMed

    Chowdhury, Goutam; Guengerich, F Peter

    2009-07-01

    Oxidative damage to DNA has been linked to aging, cancer, and other biological processes. Reactive oxygen species and various antitumor agents including bleomycin and ionizing radiation have been shown to cause oxidative DNA sugar damage. Detection of DNA lesions is important for understanding the toxicological or therapeutic consequences associated with such agents. C4'-oxidized abasic sites (C4-AP) are produced by the antitumor drug bleomycin and ionizing radiation. The currently available methods for the detection of C4-AP cannot provide both structural and sequence information. We have developed an LC-ESI-MS-based approach for specific detection and mapping of C4-AP from a mixture of lesions. We show using Fe-bleomycin-damaged DNA that C4-AP can be detected at cytosine and thymine sites by direct MS analysis. Our results reveal that collision-induced dissociation of C4-AP-containing oligonucleotides results in preferential fragmentation at C4-AP sites with the formation of the unique a* ions (18 amu more than the a-B ions) that allow mapping of the C4-AP sites. Various chemical modification strategies (e.g., reduction with NaBH4 and NaBD4 and derivatization with methoxyamine and hydrazine, followed by LC-MS analysis) were also used for unambiguous detection of C4-AP sites. Finally, we show that the methods described here can detect the presence of C4-AP at specific sites in a complex sample such as hydroxyl radical-damaged DNA. The LC-MS approach was also used for the simultaneous detection of the other C4'-oxidation end product, 3'-phosphoglycolate, at a specific site in hydroxyl radical-damaged DNA. Thus, LC-MS provides a rapid and direct approach for the detection and mapping of oxidative DNA lesions. PMID:19496605

  16. Experimental and Theoretical Studies on the Fragmentation of Gas-Phase Uranyl-, Neptunyl- and Plutonyl-Diglycolamide Complexes

    SciTech Connect

    Gong, Yu; Hu, Han-Shi; Rao, Linfeng; Li, Jun; Gibson, John K.

    2013-10-10

    Fragmentation of actinyl(VI) complexes UVIO2(L)22+, NpVIO2(L)22+ and PuVIO2(L)22+ (L = tetramethyl-3-oxa-glutaramide, TMOGA) produced by electrospray ionization was examined in the gas phase by collision induced dissociation (CID) in a quadrupole ion trap mass spectrometer. Cleavage of the C-Oether bond was observed for all three complexes, with dominant products being UVIO2(L)(L-86)+ with charge reduction, and NpVIO2(L)(L-101)2+ and PuVIO2(L)(L-101)2+ with charge conservation. The neptunyl and plutonyl complexes also exhibited substantial L+ loss to give pentavalent complexes NpVO2(L)+ and PuVO2(L)+, whereas the uranyl complex did not, consistent with the comparative An 5f-orbital energies and the AnVIO22+/AnVO2+ (An = U, Np, Pu) reduction potentials. CID of NpVO2(L)2+ and PuVO2(L)2+ was dominated by neutral ligand loss to form NpVO2(L)+ and PuVO2(L)+, which hydrated by addition of residual water in the ion trap; UVO2(L)2+ was not observed. Theoretical calculations of the structures and bonding of the AnVIO2(L)22+ complexes using density functional theory reveal that the metal centers are coordinated by six oxygen atoms from the two TMOGA ligands. The results are compared with radiolytic decomposition of TMOGA in solution.

  17. Magma Fragmentation

    NASA Astrophysics Data System (ADS)

    Gonnermann, Helge M.

    2015-05-01

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

  18. Dissociation of diatomic gases

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1991-01-01

    The Landau-Zener theory of reactive cross sections has been applied to diatomic molecules dissociating from a ladder of rotational and vibrational states. Although the preexponential factor of the Arrhenius rate expression is shown to be a complex function of the dimensionless activation energy, the average over all states in the ladder is well represented by a single factor that varies about as T exp (-n), where the coefficient n is the order of unity. This relation agrees very well with experimental data for dissociation of O2 and N2, for example. The results validate previous empirical assignment of a single preexponential factor in the Arrhenius expression and justify the extrapolation of the expression well beyond the range of data. The theory is then used to calculate the effect of vibrational nonequilibrium on dissociation rate. For Morse oscillators the results are about the same as for harmonic oscillators, and the dissociation from a ladder of equilibrium rotational and nonequilibrium vibrational states is close to an analytic approximation provided by Hammerling, Kivel, and Teare for harmonic oscillators all dissociating from the ground rotational state.

  19. Structure of olefin-imidacloprid and gas-phase fragmentation chemistry of its protonated form.

    PubMed

    Fusetto, Roberto; White, Jonathan M; Hutton, Craig A; O'Hair, Richard A J

    2016-02-01

    One of the major insect metabolites of the widely used neonicotinoid insecticide imidacloprid, 1 (1-[(6-chloro-3-pyridinyl)methyl]-N-nitro-1H-imidazol-2-amine), is the olefin 2. To better understand how the structure of olefin 2 relates to the gas-phase fragmentation of its protonated form, 2H(+), X-ray crystallography, tandem mass spectrometry experiments and DFT calculations were carried out. Olefin 2 was found to be in a tautomeric form where the proton is on the N(1) position of the imidazole ring and forms a hydrogen bond to one of the oxygen atoms of the coplanar nitroamine group. Under conditions of low-energy collision-induced dissociation (CID) in a linear ion trap, 2H(+), formed via electrospray ionization (ESI), fragments via a major loss of water, together with minor competing losses of HNO2 and NO2•.This contrasts with 1H+, which mainly undergoes bond homolysis via NO2• loss. Thus, installation of the double bond in 2 plays a key role in facilitating the loss of water. DFT calculations, carried out using the B3LYP/6-311G++(d,p) level of theory, revealed that loss of water was energetically more favourable compared to HNO2 and NO2• loss. Three multistep, energetically accessible mechanisms were identified for loss of water from 2H(+), and these have the following barriers: (I) direct proton transfer from N(5) of the pyridine to O(1) on the NO2 group (119 kJ mol(-1)); (II) rotation of the N(2)-N(4) bond (117 kJ mol(-1)); (III) 1,3-intramolecular proton transfer between the two oxygen atoms of the NO2 group (145 kJ mol(-1)). Given that the lowest barrier for the losses of HNO2 and NO2• is 156 kJ mol(-1), it is likely that all three water loss mechanisms occur concurrently. PMID:26726997

  20. Electron-impact dissociation and ionization of NO+ ions

    NASA Astrophysics Data System (ADS)

    Belic, D. S.; Urbain, X.; Cherkani-Hassani, H.; Defrance, P.

    2016-07-01

    Absolute cross sections for electron-impact ionization and dissociation of NO+ ions are reported. Simple ionization to NO2+ ion and production of singly charged N+ and O+ and doubly charged N2+ and O2+ fragments have been investigated. The animated electron-ion crossed-beam method is applied in the energy range from the respective thresholds up to 2.5 keV. The maximum of the simple ionization cross section is found to be (3.49 ± 0.07) × 10‑17 cm2 at 135 eV. The total cross sections for N+ and O+ fragments at the maximum are found to be (13.9 ± 1.0) × 10‑17 cm2 and (14.0 ± 1.4) × 10‑17 cm2, respectively, both at an energy of 85 eV. By performing careful magnetic field scans of the detected signal, contributions of dissociative excitation and dissociative ionization to N+ and O+ production are determined separately. The cross sections for asymmetric dissociative ionization to N2+ and O2+ are found to be over one order of magnitude smaller. Distributions of the kinetic energy release to the fragments are determined for all dissociation processes.

  1. Forest Fragmentation

    EPA Science Inventory

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

  2. Collision-induced fusion of two single-walled carbon nanotubes: A quantitative study

    NASA Astrophysics Data System (ADS)

    Zhang, Chao; Mao, Fei; Meng, Xiang-Rui; Wang, Dong-Qi; Zhang, Feng-Shou

    2016-07-01

    The coalescence processes of two (6, 0) single-walled carbon nanotubes are investigated via coaxial collision based on the self-consistent-charge density-functional tight-binding molecular dynamics method. According to the structure characteristics of the nanotubes, five impact cases are studied to explore the coalescence processes of the nanotubes. The simulation shows that various kinds of carbon nanomaterials, such as graphene sheets, graphene nanoribbons, and single-walled carbon nanotubes with larger diameters, are created after collision. Moreover, some defects formed in the carbon nanomaterials can be eliminated, and even the final configurations which are originally fragmented can almost become intact structures by properly quenching and annealing.

  3. Modeling of collision induced absorption spectra of CO2-CO2 pairs for planetary atmosphere of Venus

    NASA Technical Reports Server (NTRS)

    Borysow, Aleksandra

    1995-01-01

    The objective of the proposal was to model the rototranslational and rotovibrational collision induced absorption spectral bands of importance for the radiative transfer analysis of the atmosphere of Venus. Our main task has involved CO2 pairs. The approach is not straightforward: whereas computational techniques to compute CIA spectra of small linear molecules exist, and were successfully applied to molecules like H2 or N2, they fail when applied to large molecules like CO2. For small molecules one can safely assume that the interaction potential is isotropic. The same approximation does not work for CO2, and when employed, it gives an incorrect band shape and only 50 percent of the CIA intensity.

  4. Collision-induced desorption in 193-nm photoinduced reactions in (O{sub 2}+CO) adlayers on Pt(112)

    SciTech Connect

    Han Song; Ma Yunsheng; Matsushima, Tatsuo

    2005-09-01

    The spatial distribution of desorbing O{sub 2} and CO{sub 2} was examined in 193-nm photoinduced reactions in O{sub 2}+CO adlayers on stepped Pt (112)=[(s)3(111)x(001)]. The O{sub 2} desorption collimated in inclined ways in the plane along the surface trough, confirming the hot-atom collision mechanism. In the presence of CO(a), the product CO{sub 2} desorption also collimated in an inclined way, whereas the inclined O{sub 2} desorption was suppressed. The inclined O{sub 2} and CO{sub 2} desorption is explained by a common collision-induced desorption model. At high O{sub 2} coverage, the CO{sub 2} desorption collimated closely along the (111) terrace normal.

  5. Molecular Dissociation Induced by Electron Collisions

    NASA Astrophysics Data System (ADS)

    Wolf, Andreas

    2009-05-01

    Free electrons can efficiently break molecules or molecular ions in low-energy collisions by the processes of dissociative recombination or attachment. These processes make slow electrons efficient chemical agents in many environments. For dissociative recombination, in particular, studies of the underlying reaction paths and mechanisms have become possible on a uniquely elementary level in recent years both for theory and experiment. On the experimental side, collisions can be prepared at resolved collision energies down to the meV (10 Kelvin) level, increasingly gaining control also over the initial molecular quantum level, and individual events are detected and kinematically analyzed by fast-beam coincidence fragment imaging. Experiments are reported from the ion cooler ring TSR in Heidelberg. Stored beams of molecular ions cooled in their external and internal degrees of freedom are collinearly merged with intense and cold electron beams from cryogenic GaAs photocathodes, recently shown to yield fast cooling of the center-of-mass motion also for heavy and correspondingly slow molecular ion beams. To reconstruct the molecular fragmentation events multiparticle imaging can now be used systematically with collision energies set a wide range, especially aiming at specific electron capture resonances. Thus, for CF^+ it is found that the electronic state of the C fragment (^3P or ^1D) switches resonantly when the collision energy is changed by only a small fraction. As a new powerful tool, an energy-sensitive multi-strip surface-barrier detector (EMU) has been set up to measure with near-unity efficiency the masses of all fragments together with their hit positions in high-multiplicity events. Among many uses, this device allows internal molecular excitations to be derived for individual chemical channels in polyatomic fragmentation. New results will be presented in particular on the breakup of the hydronium ion (D3O^+).

  6. Electron ionization and dissociation of aliphatic amino acids

    NASA Astrophysics Data System (ADS)

    Papp, P.; Shchukin, P.; Kočíšek, J.; Matejčík, Š.

    2012-09-01

    We present experimental and theoretical study of electron ionization and dissociative ionization to the gas phase amino acids valine, leucine, and isoleucine. A crossed electron/molecular beams technique equipped with quadrupole mass analyzer has been applied to measure mass spectra and ion efficiency curves for formation of particular ions. From experimental data the ionization energies of the molecules and the appearance energies of the fragment ions were determined. Ab initio calculations (Density Functional Theory and G3MP2 methods) were performed in order to calculate the fragmentation paths and interpret the experimental data. The experimental ionization energies of parent molecules [P]+ 8.91 ± 0.05, 8.85 ± 0.05, and 8.79 ± 0.05 eV and G3MP2 ionization energies (adiabatic) of 8.89, 8.88, and 8.81 eV were determined for valine, leucine, and isoleucine, respectively, as well as the experimental and theoretical threshold energies for dissociative ionization channels. The comparison of experimental data with calculations resulted in identification of the ions as well as the neutral fragments formed in the dissociative reactions. Around 15 mass/charge ratio fragments were identified from the mass spectra by comparison of experimental appearance energies with calculated reaction enthalpies for particular dissociative reactions.

  7. Coherent dissociation of relativistic {sup 12}N nuclei

    SciTech Connect

    Kattabekov, R. R.; Mamatkulov, K. Z.; Alikulov, S. S.; Artemenkov, D. A.; Bekmirzaev, R. N.; Bradnova, V.; Zarubin, P. I. Zarubina, I. G.; Kondratieva, N. V.; Kornegrutsa, N. K.; Krivenkov, D. O.; Malakhov, A. I.; Olimov, K.; Peresadko, N. G.; Polukhina, N. G.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Kharlamov, S. P.

    2013-10-15

    The dissociation of relativistic {sup 12}N nuclei having a momentum of 2 GeV/c per nucleon and undergoing the most peripheral interactions in a track emulsion is studied. The picture of charged topology of product ensembles of relativistic fragments and special features of their angular distributions are presented.

  8. Reaction Mechanisms in Collisions Induced by Halo and/or Weakly Bound Nuclei Around the Barrier: the 13N+9Be and 6He+64Zn Collisions

    SciTech Connect

    Figuera, P.; Cardella, G.; Di Pietro, A.; Lu, J.; Marchetta, C.; Papa, M.; Tian, W.; Amorini, F.; Cherubini, S.; Lattuada, M.; Musumarra, A.; Pizzone, R. G.; Rizzo, F.; Scuderi, V.; Angulo, C.; Casarejos, E.; Pellegriti, M. G.; Raabe, R.; Sida, J. L.

    2006-08-14

    The study of reaction mechanisms in collisions induced by halo and/or weakly bound nuclei around the barrier has recently been the subject of many theoretical and experimental papers. Here we discuss our recent results concerning the study of the systems 13N+9Be and 6He+64Zn.

  9. Rates for dissociative recombination of LiH+ ions

    NASA Astrophysics Data System (ADS)

    Čurík, R.; Greene, C. H.

    2008-05-01

    We review recent progress in developing a theoretical treatment of the dissociative recombination (DR) process for the LiH+ molecule, in which a low energy electron is captured and causes the molecule to dissociate into neutral fragments. This e+LiH+ system is prototypical of the indirect class of DR processes, in which the incident electron destroys the molecule through Rydberg capture pathways. The conventional mechanism characteristic of most species with a high DR rate, which normally involves direct capture into a dissociative resonance potential curve, is entirely absent here. We have adopted ab initio multichannel quantum defect theory (MQDT) and a rovibrational frame transformation based on Siegert pseudostates to calculate indirect dissociative recombination for this simple diatomic ion. It is based on a set of ab-initio quantum defects as functions of the internuclear distance, which have been calculated using the R-matrix approach. The calculated DR rate coefficient is found to agree with recent experimental data [1].

  10. Dissociative Reactions to Incest.

    ERIC Educational Resources Information Center

    Hall, J. Mark

    In contrast to Freud's later and revised view of the etiology of hysterical, or dissociative, symptoms, it is now known that real, and not fantasized, sexual experiences in childhood are experienced in disociative symptomatology. It is useful to understand that incest involves both traumatic events, that is, incidents of sexual violation per se,…

  11. Dissociative Identity Disorder

    ERIC Educational Resources Information Center

    Schmidt, Tom

    2007-01-01

    Few psychological disorders in the Diagnostic Statistical Manual have generated as much controversy as Dissociative Identity Disorder (DID). For the past 35 years diagnoses of DID, previously referred to as Multiple Personality Disorder (MPD), have increased exponentially, causing various psychological researchers and clinicians to question the…

  12. Dissociation and psychosis in dissociative identity disorder and schizophrenia.

    PubMed

    Laddis, Andreas; Dell, Paul F

    2012-01-01

    Dissociative symptoms, first-rank symptoms of schizophrenia, and delusions were assessed in 40 schizophrenia patients and 40 dissociative identity disorder (DID) patients with the Multidimensional Inventory of Dissociation (MID). Schizophrenia patients were diagnosed with the Structured Clinical Interview for the DSM-IV Axis I Disorders; DID patients were diagnosed with the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised. DID patients obtained significantly (a) higher dissociation scores; (b) higher passive-influence scores (first-rank symptoms); and (c) higher scores on scales that measure child voices, angry voices, persecutory voices, voices arguing, and voices commenting. Schizophrenia patients obtained significantly higher delusion scores than did DID patients. What is odd is that the dissociation scores of schizophrenia patients were unrelated to their reports of childhood maltreatment. Multiple regression analyses indicated that 81% of the variance in DID patients' dissociation scores was predicted by the MID's Ego-Alien Experiences Scale, whereas 92% of the variance in schizophrenia patients' dissociation scores was predicted by the MID's Voices Scale. We propose that schizophrenia patients' responses to the MID do not index the same pathology as do the responses of DID patients. We argue that neither phenomenological definitions of dissociation nor the current generation of dissociation instruments (which are uniformly phenomenological in nature) can distinguish between the dissociative phenomena of DID and what we suspect are just the dissociation-like phenomena of schizophrenia. PMID:22651674

  13. Pathological Dissociation as Measured by the Child Dissociative Checklist

    ERIC Educational Resources Information Center

    Wherry, Jeffrey N.; Neil, Debra A.; Taylor, Tamara N.

    2009-01-01

    The component structure of the Child Dissociative Checklist was examined among abused children. A factor described as pathological dissociation emerged that was predicted by participants being male. There also were differences in pathological dissociation between groups of sexually abused and physically abused children. Replication of this factor…

  14. On the dissociation energy of Mg2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Pettersson, Lars G. M.; Mclean, A. D.; Liu, Bowen

    1990-01-01

    The bonding in the X 1Sigma(+)g state of Mg2 is investigated using near-complete valence one-particle Slater and Gaussian basis sets containing up to h functions. It is shown that the four-electron complete CI limit can be approached using a sequence of either second-order CI (SOCI) or interacting correlated fragment (ICF) calculations. At the valence level, the best estimate of the dissociation energy D(e) was 464/cm. This is a lower limit and is probably within 5/cm of the complete basis value.

  15. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

    Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.

    2014-05-14

    The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.

  16. Direct Photo Double Ionization of Water and Subsequent Fragmentation

    NASA Astrophysics Data System (ADS)

    Reedy, D.; Gaire, B.; Gatton, A.; Sartor, J.; Berry, B.; Weller, M.; Bauer, T.; Burzynski, P.; Henrichs, K.; Dorner, R.; Williams, J. B.; Weber, Th.; Landers, A. L.

    2016-05-01

    We have measured and imaged the dissociation of water in the gas phase following direct double photoionization by a 57 eV photon. The dissociation left the dication in a range of several energetically available excited states. The momenta of the resulting dication fragments and photoelectrons were measured in coincidence with Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS). The different states of the dication result in marked differences in photoelectron energies, kinetic energy release, and bond angle at the time of the fragmentation, as well as leaving the neutral oxygen fragment in one of several indirectly observed excited states.

  17. Dissociation of gaseous zwitterion glycine-betaine by slow electrons.

    PubMed

    Kopyra, J; Abdoul-Carime, H

    2010-05-28

    In this work, we investigate dissociation processes induced by low-energy electrons to gas phase N,N,N-trimethylglycine [glycine-betaine, (CH(3))(3)N(+)CH(2)COO(-)] molecules. Glycine-betaine represents a model system for zwitterions. All negative fragments are observed to be produced only at subelectronic excitation energies (<4 eV). With the exception of the loss of a neutral H atom that could arise from any C[Single Bond]H bond breaking, we tentatively suggest that the zwitterion dissociates exclusively from the fragmentation of the cation site of the molecule, subsequent to the attachment of the excess electron. Within the context of radiation induced damage to biological systems, the present findings contribute to a more complete description of the fragmentation mechanism occurring to amino acids, peptides, and proteins since they adopt usually a zwitterion structure. PMID:20515090

  18. Three dimensions of dissociative amnesia.

    PubMed

    Dell, Paul F

    2013-01-01

    Principal axis factor analysis with promax rotation extracted 3 factors from the 42 memory and amnesia items of the Multidimensional Inventory of Dissociation (MID) database (N = 2,569): Discovering Dissociated Actions, Lapses of Recent Memory and Skills, and Gaps in Remote Memory. The 3 factors' shared variance ranged from 36% to 64%. Construed as scales, the 3 factor scales had Cronbach's alpha coefficients of .96, .94, and .93, respectively. The scales correlated strongly with mean Dissociative Experiences Scale scores, mean MID scores, and total scores on the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised (SCID-D-R). What is interesting is that the 3 amnesia factors exhibited a range of correlations with SCID-D-R Amnesia scores (.52, .63, and .70, respectively), suggesting that the SCID-D-R Amnesia score emphasizes gaps in remote memory over amnesias related to dissociative identity disorder. The 3 amnesia factor scales exhibited a clinically meaningful pattern of significant differences among dissociative identity disorder, dissociative disorder not otherwise specified-1, dissociative amnesia, depersonalization disorder, and nonclinical participants. The 3 amnesia factors may have greater clinical utility for frontline clinicians than (a) amnesia as discussed in the context of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, nosology of the dissociative disorders or (b) P. Janet's (1893/1977 ) 4-fold classification of dissociative amnesia. The author recommends systematic study of the phenomenological differences within specific dissociative symptoms and their differential relationship to specific dissociative disorders. PMID:23282045

  19. Fragmentation of mercury compounds under ultraviolet light irradiation

    SciTech Connect

    Kokkonen, E.; Hautala, L.; Jänkälä, K.; Huttula, M.; Löytynoja, T.

    2015-08-21

    Ultraviolet light induced photofragmentation of mercury compounds is studied experimentally with electron energy resolved photoelectron-photoion coincidence techniques and theoretically with computational quantum chemical methods. A high resolution photoelectron spectrum using synchrotron radiation is presented. Fragmentation of the molecule is studied subsequent to ionization to the atomic-mercury-like d orbitals. State dependent fragmentation behaviour is presented and specific reactions for dissociation pathways are given. The fragmentation is found to differ distinctly in similar orbitals of different mercury compounds.

  20. Dissociation and psychotic symptoms.

    PubMed

    Steingard, S; Frankel, F H

    1985-08-01

    The literature on hysterical or brief reactive psychosis reflects great diversity both in clinical description and theoretical formulation. The authors describe the case of a 17-year-old girl who presented with a diagnosis of bipolar affective disorder, rapid cycling type, but who, in fact, was experiencing dissociative episodes manifested as psychotic states. The patient's successful treatment with hypnosis is described, along with the clinical and theoretical implications of the case. PMID:4025593

  1. Three-dimensional momentum imaging of delayed dissociation of metastable molecular ions

    NASA Astrophysics Data System (ADS)

    Malakar, Y.; Jochim, Bethany; Erdwien, Reid; Carnes, K. D.; Pearson, W. L.; Rudenko, A.; Ben-Itzhak, I.

    2016-05-01

    Coincidence three-dimensional momentum imaging has been a powerful technique in studies of molecular fragmentation following ionization by ultrashort intense laser pulses, fast ion or electron impact, etc. On occasion, the fragmentation process of the intermediate molecular ion can be delayed by a significant fraction of the flight time to the detector due to the presence of metastable states. We focus on the signatures of delayed dissociation into an ion pair observed in coincidence spectra obtained using cold target recoil ion momentum spectrometry (COLTRIMS). Moreover, we present a method for recovering the complete 3D momenta of the dissociating fragments as well as the time delay of the dissociation. Laser-induced dissociation of hydrocarbon dications, for example C2 H42+ --> H+ + C2 H3+,is used to demonstrate the method. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy.

  2. Perturbative fragmentation

    SciTech Connect

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

    2008-03-01

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

  3. Energy and Entropy Effects in Dissociation of Peptide Radical Anions

    SciTech Connect

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

    2012-04-15

    Time- and collision energy-resolved surface-induced dissociation (SID) of peptide radical anions was studied for the first time using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for SID experiments. Peptide radical cations and anions were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. The effect of the charge, radical, and the presence of a basic residue on the energetics and dynamics of dissociation of peptide ions was examined using RVYIHPF (1) and HVYIHPF (2) as model systems. Comparison of the survival curves for of [M+H]{sup +}, [M-H]{sup -}, M{sup +{sm_bullet}}, and [M-2H]{sup -{sm_bullet}} ions of these precursors demonstrated that even-electron ions are more stable towards fragmentation than their odd-electron counterparts. RRKM modeling of the experimental data demonstrated that the lower stability of the positive radicals is mainly attributed to lower dissociation thresholds while entropy effects are responsible the relative instability of the negative radicals. Substitution of arginine with less basic histidine residue has a strong destabilizing effect on the [M+H]{sup +} ions and a measurable stabilizing effect on the odd-electron ions. Lower threshold energies for dissociation of both positive and negative radicals of 1 are attributed to the presence of lower-energy dissociation pathways that are most likely promoted by the presence of the basic residue.

  4. Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes

    SciTech Connect

    Rios, Daniel; Schoendorff, George E.; Van Stipdonk, Michael J.; Gordon, Mark S.; Windus, Theresa L.; Gibson, John K.; De Jong, Wibe A.

    2012-12-03

    Combined collision-induced dissociation mass-spectrometry experiments and DFT calculations were employed to elucidate the molecular structure of "hypercoordinated" species and the energetics of water-elimination reactions of uranyl acetone complexes observed in earlier work (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). It is shown that the "hypercoordinated" species contain diacetone alcohol ligands bonded in either bidentate or monodentate fashion, which are indistinguishable from (acetone)2 in mass spectrometry. Calculations confirm that four diacetone ligands can form stable complexes, but that the effective number of atoms coordinating with uranium in the equatorial plane does not exceed five. Diacetone alcohol ligands are shown to form mesityl oxide ligands and alkoxide species through the elimination of water, providing an explanation for the observed water-elimination reactions.

  5. Infrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexes.

    PubMed

    Verkerk, Udo H; Zhao, Junfang; Saminathan, Irine S; Lau, Justin Kai-Chi; Oomens, Jos; Hopkinson, Alan C; Siu, K W Michael

    2012-04-16

    Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative. PMID:22455512

  6. Dissociative Recombination Dynamics of the Ozone Cation

    SciTech Connect

    Zhaunerchyk, Vitali; Geppert, W.; sterdahl, F.; Larsson, Mats; Thomas, R. D.; Bahati Musafiri, Eric; Bannister, Mark E; Fogle, Mark R.; Vane, C Randy

    2008-02-01

    The dissociative recombination of the ozone cation has been studied at the heavy-ion storage ring CRYRING. The total cross section and branching fractions have been measured. The cross section from {approx}0eV to 0.2 eV follows a nearly E{sup -1} dependence, which was theoretically predicted to be a characteristic of the direct dissociative recombination mechanism. The thermal rate coefficient has been deduced from the cross section to be 7.37x10{sup -7}(T/300){sup -0.55}cm{sup 3}s{sup -1}. The branching fraction analysis carried out at {approx}0eV interaction energy has shown a strong propensity (94%) to dissociate through the three-body channel. Due to the overwhelming dominance of this channel it has been investigated in more detail. Of the six energetically available three-body pathways only three are significantly populated, such that the production of O(S1) is highly unfavored and all atomic oxygen fragments are predominantly formed in P3 and D1 states. Analysis of the breakup geometries has been performed by means of the Dalitz plot. It is observed that the molecules dissociating through the O(P3)+O(P3)+O(P3) and O(P3)+O(P3)+O(D1) channels have an open linear geometry where the cleavage of two valence bonds occurs preferentially in unison, while the O(P3)+O(D1)+O(D1) breakup might proceed partly through a sequential mechanism.

  7. Spectral Moments of Collision-Induced Absorption of CO2 Pairs: The Role of the Intermolecular Potential

    NASA Technical Reports Server (NTRS)

    Gruszka, Marcin; Borysow, Aleksandra

    1994-01-01

    In this paper we examine the role of the anisotropy of the intermolecular potential in the rototranslational collision-induced absorption of the CO2 pairs. Using newly developed formulas that include the effects of anisotropy of the potential to all orders, we calculate the two lowest spectral moments gamma(prime), and alpha(prime), for four different classes of C02 pair potentials and compare the results with the experimental values. We assumed only multipolar induction in the process of forming the induced dipole, with the second-order contributions included. Using a site-site LJ and a site-site semi-ab initio intermolecular potentials we were able to reproduce the experimental values of gamma(prime), and alpha(prime) moments over entire temperature range from 230 to 330 K. Also, the role of an electrostatic interaction between two C02 molecules and its impact on the spectral moments is thoroughly investigated. An isotropic core with a point quadrupole centered at each molecule is shown to be an inadequate representation of the C02-CO2 potential. Additionally, we show the results obtained with the first- and second-order perturbation theory to be more than twice too small.

  8. New line narrowing effects in the infrared collision-induced spectra of molecular hydrogens in liquid neon.

    PubMed

    Herrebout, W A; van der Veken, B J; Kouzov, A P

    2008-08-29

    The first spectroscopic observation of the relative (solute-solute) diffusion in a fluid environment is reported. New, unusually sharp Q1q(J) lines developing against the diffuse background in the collision-induced fundamental IR bands of hydrogen isotopomers (H2, D2, and HD) dissolved in liquid Ne (T approximately 25 K) are studied as functions of the solute concentration x. In all cases, the Q1q intensity parabolically scales with x, accompanied by a striking narrowing of the line shapes. The narrowing, as revealed by the p-H2 solution studies, is due to a faster growth with x of the sharper solute-solute induced component of the single Q1q(0) line. The latter as well as other observed solute-solute lines are strongly narrowed by fast velocity decorrelations and are signatures of microscopic-scale diffusion. Also, a first observation of the solute-solvent induced J-->J + 4 transitions is reported. PMID:18851607

  9. Collision-induced Raman scattering and the peculiar case of neon: anisotropic spectrum, anisotropy, and the inverse scattering problem.

    PubMed

    Dixneuf, Sophie; Rachet, Florent; Chrysos, Michael

    2015-02-28

    Owing in part to the p orbitals of its filled L shell, neon has repeatedly come on stage for its peculiar properties. In the context of collision-induced Raman spectroscopy, in particular, we have shown, in a brief report published a few years ago [M. Chrysos et al., Phys. Rev. A 80, 054701 (2009)], that the room-temperature anisotropic Raman lineshape of Ne-Ne exhibits, in the far wing of the spectrum, a peculiar structure with an aspect other than a smooth wing (on a logarithmic plot) which contrasts with any of the existing studies, and whose explanation lies in the distinct way in which overlap and exchange interactions interfere with the classical electrostatic ones in making the polarizability anisotropy, α∥ - α⊥. Here, we delve deeper into that study by reporting data for that spectrum up to 450 cm(-1) and for even- and odd-order spectral moments up to M6, as well as quantum lineshapes, generated from SCF, CCSD, and CCSD(T) models for α∥ - α⊥, which are critically compared with the experiment. On account of the knowledge of the spectrum over the augmented frequency domain, we show how the inverse scattering problem can be tackled both effectively and economically, and we report an analytic function for the anisotropy whose quantum lineshape faithfully reproduces our observations. PMID:25725726

  10. Rototranslational collision-induced absorption by H2-H2 pairs at temperatures from 600 to 7000 K

    NASA Technical Reports Server (NTRS)

    Zheng, Chunguang; Borysow, Aleksandra

    1995-01-01

    The computation of the far-infrared, rototranslational (RT) collision-induced absorption (CIA) spectra of H2-H2 pairs is presented at temperatures from 600 to 7000 K for the first time. Theoretical results are based on the quantum mechanical and semiclassical, three lowest translational spectral moments obtained for H2 pairs. The effective, isotropic H2-H2 interaction potential, suitable for the high-temperature computations, and the ab initio induced dipoles, have been used as input. Special effort has been made to account for the rotational and vibrational states dependence of the dipoles, since it was found to be relevant at the high temperatures employed. The computations of the entire RT band account for all populated vibrational states of hydrogen molecule and include vibrational transitions v tends towards v-prime = v, with v = 0, 1, 2 and 3. The described method makes use of the adequately selected model line shapes with the temperature-dependent parameters. The presented model is useful for the 'model atmospheres' of zero- and low-metallicity, cool and dense stellar atmospheres, where CIA is known to be imporatnt.

  11. Relativistic MHD simulations of collision-induced magnetic dissipation in Poynting-flux-dominated jets/outflows

    SciTech Connect

    Deng, Wei

    2015-07-21

    The question of the energy composition of the jets/outflows in high-energy astrophysical systems, e.g. GRBs, AGNs, is taken up first: Matter-flux-dominated (MFD), σ < 1, and/or Poynting-flux-dominated (PFD), σ >1? The standard fireball IS model and dissipative photosphere model are MFD, while the ICMART (Internal-Collision-induced MAgnetic Reconnection and Turbulence) model is PFD. Motivated by ICMART model and other relevant problems, such as “jets in a jet” model of AGNs, the author investigates the models from the EMF energy dissipation efficiency, relativistic outflow generation, and σ evolution points of view, and simulates collisions between high-σ blobs to mimic the situation of the interactions inside the PFD jets/outflows by using a 3D SRMHD code which solves the conservative form of the ideal MHD equations. σb,f is calculated from the simulation results (threshold = 1). The efficiency obtained from this hybrid method is similar to the efficiency got from the energy evolution of the simulations (35.2%). Efficiency is nearly σ independent, which is also confirmed by the hybrid method. σb,i - σb,f provides an interesting linear relationship. Results of several parameter studies of EMF energy dissipation efficiency are shown.

  12. The Generation of Hot Galactic Halos: Multi-Phase Simulations including Collision-Induced Shock Heating, and Comparisons with Observations

    NASA Astrophysics Data System (ADS)

    Hearn, Nathan C.; Lamb, Susan A.

    2001-09-01

    The presence of hot halos around some colliding and supposed merging galaxies, as detected in X-rays, suggests that galaxy interactions may be responsible for the production of significant amounts of hot-phase interstellar gas in some systems. Possible mechanisms for producing this hot material are large-scale shock heating due to the collision itself, as well as the subsequent supernova explosions and intense stellar winds from the massive stars that are formed in collision-induced starbursts. We are using numerical simulations of galaxy collisions and mergers to explore the possible contribution of these various physical mechanisms. These simulations are compared with observations of real systems. Here we report on results from the application of a new N-body/smoothed particle hydrodynamics simulation code that has been constructed to allow the representation of multiple phases in the interstellar medium (Hearn et al, in preparation). This simulation code has been used to explore the generation of hot interstellar gas due to the large-scale shock heating that occurs during the collision and merger of two gas-rich disk galaxies. This current study allows us to place limits on the effect of the collision itself (as opposed to the results of subsequent star formation) on the generation of hot halos. We compare our numerical results to the extensive observations of the collisional merging system Arp 220 and, in particular, with our recent Chandra observations of its extended X-ray halo (McDowell et al, in preparation).

  13. Collision-induced Raman scattering and the peculiar case of neon: Anisotropic spectrum, anisotropy, and the inverse scattering problem

    SciTech Connect

    Dixneuf, Sophie; Rachet, Florent; Chrysos, Michael

    2015-02-28

    Owing in part to the p orbitals of its filled L shell, neon has repeatedly come on stage for its peculiar properties. In the context of collision-induced Raman spectroscopy, in particular, we have shown, in a brief report published a few years ago [M. Chrysos et al., Phys. Rev. A 80, 054701 (2009)], that the room-temperature anisotropic Raman lineshape of Ne–Ne exhibits, in the far wing of the spectrum, a peculiar structure with an aspect other than a smooth wing (on a logarithmic plot) which contrasts with any of the existing studies, and whose explanation lies in the distinct way in which overlap and exchange interactions interfere with the classical electrostatic ones in making the polarizability anisotropy, α{sub ∥} − α{sub ⊥}. Here, we delve deeper into that study by reporting data for that spectrum up to 450 cm{sup −1} and for even- and odd-order spectral moments up to M{sub 6}, as well as quantum lineshapes, generated from SCF, CCSD, and CCSD(T) models for α{sub ∥} − α{sub ⊥}, which are critically compared with the experiment. On account of the knowledge of the spectrum over the augmented frequency domain, we show how the inverse scattering problem can be tackled both effectively and economically, and we report an analytic function for the anisotropy whose quantum lineshape faithfully reproduces our observations.

  14. Reaction of Cu+ with dimethoxyethane: Competition between association and multiple dissociation channels

    NASA Astrophysics Data System (ADS)

    Koizumi, Hideya; Muntean, Felician; Armentrout, P. B.

    2004-01-01

    The reaction of Cu+ with dimethoxyethane (DXE) is studied using kinetic-energy dependent guided ion beam mass spectrometry. The bimolecular reaction forms an associative Cu+(DXE) complex that is long-lived and dissociates into several competitive channels: C4H9O2++CuH, Cu+(C3H6O)+CH3OH, back to reactants, and other minor channels. The kinetic-energy dependences of the cross sections for the three largest product channels are interpreted with several different models (including rigorous phase space theory) to yield 0 K bond energies after accounting for the effects of multiple ion-molecule collisions, internal energy of the reactant ions, Doppler broadening, and dissociation lifetimes. These values are compared with bond energies obtained from collision-induced dissociation (CID) studies of the Cu+(DXE) complex and found to be self-consistent. Although all models provide reasonable thermochemistry, phase space theory reproduces the details of the cross sections most accurately. We also examine the dynamics of this reaction using time-of-flight methods and a retarding potential analysis. This provides additional insight into the unimolecular decay of the long-lived Cu+(DXE) association complex. Comparison of results from this study with those from the complementary CID study, thus forming the same energized Cu+(DXE) complex in two distinct ways, allows an assessment of the models used to interpret CID thresholds.

  15. Recurrent dissociative fugue.

    PubMed

    Mamarde, Abhishek; Navkhare, Praveen; Singam, Amrita; Kanoje, Akash

    2013-10-01

    Dissociative fugue is a rarely reported diagnostic entity. It is one of the least understood and yet clinically one of the most fascinating disorders in mental health. Here, we describe a case of fugue in a 32-year-old man who was brought to mental hospital with complete loss of memory for events pertaining to identity of self. This case illustrates the nature of presentation in hospital setting like mental hospital and effort taken to reintegrate his identity and reunite with his family. PMID:24379504

  16. Absorption and dissociative photoionization cross sections of NH3 from 80 to 1120 A

    NASA Technical Reports Server (NTRS)

    Samson, James A. R.; Haddad, G. N.; Kilcoyne, L. D.

    1987-01-01

    The total absorption, photoionization, and dissociative photoionization cross sections of ammonia have been measured from 80 to 1120 A. All possible fragment ions have been observed including doubly ionized ammonia. The absolute ionization efficiencies have also been measured in this spectral range. The appearance potentials of the fragment ions have been measured and are compared with the calculated appearance potentials derived from published heats of formation and ionization potentials of the fragments.

  17. Dissociative Electron Attachment

    NASA Astrophysics Data System (ADS)

    Arreola, Esmeralda; Esmeralda Arreola Collaboration; Leigh Hargreaves Collaboration

    Since the pioneering work of Boudiaffa et al., it has been understood that electrons, even with energies near or below the ionization threshold, are capable of initiating strand-breaks in human DNA. This discovery raised important questions for cancer treatments, since sub-ionizing electrons are known to be the most copiously produced secondary product of radiation therapy. But even to date these factors are largely excluded from dosimetry calculations. This lack of inclusion is, at least in part, certainly due to the dearth of fundamental data describing low-energy electron interactions with nucleotide molecules that form the basis of DNA. Understanding of how such slow electrons are able to damage DNA remains incomplete, but the strongly peaked nature of Boudiaffa et al.'s data gives strong hints at resonantly driven collision processes. DNA damage is therefore most likely driven by ``dissociative electron attachment'' (DEA). DEA is a rather complicated process to model due to the coupling of electronic and nuclear degrees of freedom in the molecule. At the California State University Fullerton, we are currently commissioning a new spectrometer to study dissociation channels, reaction rates and orientation effects in DEA collisions between slow electrons and nucleotide molecules. At the meeting we will present design parameters and commissioning data for this new apparatus.

  18. Hyperglycemia associated dissociative fugue (organic dissociative disorder) in an elderly

    PubMed Central

    Ram, Dushad; Ashoka, H. G; Gowdappa, Basavnna

    2015-01-01

    Inadequate glycemic control in patients with diabetes is known to be associated with psychiatric disorders such as depression, anxiety disorder, and cognitive impairment. However, dissociative syndrome has not been reported so far. Here we are reporting a case of repeated dissociative fugue associated with hyperglycemia, in an elderly with type II diabetes. Possible neurobiological mechanism has been discussed. PMID:26286620

  19. Reaction paths of phosphine dissociation on silicon (001)

    NASA Astrophysics Data System (ADS)

    Warschkow, O.; Curson, N. J.; Schofield, S. R.; Marks, N. A.; Wilson, H. F.; Radny, M. W.; Smith, P. V.; Reusch, T. C. G.; McKenzie, D. R.; Simmons, M. Y.

    2016-01-01

    Using density functional theory and guided by extensive scanning tunneling microscopy (STM) image data, we formulate a detailed mechanism for the dissociation of phosphine (PH3) molecules on the Si(001) surface at room temperature. We distinguish between a main sequence of dissociation that involves PH2+H, PH+2H, and P+3H as observable intermediates, and a secondary sequence that gives rise to PH+H, P+2H, and isolated phosphorus adatoms. The latter sequence arises because PH2 fragments are surprisingly mobile on Si(001) and can diffuse away from the third hydrogen atom that makes up the PH3 stoichiometry. Our calculated activation energies describe the competition between diffusion and dissociation pathways and hence provide a comprehensive model for the numerous adsorbate species observed in STM experiments.

  20. The return of dissociation as absence within absence.

    PubMed

    Gurevich, Hayuta

    2014-12-01

    My aim is to translate Ferenczi's central concepts of the intrapsychic impact and imprint of early developmental trauma into both revived and contemporary conceptualizations. The concept of dissociation was renounced by Freud, yet it is returning as a cornerstone of recent trauma theories. Ferenczi used the concept of "repression," but used it in the sense of an intrapsychic imprint of early external trauma that fragments consciousness, that is, as dissociation. Furthermore, early trauma is double: an absence of protection that threatens existence of the self, combined with an absence of attachment and of recognition of this threat and terror; thus it is an absence-within-absence. This contemporary conceptualization entails a widening of the intrapsychic realm to include an intersubjective one, and regards dissociation as a unique and complex intrapsychic absence, which is a negative of the external absence-within-absence in the early environment. PMID:25434884

  1. Fragmentation of Integral Membrane Proteins in the Gas Phase

    PubMed Central

    2015-01-01

    Integral membrane proteins (IMPs) are of great biophysical and clinical interest because of the key role they play in many cellular processes. Here, a comprehensive top down study of 152 IMPs and 277 soluble proteins from human H1299 cells including 11 087 fragments obtained from collisionally activated dissociation (CAD), 6452 from higher-energy collisional dissociation (HCD), and 2981 from electron transfer dissociation (ETD) shows their great utility and complementarity for the identification and characterization of IMPs. A central finding is that ETD is ∼2-fold more likely to cleave in soluble regions than threshold fragmentation methods, whereas the reverse is observed in transmembrane domains with an observed ∼4-fold bias toward CAD and HCD. The location of charges just prior to dissociation is consistent with this directed fragmentation: protons remain localized on basic residues during ETD but easily mobilize along the backbone during collisional activation. The fragmentation driven by these protons, which is most often observed in transmembrane domains, both is of higher yield and occurs over a greater number of backbone cleavage sites. Further, while threshold dissociation events in transmembrane domains are on average 10.1 (CAD) and 9.2 (HCD) residues distant from the nearest charge site (R, K, H, N-terminus), fragmentation is strongly influenced by the N- or C-terminal position relative to that site: the ratio of observed b- to y-fragments is ∼1:3 if the cleavage occurs >7 residues N-terminal and ∼3:1 if it occurs >7 residues C-terminal to the nearest basic site. Threshold dissociation products driven by a mobilized proton appear to be strongly dependent on not only relative position of a charge site but also N- or C-terminal directionality of proton movement. PMID:24689519

  2. Collision-induced basalt eruptions at Pleiku and Buôn Mê Thuột, south-central Viet Nam

    NASA Astrophysics Data System (ADS)

    Hoàng, Nguyễn; Flower, Martin F. J.; Chí, Cung Thu'ọ'ng; Xuân, Phạm Tích; Quý, Hoàng Văn; Sơn, Trần Thanh

    2013-09-01

    Neogene-Quaternary basalts occur as dispersed volcanic clusters in the vicinity of the Tethyan tectonic belt, possibly representing 'far-field' effects of the Early Tertiary collisions of Gondwana fragments with the southern margin of Eurasia. In Indochina, such a 'Diffuse Igneous Province' post-dates the 45-42 Ma 'hard' India-Asia collision and southeastward, collision induced (c. 30-17 Ma.), extrusion of Indochina. Extrusion was accommodated by left-lateral strike-slip shearing on the Ailao Shan-Red River Fault, coeval with seafloor spreading in the East Viet Nam (South China) Sea. The Indochina basalts mostly comprise shield-building tholeiites capped by small-volume undersaturated types, the latter often bearing mantle xenoliths and 'exotic' xenocrysts such as sapphire, zircon. They appeared at c. 17 Ma, more-or-less coinciding with the cessation of both continental extrusion and seafloor spreading. At this point extensional stress appears to have shifted westwards to continental Indochina, with magmatic activity appearing, characteristically, at 'pull-apart' basins. However, the relationship of mantle melting beneath this region to its geodynamic setting is controversial, being variously attributed to mantle plumes, extreme lithospheric stretching, and lateral asthenospheric displacement. There is little or no definitive evidence for regional mantle upwelling while lithosphere stretching alone appears to be insufficient to allow for melting, Here, we present geochemical and Sr, Nd, and Pb isotopic (and paleomagnetic data), for cored sections from the Pleiku and Buon Mê Thuột plateaus in south-central Viet Nam, representative in most respects of the Indochina province as a whole. In the Pleiku shield olivine tholeiite flows are intercalated with quartz tholeiites while, in contrast, alkali basalts predominate over olivine tholeiite in the Buon Mê Thuột (BMT) shield. The first of these features (in Pleiku) probably reflects crustal wall-rock reaction while

  3. Temperature dependences of mechanisms responsible for the water-vapor continuum absorption. II. Dimers and collision-induced absorption.

    PubMed

    Leforestier, C; Tipping, R H; Ma, Q

    2010-04-28

    We investigated the magnitude and temperature dependence (T dependence) of the dimer absorption in the region of 0-600 cm(-1) and the collision-induced absorption (CIA) in the region of 0-1150 cm(-1). Together with our previous study of the self water-vapor continuum contributions resulting from far-wing line shapes of the allowed H(2)O lines in the infrared window between 800 and 1150 cm(-1), we find that the three mechanisms have completely different T dependence behaviors. The dimer absorption has the strongest negative T dependence and the continuum absorption from far wings of the allowed lines has a moderately strong negative one. Meanwhile, the CIA exhibits a mild T dependence. In addition, their T dependence patterns are quite different. The T dependence of the far-wing theory varies significantly as the frequency of interest omega varies. For CIA, in general, its T dependence is mildly negative, but becomes slightly positive in the window region between the H(2)O bands. In contrast, the T dependence of the dimer absorption varies slightly as omega varies. In the microwave and submillimeter region, its T dependence becomes uniform. Concerning the relative importance for each of these three mechanisms, we find that in the infrared widow, the far-wing contributions are the dominant source of the self-continuum. Within the band, its contributions are definitely responsible for the measured continuum data. But, it is impossible to draw quantitatively conclusions on its relative importance unless one is able to improve the accuracy of the local line calculations significantly. On the other hand, within the pure rotational band, the dimer absorptions are a minor contributor to the self-continuum measurements, and its role becomes more important in the microwave and submillimeter regions. Finally, based on our study we conclude that contributions to the self-continuum from CIA in the frequency region of 0-1150 cm(-1) are negligible. PMID:20441270

  4. Dissociative excitation of molecular hydrogen by electron impact.

    NASA Technical Reports Server (NTRS)

    Misakian, M.; Zorn, J. C.

    1972-01-01

    A pulsed electron beam was employed in the experiment to excite a diffuse gas of hydrogen molecules. The energy resolution of the electron gun permitted careful measurements of the thresholds for the production of slow and fast H(2s) atoms. The experiment was conducted in a vacuum system that facilitated a systematic study of the angular distribution of the fragments in the dissociative excitation process. The results permit the identification of the several excited states that are involved in the production of the H(2s) fragments.

  5. Dissociative attachment of electrons with Si2H6

    NASA Technical Reports Server (NTRS)

    Krishnakumar, E.; Srivastava, S. K.; Iga, I.

    1991-01-01

    Cross-sections for the production of negative ion fragments by electron attachment to Si2H6 and ion pair formation from it have been measured by utilizing the crossed electron beam-molecular beam collision technique. The negative ions are mass-analyzed by employing a quadrupole mass spectrometer. There are serious disagreements between the present and two previously published results. In the present paper cross-section values, appearance potentials, and the various channels of dissociation for the formation of negative monosilane fragments are presented.

  6. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-04-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

  7. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study.

    PubMed

    Shaffer, Christopher J; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-07-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed. Graphical Abstract ᅟ. PMID:27059977

  8. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-07-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

  9. Dissociation dynamics of core excited N[sub 2]O

    SciTech Connect

    LeBrun, T. DRECAM, SPAM, CEA, CEN Saclay, 9119, Gif sur Yvette Cedex Physics Division, Argonne National Laboratory, Argonne, Illinois 60439 ); Lavollee, M. ); Simon, M.; Morin, P. DRECAM, SPAM, CEA, CEN Saclay, 9119, Gif sur Yvette Cedex )

    1993-02-15

    Fragmentation of N[sub 2]O after selective core excitation of terminal and central nitrogen, has been studied by a multicoincidence technique (PEPIPICO) using synchrotron radiation. We show that dissociation dynamics is dependent upon the excited site, especially in the case of the atomization'' of the molecule. The central nitrogen is always found with very little kinetic energy, except after Nt[r arrow][Pi]* transition. A bent intermediate geometry is proposed to explain this observation.

  10. Dissociative States and Neural Complexity

    ERIC Educational Resources Information Center

    Bob, Petr; Svetlak, Miroslav

    2011-01-01

    Recent findings indicate that neural mechanisms of consciousness are related to integration of distributed neural assemblies. This neural integration is particularly vulnerable to past stressful experiences that can lead to disintegration and dissociation of consciousness. These findings suggest that dissociation could be described as a level of…

  11. Absolute total and partial dissociative cross sections of pyrimidine at electron and proton intermediate impact velocities

    SciTech Connect

    Wolff, Wania Luna, Hugo; Sigaud, Lucas; Montenegro, Eduardo C.; Tavares, Andre C.

    2014-02-14

    Absolute total non-dissociative and partial dissociative cross sections of pyrimidine were measured for electron impact energies ranging from 70 to 400 eV and for proton impact energies from 125 up to 2500 keV. MOs ionization induced by coulomb interaction were studied by measuring both ionization and partial dissociative cross sections through time of flight mass spectrometry and by obtaining the branching ratios for fragment formation via a model calculation based on the Born approximation. The partial yields and the absolute cross sections measured as a function of the energy combined with the model calculation proved to be a useful tool to determine the vacancy population of the valence MOs from which several sets of fragment ions are produced. It was also a key point to distinguish the dissociation regimes induced by both particles. A comparison with previous experimental results is also presented.

  12. Dissociative electron attachments to ethanol and acetaldehyde: A combined experimental and simulation study

    NASA Astrophysics Data System (ADS)

    Wang, Xu-Dong; Xuan, Chuan-Jin; Feng, Wen-Ling; Tian, Shan Xi

    2015-02-01

    Dissociation dynamics of the temporary negative ions of ethanol and acetaldehyde formed by the low-energy electron attachments is investigated by using the anion velocity map imaging technique and ab initio molecular dynamics simulations. The momentum images of the dominant fragments O-/OH- and CH3- are recorded, indicating the low kinetic energies of O-/OH- for ethanol while the low and high kinetic energy distributions of O- ions for acetaldehyde. The CH3- image for acetaldehyde also shows the low kinetic energy. With help of the dynamics simulations, the fragmentation processes are qualitatively clarified. A new cascade dissociation pathway to produce the slow O- ion via the dehydrogenated intermediate, CH3CHO- (acetaldehyde anion), is proposed for the dissociative electron attachment to ethanol. After the electron attachment to acetaldehyde molecule, the slow CH3- is produced quickly in the two-body dissociation with the internal energy redistributions in different aspects before bond cleavages.

  13. HCD Fragmentation of Glycated Peptides.

    PubMed

    Keilhauer, Eva C; Geyer, Philipp E; Mann, Matthias

    2016-08-01

    Protein glycation is a concentration-dependent nonenzymatic reaction of reducing sugars with amine groups of proteins to form early as well as advanced glycation (end-) products (AGEs). Glycation is a highly disease-relevant modification but is typically only studied on a few blood proteins. To complement our blood proteomics studies in diabetics, we here investigate protein glycation by higher energy collisional dissociation (HCD) fragmentation on Orbitrap mass spectrometers. We established parameters to most efficiently fragment and identify early glycation products on in vitro glycated model proteins. Retaining standard collision energies does not degrade performance if the most dominant neutral loss of H6O3 is included into the database search strategy. Glycation analysis of the entire HeLa proteome revealed an unexpected intracellular preponderance for arginine over lysine modification in early and advanced glycation (end-) products. Single-run analysis from 1 μL of undepleted and unenriched blood plasma identified 101 early glycation sites as well as numerous AGE sites on diverse plasma proteins. We conclude that HCD fragmentation is well-suited for analyzing glycated peptides and that the diabetic status of patients can be directly diagnosed from single-run plasma proteomics measurements. PMID:27425404

  14. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions.

    PubMed

    Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability

  15. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions

    NASA Astrophysics Data System (ADS)

    Bender, Jason D.; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G.; Schwartzentruber, Thomas; Candler, Graham V.

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 109 trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature Tv. The rate constant depends more strongly on T when Tv is low, and it depends more strongly on Tv when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = Tv and a nonequilibrium test set in which Tv < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as Tv decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v

  16. Does Electron Capture Dissociation Cleave Protein Disulfide Bonds?

    PubMed Central

    Ganisl, Barbara; Breuker, Kathrin

    2012-01-01

    Peptide and protein characterization by mass spectrometry (MS) relies on their dissociation in the gas phase into specific fragments whose mass values can be aligned as ‘mass ladders’ to provide sequence information and to localize possible posttranslational modifications. The most common dissociation method involves slow heating of even-electron (M+n H)n+ ions from electrospray ionization by energetic collisions with inert gas, and cleavage of amide backbone bonds. More recently, dissociation methods based on electron capture or transfer were found to provide far more extensive sequence coverage through unselective cleavage of backbone N–Cα bonds. As another important feature of electron capture dissociation (ECD) and electron transfer dissociation (ETD), their unique unimolecular radical ion chemistry generally preserves labile posttranslational modifications such as glycosylation and phosphorylation. Moreover, it was postulated that disulfide bond cleavage is preferred over backbone cleavage, and that capture of a single electron can break both a backbone and a disulfide bond, or even two disulfide bonds between two peptide chains. However, the proposal of preferential disulfide bond cleavage in ECD or ETD has recently been debated. The experimental data presented here reveal that the mechanism of protein disulfide bond cleavage is much more intricate than previously anticipated. PMID:24363980

  17. Electron-Impact Dissociation of Ozone Cations O3+

    SciTech Connect

    Deng, Shihu; Vane, C Randy; Bannister, Mark E; FogleJr, Michael R

    2010-01-01

    Absolute cross sections for electron-impact dissociation of O3+ ions yielding O+ and O2+ fragment ions have been measured using a crossed electron-ion beams method for energies from about 3 eV to 100 eV. While the O2+ channel dominates the dissociation cross section over the measured energy range, a strong enhancement is observed in the O+ channel at low energy.

  18. Coherent dissociation of relativistic {sup 9}C nuclei in nuclear track emulsion

    SciTech Connect

    Krivenkov, D. O.; Artemenkov, D. A.; Bradnova, V.; Kattabekov, R. R.; Kondratieva, N. V.; Mamatkulov, K. Z.; Malakhov, A. I.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Zarubin, P. I.; Zarubina, I. G.; Haiduc, M.; Kharlamov, S. P.; Orlova, G. I.; Peresadko, N. G.; Polukhina, N. G.; Moiseenko, A. A.; Sarkisyan, V. R.; Vokal, S.

    2010-04-30

    For the first time nuclear track emulsion is exposed to relativistic {sup 9}C nuclei. A systematic pattern of the distributions of charge combinations of fragments in the peripheral interactions of {sup 9}C nuclei in a nuclear track emulsion has been obtained. The main conclusion is that the contribution of the channel {sup 9}C->{sup 8}B+p and {sup 9}C->{sup 7}Be+2p is most important in events that do not involve the production of target-nucleus fragments or mesons (coherent dissociation). It can be concluded that in the peripheral {sup 9}C dissociation the picture hitherto obtained for {sup 8}B and {sup 7}Be with the addition of one or two protons, respectively, is reproduced. Three coherent dissociation events {sup 9}C->3{sup 3}He accompanied by neither target fragments of the nucleus target nor charged mesons are identified.

  19. Light-scattering investigation of the dissociation behavior of Lunatia heros and Littorina littorea hemocyanins

    SciTech Connect

    Herskovits, T.T.; Mazzella, L.J.; Villanueva, G.B.

    1985-07-16

    The subunit structure and dissociation of the hemocyanins of two marine snails, Lunatia heros and Littorina littorea, were investigated by light-scattering molecular weight methods. The hemocyanins of both species of snails are readily dissociated to fragments of one-tenth and one-twentieth of the parent proteins of close to 9 X 10(6) daltons by either increasing the pH or using dissociating reagents of the hydrophobic urea series or some of the Hofmeister salts. The two hemocyanins investigated possess beta-type subunits, which are known to be resistant to NaCl dissociation. The molecular weight profiles obtained with the various dissociating reagents were single inverted sigmoidal-shaped curves for both Lunatia and Littorina hemocyanins, suggesting overlapping transitions. The ultracentrifugation patterns and the species-distribution plots based on the urea dissociation data of Littorina hemocyanin suggest the presence of whole, half, and one-tenth molecular weight species in the dissociation transition region. Fitting of the urea dissociation data of Littorina hemocyanin obtained at both pH 5.7 and pH 8.0, assuming a sequential two-step dissociation scheme was found to be consistent with a model of a few hydrophobic binding sites at the contact areas of the half-molecules and a much larger apparent number of binding sites (Napp) at the side to side contacts of the one-tenth molecules.

  20. 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

  1. Dissociative absorption: An empirically unique, clinically relevant, dissociative factor.

    PubMed

    Soffer-Dudek, Nirit; Lassri, Dana; Soffer-Dudek, Nir; Shahar, Golan

    2015-11-01

    Research of dissociative absorption has raised two questions: (a) Is absorption a unique dissociative factor within a three-factor structure, or a part of one general dissociative factor? Even when three factors are found, the specificity of the absorption factor is questionable. (b) Is absorption implicated in psychopathology? Although commonly viewed as "non-clinical" dissociation, absorption was recently hypothesized to be specifically associated with obsessive-compulsive symptoms. To address these questions, we conducted exploratory and confirmatory factor analyses on 679 undergraduates. Analyses supported the three-factor model, and a "purified" absorption scale was extracted from the original inclusive absorption factor. The purified scale predicted several psychopathology scales. As hypothesized, absorption was a stronger predictor of obsessive-compulsive symptoms than of general psychopathology. In addition, absorption was the only dissociative scale that longitudinally predicted obsessive-compulsive symptoms. We conclude that absorption is a unique and clinically relevant dissociative tendency that is particularly meaningful to obsessive-compulsive symptoms. PMID:26241024

  2. Modeling of collision-induced infrared absorption spectra of H2-H2 pairs in the fundamental band at temperatures from 20 to 300 K. [Planetary atmospheres

    SciTech Connect

    Borysow, A. )

    1991-08-01

    The 20-300 K free-free rotovibrational collision-induced absorption (RV CIA) spectra of H2-H2 pairs are presently obtained by a numerical method which, in addition to closely matching known CIA spectra of H2-H2, can reproduce the results of the quantum-mechanical computations to within a few percent. Since the spectral lineshape parameters are derivable by these means from the lowest three quantum-mechanical spectral moments, these outer-planet atmosphere-pertinent model spectra may be computed on even small computers. 35 refs.

  3. Analysis of the collision-induced absorption spectra in the second overtone region of H2-H2 at 298 K

    NASA Astrophysics Data System (ADS)

    Abu-Kharma, M.

    2015-02-01

    The collision-induced absorption (CIA) spectra of the second overtone band of normal hydrogen in a pure gas were recorded for a number of gas densities up to 750 amagat (1 amagat = 44.614981 mol/m3) with a two meter stainless steel absorption cell at 298 K. The profile analyses of these spectra were carried out using the Birnbaum-Cohen line shape function for the quadrupolar vibrational transitions and the Levine-Birnbaum line shape function for the overlap transitions.

  4. Multiphoton dissociation of electrosprayed megadalton-sized DNA ions in a charge-detection mass spectrometer.

    PubMed

    Doussineau, Tristan; Paletto, Pierre; Dugourd, Philippe; Antoine, Rodolphe

    2015-01-01

    Charge detection mass spectrometry in combination with a linear electrostatic ion trap coupled to a continuous wavelength infrared CO2 laser has been used to study the multiphoton dissociation of DNA macromolecular ions. Samples, with masses ranging from 2.23 to 31.5 MDa, include single strand circular M13mp18, double strand circular M13mp18, and double strand linear LambdaPhage DNA fragments. Their activation energies for unimolecular dissociation were determined. Activation energy values slightly increase as a function of the molecular weight. The most important result is the difference between the fragmentations observed for hybridized double-strands and dimers of single strands. PMID:25348472

  5. Infrared Multiple-Photon Dissociation spectroscopy of group II metal complexes with salicylate

    SciTech Connect

    Ryan P. Dain; Gary Gresham; Gary S. Groenewold; Jeffrey D. Steill; Jos Oomens; Michael J. van Stipdonk

    2011-07-01

    Ion-trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations were used to characterize singly-charged, 1:1 complexes of Ca2+, Sr2+ and Ba2+ with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO2 and (b) formation of [MOH]+ where M=Ca2+, Sr2+ or Ba2+. DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cation is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 – 1650 cm-1, and the best correlation between theoretical and experimental spectra for the structure that features coordination of the metal ion by phenoxide and the carbonyl group of the carboxylic acid group, consistent with calculated energies for the respective species.

  6. Roles of acetone and diacetone alcohol in coordination and dissociation reactions of uranyl complexes.

    PubMed

    Rios, Daniel; Schoendorff, George; Van Stipdonk, Michael J; Gordon, Mark S; Windus, Theresa L; Gibson, John K; de Jong, Wibe A

    2012-12-01

    Combined collision-induced dissociation mass spectrometry experiments with DFT and MP2 calculations were employed to elucidate the molecular structures and energetics of dissociation reactions of uranyl species containing acetone and diacetone alcohol ligands. It is shown that solutions containing diacetone alcohol ligands can produce species with more than five oxygen atoms available for coordination. Calculations confirm that complexes with up to four diacetone alcohol ligands can be energetically stable but that the effective number of atoms coordinating with uranium in the equatorial plane does not exceed five. Water elimination reactions of diacetone alcohol ligands are shown to have two coordination-dependent reaction channels, through formation of mesityl oxide ligands or formation of alkoxide and protonated mesityl oxide species. The present results provide an explanation for the implausible observation of "[UO(2)(ACO)(6,7,8)](2+)" in and observed water-elimination reactions from purportedly uranyl-acetone complexes (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). PMID:23146003

  7. Recurrent Episodes of Dissociative Fugue

    PubMed Central

    Angothu, Hareesh; Pabbathi, Lokeswar Reddy

    2016-01-01

    Dissociative fugue is rare entity to encounter with possible differentials of epilepsy and malingering. It is one of the dissociative disorders rarely seen in clinical practice more often because of the short lasting nature of this condition. This might also be because of organized travel of the individuals during the episodes and return to their families after the recovery from episodes. This is a case description of a patient who has experienced total three episodes of dissociative fugue. The patient has presented during the third episode and two prior episodes were diagnosed as fugue episodes retrospectively based on the history. Planned travel in this case by the patient to a distant location was prevented because of early diagnosis and constant vigilance till the recovery. As in this case, it may be more likely that persons with Dissociative fugue may develop similar episodes if they encounter exceptional perceived stress. However, such conclusions may require follow-up studies. PMID:27114633

  8. Soft x-ray ionization induced fragmentation of glycine

    SciTech Connect

    Itälä, E.; Kooser, K.; Rachlew, E.; Huels, M. A.; Kukk, E.

    2014-06-21

    X-ray absorption commonly involves dissociative core ionization producing not only momentum correlated charged fragments but also low- and high-energy electrons capable of inducing damage in living tissue. This gives a natural motivation for studying the core ionization induced fragmentation processes in biologically important molecules such as amino acids. Here the fragmentation of amino acid glycine following carbon 1s core ionization has been studied. Using photoelectron-photoion-photoion coincidence technique, a detailed analysis on fragmentation of the sample molecule into pairs of momentum correlated cations has been carried out. The main characteristics of core ionization induced fragmentation of glycine were found to be the rupture of the C–C{sub α} bond and the presence of the CNH{sub 2}{sup +} fragment.

  9. Soft x-ray ionization induced fragmentation of glycine

    NASA Astrophysics Data System (ADS)

    Itälä, E.; Kooser, K.; Rachlew, E.; Huels, M. A.; Kukk, E.

    2014-06-01

    X-ray absorption commonly involves dissociative core ionization producing not only momentum correlated charged fragments but also low- and high-energy electrons capable of inducing damage in living tissue. This gives a natural motivation for studying the core ionization induced fragmentation processes in biologically important molecules such as amino acids. Here the fragmentation of amino acid glycine following carbon 1s core ionization has been studied. Using photoelectron-photoion-photoion coincidence technique, a detailed analysis on fragmentation of the sample molecule into pairs of momentum correlated cations has been carried out. The main characteristics of core ionization induced fragmentation of glycine were found to be the rupture of the C-Cα bond and the presence of the CNH_2^+ fragment.

  10. Dissociative Recombination of Molecular Ions for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Savin, Daniel W.; Novotný, O.; Becker, A.; Buhr, H.; Geppert, W.; Hamberg, M.; Krantz, C.; Kreckel, H.; Schwalm, D.; Spruck, K.; Stützel, J.; Wolf, A.; Yang, B.

    2013-06-01

    Dissociative recombination (DR) of molecular ions is a key chemical process in the cold interstellar medium (ISM). DR affects the composition, charge state, and energy balance of such environments. Astrochemical models of the ISM require reliable total DR cross sections as well as knowledge of the chemical composition and excitation states of the neutral DR products. Theory cannot reliably provide these data. We have systematically measured DR for many astrophysically relevant molecular ions utilizing the TSR storage ring at the Max-Planck-Institute for Nuclear Physics in Heidelberg, Germany. We used the merged ion-electron beam technique combined with an energy- and position-sensitive imaging detector and are able to study DR down to plasma temperatures of 10 K. The DR count rate is used to obtain absolute DR rate coefficient. Additionally we determine the masses of the DR products by measuring their kinetic energy. This allows us to assign particular DR fragmentation channels and to obtain their branching ratios. Moreover, the distribution of detected fragment distances provides information on the kinetic energy released in DR and thus also on the internal excitation of the DR products. All this information is particularly important for understanding DR of heteronuclear polyatomic ions. We will present DR results for several ions recently investigated at TSR. This work is supported in part by NASA and the NSF.

  11. "Diabodies": small bivalent and bispecific antibody fragments.

    PubMed Central

    Holliger, P; Prospero, T; Winter, G

    1993-01-01

    Bivalent and bispecific antibodies and their fragments have immense potential for practical application. Here we describe the design of small antibody fragments with two antigen-binding sites. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) on the same polypeptide chain (VH-VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. As indicated by a computer graphic model of the dimers, the two pairs of domains can pack together with the antigen-binding sites pointing in opposite directions. The dimeric antibody fragments, or "diabodies," can be designed for bivalent or bispecific interactions. Starting from the monoclonal antibodies NQ11.7.22 (NQ11) and D1.3 directed against the hapten phenyloxazolone and hen egg lysozyme, respectively, we built bivalent fragments (VHNQ11-VLNQ11)2 and (VHD1.3-VLD1.3)2 and bispecific fragments VHNQ11-VLD1.3 and VHD1.3-VLNQ11. The fragments were expressed by secretion from bacteria and shown to bind specifically to the hapten and/or antigen. Those with 5- and 15-residue linkers had similar binding affinities to the parent antibodies, but a fragment with the VH domain joined directly to the VL domain was found to have slower dissociation kinetics and an improved affinity for hapten. Diabodies offer a ready means of constructing small bivalent and bispecific antibody fragments in bacteria. Images Fig. 1 Fig. 3 PMID:8341653

  12. Collision-induced line-shape effects limiting the accuracy in Doppler-limited spectroscopy of H2

    NASA Astrophysics Data System (ADS)

    Wcisło, P.; Gordon, I. E.; Cheng, C.-F.; Hu, S.-M.; Ciuryło, R.

    2016-02-01

    Recent advances in theoretical calculations of H2 dissociation energies and ultra-accurate measurements of H2 transition frequencies give possibilities not only for testing QED and relativistic effects, but also for searching for physics beyond the standard model. In this paper we show that at the level of 10-4cm-1 the uncertainty of the Doppler-limited H2 line position determination is dominated by collisional line-shape effects. We question the paradigm that the unperturbed transition energy can be determined from linear extrapolation of the line shift to zero pressure.

  13. Global functioning and disability in dissociative disorders.

    PubMed

    Mueller-Pfeiffer, Christoph; Rufibach, Kaspar; Perron, Noelle; Wyss, Daniela; Kuenzler, Cornelia; Prezewowsky, Cornelia; Pitman, Roger K; Rufer, Michael

    2012-12-30

    Dissociative disorders are frequent comorbid conditions of other mental disorders. Yet, there is controversy about their clinical relevance, and little systematic research has been done on how they influence global functioning. Outpatients and day care patients (N=160) of several psychiatric units in Switzerland were assessed with the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV Axis I Disorders, Structured Clinical Interview for DSM-IV Dissociative Disorders, Global Assessment of Functioning Scale, and World Health Organization Disability Assessment Schedule-II. The association between subjects with a dissociative disorder (N=30) and functional impairment after accounting for non-dissociative axis I disorders was evaluated by linear regression models. We found a proportion of 18.8% dissociative disorders (dissociative amnesia=0%, dissociative fugue=0.6%, depersonalization disorder=4.4%, dissociative identity disorder=7.5%, dissociative disorder-not-otherwise-specified=6.3%) across treatment settings. Adjusted for other axis I disorders, subjects with a comorbid dissociative identity disorder or dissociative disorder-not-otherwise-specified had a median global assessment of functioning score that was 0.86 and 0.88 times, respectively, the score of subjects without a comorbid dissociative disorder. These findings support the hypothesis that complex dissociative disorders, i.e., dissociative identity disorder and dissociative disorder-not-otherwise-specified, contribute to functional impairment above and beyond the impact of co-existing non-dissociative axis I disorders, and that they qualify as "serious mental illness". PMID:22578820

  14. Ionization and Fragmentation of 5-Chlorouracil induced by 100 keV protons collisions

    SciTech Connect

    Cafarelli, Pierre; Champeaux, Jean-Philippe; Le Padellec, Arnaud; Moretto-Capelle, Patrick; Rabier, Julien; Sence, Martine; Carcabal, Pierre

    2008-12-08

    We present preliminary experimental results on the dissociation of singly and doubly ionized 5-Chlorouracil induced by collisions with proton of 100 keV energy. Multiple coincidence techniques are used to detect the ionic fragments from single dissociation events. This enables a thorough analysis of kinetic momentums of the charged and neutral species involved in the dissociation. In many cases, this leads to the establishment of the scenario the molecule undergoes after ionization as well as the determination of the nature of intermediate (undetected) species. In other cases, the dissociation scenario cannot be unambiguously identified and further analysis as well as theoretical support is needed.

  15. Dissociative experiences and dissociative minds: Exploring a nomological network of dissociative functioning.

    PubMed

    Schimmenti, Adriano

    2016-01-01

    In this study, the psychometric properties of the Dissociative Experiences Scale-II (DES-II) were tested in a sample of Italian adults, and a nomological network of dissociative functioning based on current psychodynamic research was examined. A total of 794 participants (55% females) ranging in age from 18 to 64 completed the DES-II and other measures of theory of mind, alexithymia, attachment style, and empathy. The Italian translation of the DES-II showed high internal consistency, adequate item-to-scale homogeneity, and good split-half reliability. A single-factor solution including the 8 items of pathological dissociation (DES-T) adequately fit the data. Participants who reported higher levels of dissociative experiences showed significantly lower scores on theory of mind and empathy than other participants. They also showed significantly higher scores on alexithymia, preoccupied attachment, and fearful attachment. Results of the study support the view that people who suffer from severe dissociative experiences may also have difficulties mentalizing and regulating affects and that they may feel uncomfortable in close relationships because they have a negative view of the self. This can inform clinical work with dissociative individuals, who could benefit from therapies that consider their potential problems with mentalization, empathy, affect regulation, and attachment. PMID:26507547

  16. Dissociative ionization of the 1-propanol dimer in a supersonic expansion under tunable synchrotron VUV radiation.

    PubMed

    Tao, Yanmin; Hu, Yongjun; Xiao, Weizhan; Guan, Jiwen; Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi

    2016-05-11

    Photoionization and dissociation of the 1-propanol dimer and subsequent fragmentations have been investigated by synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry and theoretical calculations. Besides the protonated monomer cation (C3H7OH)·H(+) (m/z = 61) and Cα-Cβ bond cleavage fragment CH2O·(C3H7OH)H(+) (m/z = 91), the measured mass spectrum at an incident photon energy of 13 eV suggests a new dissociation channel resulting in the formation of the (C3H7OH)·H(+)·(C2H5OH) (m/z = 107) fragment. The appearance energies of the fragments (C3H7OH)·H(+), CH2O·(C3H7OH)H(+) and (C3H7OH)·H(+)·(C2H5OH) are measured at 10.05 ± 0.05 eV, 9.48 ± 0.05 eV, and 12.8 ± 0.1 eV, respectively, by scanning photoionization efficiency (PIE) spectra. The 1-propanol ion fragments as a function of VUV photon energy were interpreted with the aid of theoretical calculations. In addition to O-H and Cα-Cβ bond cleavage, a new dissociation channel related to Cβ-Cγ bond cleavage opens. In this channel, molecular rearrangement (proton transfer and hydrogen transfer after surmounting an energy barrier) gives rise to the generated complex, which then dissociates to produce the mixed propanol/ethanol proton bound cation (C3H7OH)·H(+)·(C2H5OH). This new dissociation channel has not been reported in previous studies of ethanol and acetic acid dimers. The photoionization and dissociation processes of the 1-propanol dimer are described in the photon energy range of 9-15 eV. PMID:27141555

  17. Dissociative photodetachment dynamics of the iodide-aniline cluster

    NASA Astrophysics Data System (ADS)

    Bowen, M. Shane; Becucci, Maurizio; Continetti, Robert E.

    2006-10-01

    The photodetachment dynamics of the iodide-aniline cluster, I-(C6H5NH2), were investigated using photoelectron-photofragment coincidence spectroscopy at several photon energies between 3.60 and 4.82eV in concert with density functional theory calculations. Direct photodetachment from the solvated I- chromophore and a wavelength-independent autodetachment process were observed. Autodetachment is attributed to a charge-transfer-to-solvent reaction in which incipient continuum electrons photodetached from I- are temporarily captured by the nascent neutral iodine-aniline cluster configured in the anion geometry. Subsequent dissociation of the neutral cluster removes the stabilization, leading to autodetachment of the excess electron. The dependence of the dissociative photodetachment (DPD) and autodetachment dynamics on the final spin-orbit electronic state of the iodine fragment is characterized. The dissociation dynamics of the neutral fragments correlated with autodetached electrons were found to be identical to the DPD dynamics of the I atom product spin-orbit state closest to threshold at a given photon energy, lending support to the proposed sequential mechanism.

  18. Dissociative ionization of sodium molecules via repulsive Rydberg states

    NASA Astrophysics Data System (ADS)

    Chen, Hong

    In this thesis, an investigation of two color resonance multiphoton ionization (REMPI) and fragmentation processes in Na2 has been performed in combination with Linear Time-of-Flight Mass Spectrometry technique. The ionization and dissociative ionizations channels in the energy range up to 2500cm -1 above the dissociative ionization threshold into Na(3s)+Na ++e have been studied. After a mild supersonic expansion from the beam source, neutral sodium dimers in the ground state have been produced. Two tunable, pulsed lasers excite Na2 molecules via the intermediate A1S+u state to a single ro-vibrational level of the second intermediate 21pig state. Following absorption of a third photon, the total energy is above the dissociation limit into Na(3s) + Na+ + e. Typically, a small portion of atomic ions is produced under our experimental conditions. By varying the total available energy below and through the doubly excited states correlating with the Na(3p)+Na(4s) atom pair, there is no evidence that the doubly excited states positioned in the ionic continuum get involved. By calculation of the expected transition probabilities for all possible channels which can decay directly and indirectly into atomic ions, I find that direct dissociative ionization via 12S+u is impossible. The transition probabilities for dissociative ionization via the repulsive Rydberg states with principal quantum numbers n from 5˜12 converging toward the 12S+u state are three to four orders of magnitude larger than those for direct ionization into the continuum of the X2S+g ground state. These repulsive Rydberg states are much more likely to play a role in the photo-ionization through the intermediate 21Pg state. A semi-classical model which was originally developed for negative ion dissociative attachment (O'MAL'67) describes how dissociative ionization occurs along the repulsive Rydberg states. Its prediction concerning the ratio of atomic to molecular ion production as a function of initial

  19. Dissociative symptomatology in cancer patients

    PubMed Central

    Civilotti, Cristina; Castelli, Lorys; Binaschi, Luca; Cussino, Martina; Tesio, Valentina; Di Fini, Giulia; Veglia, Fabio; Torta, Riccardo

    2015-01-01

    Introduction: The utilization of the post-traumatic stress disorder (PTSD) diagnostic spectrum is currently being debated to categorize psychological adjustment in cancer patients. The aims of this study were to: (1) evaluate the presence of cancer-related traumatic dissociative symptomatology in a sample of cancer patients; (2) examine the correlation of cancer-related dissociation and sociodemographic and medical variables, anxiety, depression, and post-traumatic stress symptomatology; (3) investigate the predictors of cancer-related dissociation. Methods: Ninety-two mixed cancer patients (mean age: 58.94, ds = 10.13) recruited from two hospitals in northern Italy were administered a questionnaire on sociodemographic and medical characteristics, the Karnofsky Scale to measure the level of patient activity and medical care requirements, the Hospital Anxiety and Depression Scale (HADS) to evaluate the presence of anxiety and depression, the Impact of Event Scale Revised (IES-R) to assess the severity of intrusion, avoidance, and hypervigilance, and the Peritraumatic Dissociative Experiences Questionnaire (PDEQ) to quantify the traumatic dissociative symptomatology. Results: 31.5% of participants report a PDEQ score above the cutoff. The results indicated that dissociative symptomatology was positively correlated with HADS scores (HADS-Anxiety: r = 0.476, p < 0.001; HADS-Depression: r = 0.364, p < 0.001) and with IES-R scores (IES-R-Intrusion: r = 0.698, p < 0.001; IES-R-Avoidance: r = 0.619, p < 0.001; IES-R- Hypervigilance: r = 0.681, p < 0.001). A stepwise regression analysis was performed in order to find the predictors of cancer-related traumatic dissociative symptomatology. The results converged on a three predictor model revealing that IES-R-Intrusion, IES-R-Avoidance, and IES-R-Hyperarousal accounted for 53.9% of the explained variance. Conclusion: These findings allow us to hypothesize a specific psychological reaction which may be ascribed to the traumatic

  20. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes.

    PubMed

    Loo, Rachel R Ogorzalek; Loo, Joseph A

    2016-06-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ. PMID:27052739

  1. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes

    NASA Astrophysics Data System (ADS)

    Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2016-04-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes.

  2. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes

    NASA Astrophysics Data System (ADS)

    Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2016-06-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes.

  3. Action Spectroscopy and Dissociation Energy of Ammonia Trimer

    NASA Astrophysics Data System (ADS)

    Heid, Cornelia G.; Case, Amanda S.; Western, Colin M.; Crim, F. Fleming

    2012-06-01

    We have investigated the energy dependence for the vibrational predissociation of ammonia trimer, (NH_3)_3 → (NH_3)_2 + NH_3, using infrared-action spectroscopy. The action spectra come from detecting specific rovibrational states of the monomer fragment via (2+1) resonance enhanced multiphoton excitation (REMPI) while scanning the IR excitation laser over the NH stretch transitions of the trimer as well as the dimer. The relative intensities of the dimer and trimer features in the action spectra depend on the amount of energy available for breaking the hydrogen bonds in the clusters. For example, the action spectra of ammonia fragments with large amounts of internal energy (v_2=3) show almost no trimer contribution since there is not enough energy available to break two bonds in the cyclic trimer. The action spectra for fragments with low internal energies (v_2=1), on the other hand, exhibit a substantial trimer component as more energy remains available to dissociate the cluster. Using the threshold at which the trimer feature becomes apparent in our spectra as an upper limit (Edissmax = hνvib-Eint(NH_3)), we determine the dissociation energy of ammonia trimer to be in the range between 1700-1800 cm-1. This range agrees well with theoretical predictions.

  4. Diffraction dissociation at the LHC

    NASA Astrophysics Data System (ADS)

    Jenkovszky, László; Orava, Risto; Salii, Andrii

    2013-04-01

    We report on recent calculations of low missing mass single (SD) and double (DD) diffractive dissociation at LHC energies. The calculations are based on a dual-Regge model, dominated by a single Pomeron exchange. The diffractively excited states lie on the nucleon trajectory N*, appended by the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing mass dependence of the differential and integrated single-and double diffraction dissociation in the kinematical range of present and future LHC measurements are given.

  5. Diffraction dissociation at the LHC

    SciTech Connect

    Jenkovszky, Laszlo; Orava, Risto; Salii, Andrii

    2013-04-15

    We report on recent calculations of low missing mass single (SD) and double (DD) diffractive dissociation at LHC energies. The calculations are based on a dual-Regge model, dominated by a single Pomeron exchange. The diffractively excited states lie on the nucleon trajectory N*, appended by the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing mass dependence of the differential and integrated single-and double diffraction dissociation in the kinematical range of present and future LHC measurements are given.

  6. Dissociation of pleasure in psychopathology.

    PubMed

    Brown, S L

    1981-01-01

    This paper analyzes the development of the concept of dissociation from 19th century psychological theory through 20th century neurophysiological thought. Recent research is discussed, indicating that normal individuals show an "association" between emitted pleasurable behavior and self-perception of pleasurable activity, whereas depressives and schizophrenics show a lack of association, or "dissociation," between these measures. concomitantly, depressives show an abnormal degree of association between the experience and expression of negative affect. Such a discrepancy in systems of affect is considered as both an important pathological element in mental disorder and also as a valuable new research tool for studying etiology, differential diagnosis, and therapeutic efficacy in psychobiological illness. PMID:7005394

  7. Electron-nuclear energy sharing in above-threshold multiphoton dissociative ionization of H2.

    PubMed

    Wu, J; Kunitski, M; Pitzer, M; Trinter, F; Schmidt, L Ph H; Jahnke, T; Magrakvelidze, M; Madsen, C B; Madsen, L B; Thumm, U; Dörner, R

    2013-07-12

    We report experimental observation of the energy sharing between electron and nuclei in above-threshold multiphoton dissociative ionization of H2 by strong laser fields. The absorbed photon energy is shared between the ejected electron and nuclei in a correlated fashion, resulting in multiple diagonal lines in their joint energy spectrum governed by the energy conservation of all fragment particles. PMID:23889391

  8. 8Be and 9B nuclei in dissociation of relativistic 10B and 11C nuclei

    NASA Astrophysics Data System (ADS)

    Artemenkov, D. A.; Bradnova, V.; Firu, E.; Kornegrutsa, N. K.; Haiduc, M.; Mamatkulov, K. Z.; Kattabekov, R. R.; Neagu, A.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.

    2016-02-01

    Progress in the study of nuclear clustering in the relativistic 10B and 11C nuclei dissociation in nuclear track emulsion is presented. The contribution of the unbound 8Be and 9B nuclei to their structure is determined on the basis of measurements of the emission angles of relativistic He and H fragments.

  9. 8Be and 9B nuclei in dissociation of relativistic 10C and 11C nuclei

    NASA Astrophysics Data System (ADS)

    Artemenkov, D. A.; Bradnova, V.; Firu, E.; Kornegrutsa, N. K.; Haiduc, M.; Mamatkulov, K. Z.; Kattabekov, R. R.; Neagu, A.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.

    2016-05-01

    Progress in the study of nuclear clustering in the relativistic 10C and 11C nuclei dissociation in nuclear track emulsion is presented. The contribution of the unbound 8Be and 9B nuclei to their structure is determined on the basis of measurements of the emission angles of relativistic He and H fragments.

  10. Effect of the Basic Residue on the Energetics and Dynamics of Dissociation of Phosphopeptides

    SciTech Connect

    Laskin, Julia; Kong, Ricky; Song, Tao; Chu, Ivan K.

    2012-12-15

    Time- and collision-energy-resolved surface-induced dissociation (SID) of protonated peptides containing phosphoserine (s) was studied using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer configured for SID experiments. We examined fragmentation of three singly protonated peptides: GGGsGGG, KGGsGGG, and RGGsGGG. Fragmentation of GGGsGGG occurs under the mobile proton condition, while the ionizing proton is sequestered by the basic residue, resulting in the nonmobile proton condition in dissociation of the two basic peptides: KGGsGGG and RGGsGGG. RRKM modeling of the experimental data demonstrates that the energetics and dynamics of H3PO4 loss are different under mobile and nonmobile proton conditions. Specifically, fragmentation of GGGsGGG is characterized by a higher dissociation barrier, 1.68 eV, and higher activation entropy, 11 e.u. (e.u. = entropy unit), than fragmentation of the basic peptides. Similar threshold energies of 1.36 eV and 1.40 eV and activation entropies of -4.9 e.u. and 0.3 e.u. were obtained for KGGsGGG and RGGsGGG, respectively. We propose that the loss of H3PO4 from phosphoserine is a two-step process, in which the phosphate abstraction from the phosphorylated side chain is followed by dissociation of the ion-molecule complex.

  11. THERMOSPRAY IONIZATION WITH REPELLER-INDUCED COLLISIONALLY ACTIVATED DISSOCIATION OF DYES

    EPA Science Inventory

    Thermospray ionization with repeller-induced collisionally activated dissociation (repeller-CAD) has been used to acquire mass spectra of a series of dyes. hese were obtained by applying a voltage of 400 V on the wire repeller. he mass spectra contained arge number of fragment io...

  12. Hydrocarbon rate coefficients for proton and electron impact ionization, dissociation, and recombination in a hydrogen plasma.

    SciTech Connect

    Alman, D.A.; Brooks, J.N.; Ruzic, D.N.; Wang, Z.

    1999-07-21

    We estimate cross sections and rate coefficients for proton and electron impact ionization, dissociation, and recombination of neutral and ionized hydrocarbon molecules and fragments of the form C{sub x}H{sub y}{sup k}, x = 1-3, y = 1-6, k = 0,1 in a thermalized hydrogen-electron plasma.

  13. Using Dual-Task Methodology to Dissociate Automatic from Nonautomatic Processes Involved in Artificial Grammar Learning

    ERIC Educational Resources Information Center

    Hendricks, Michelle A.; Conway, Christopher M.; Kellogg, Ronald T.

    2013-01-01

    Previous studies have suggested that both automatic and intentional processes contribute to the learning of grammar and fragment knowledge in artificial grammar learning (AGL) tasks. To explore the relative contribution of automatic and intentional processes to knowledge gained in AGL, we utilized dual-task methodology to dissociate automatic and…

  14. Revealing Dissociative Electron Attachment Dynamics in Polyatomic Molecules Using Momentum Imaging Experiments and Electron Scattering Calculations

    NASA Astrophysics Data System (ADS)

    Belkacem, Ali; Slaughter, Daniel

    2015-05-01

    Understanding electron-driven chemical reactions is important for improving a variety of technological applications such as materials processing and the important role they play in the radiation damage in bulk matter. Furthermore, dissociative electron attachment often exhibits site-selective bond cleavage, which holds promise for prediction and precise control of electron-driven chemical reactions. Recent dynamical studies of these reactions have demonstrated that an understanding of anion dissociation dynamics beyond simple one-dimensional models is crucial in interpreting the measured fragment angular distributions. We combine ion fragment momentum imaging experiments with electron attachment entrance amplitude calculations to interrogate the non-Born-Oppenheimer dynamics of dissociative electron attachment in polyatomic molecules. We will report recent experimental developments in molecules of technological interest including methanol, methane and uracil. Work supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  15. Fragmentation of methyl chloride photoexcited near Cl (2p) by mass spectrometry

    NASA Astrophysics Data System (ADS)

    Thissen, Roland; Simon, Marc; Hubin-Franskin, M.-J.

    1994-11-01

    The evolution of the fragmentation pathways of the methylchloride around the Cl 2p edge has been studied by use of charge separation mass spectrometry. Some fragmentation patterns are discussed in the frame of rapid fragmentation of the neutral and dissociation pathways characteristic of singly or multiply charged species. The correlation of the evolution of the charge separation spectra with the initial excitation process is used to give a definitive attribution to the pre-edge features present in the absorption spectrum.

  16. 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.

  17. Selectable fragmentation warhead

    SciTech Connect

    Bryan, C.S.; Paisley, D.L.; Montoya, N.I.; Stahl, D.B.

    1992-12-31

    This report discusses a selectable fragmentation warhead which is capable of producing a predetermined number of fragments from a metal plate, and accelerating the fragments toward a target. A first explosive located adjacent to the plate is detonated at selected number of points by laser-driven slapper detonators. In one embodiment, a smoother-disk and a second explosive, located adjacent to the first explosive, serve to increase acceleration of the fragments toward a target. The ability to produce a selected number of fragments allows for effective destruction of a chosen target.

  18. Knowledge-based probabilistic representations of branching ratios in chemical networks: The case of dissociative recombinations

    SciTech Connect

    Plessis, Sylvain; Carrasco, Nathalie; Pernot, Pascal

    2010-10-07

    Experimental data about branching ratios for the products of dissociative recombination of polyatomic ions are presently the unique information source available to modelers of natural or laboratory chemical plasmas. Yet, because of limitations in the measurement techniques, data for many ions are incomplete. In particular, the repartition of hydrogen atoms among the fragments of hydrocarbons ions is often not available. A consequence is that proper implementation of dissociative recombination processes in chemical models is difficult, and many models ignore invaluable data. We propose a novel probabilistic approach based on Dirichlet-type distributions, enabling modelers to fully account for the available information. As an application, we consider the production rate of radicals through dissociative recombination in an ionospheric chemistry model of Titan, the largest moon of Saturn. We show how the complete scheme of dissociative recombination products derived with our method dramatically affects these rates in comparison with the simplistic H-loss mechanism implemented by default in all recent models.

  19. [Gender differences in dissociative disorders].

    PubMed

    Spitzer, C; Freyberger, H J

    2008-01-01

    The relationship between mental illness, on the one hand, and sex and gender, on the other hand, has received interest since the beginning of medicine in antique times. A prototypical example of a seemingly woman-specific disease is hysteria. The term itself, which is derived from the Greek word for womb, denotes a psychosexual dimension comprising the current attitude towards sexuality and the dominating gender relationship. In addition, the colourful history of hysteria indicates that illness is not exclusively determined by biological factors, but also significantly by socio-cultural influences, for example in the treatment of hysterical women. Even nowadays, there is a wide-spread belief that dissociative symptoms and disorders, which have succeeded hysteria in current classification systems, are predominantly seen in women. However, empirical studies in the general population and in different clinical samples using sound instruments have indicated that dissociative symptoms do not differ between the genders. The seemingly dominance of dissociative disorders in women may also depend on the socio-cultural context, because men with dissociative disorders usually do not enter the general health system, but rather the legal system, i.e. they can be found in jail or forensic institutions. PMID:18185968

  20. Roles of deformation and orientation in heavy-ion collisions induced by light deformed nuclei at intermediate energy

    SciTech Connect

    Cao, X. G.; Zhang, G. Q.; Cai, X. Z.; Ma, Y. G.; Guo, W.; Chen, J. G.; Tian, W. D.; Fang, D. Q.; Wang, H. W.

    2010-06-15

    The reaction dynamics of axisymmetric deformed {sup 24}Mg+{sup 24}Mg collisions has been investigated systematically by an isospin-dependent quantum molecular dynamics model. It is found that different deformations and orientations result in apparently different properties of reaction dynamics. We reveal that some observables such as nuclear stopping power (R), multiplicity of fragments, and elliptic flow are very sensitive to the initial deformations and orientations. There exists an eccentricity scaling of elliptic flow in central body-body collisions with different deformations. In addition, the tip-tip and body-body configurations turn out to be two extreme cases in central reaction dynamical process.

  1. Collision-induced infrared spectra of H2-He pairs at temperatures from 18 to 7000 K. II. Overtone and hot bands

    SciTech Connect

    Borysow, A.; Frommhold, L.; Texas Univ., Austin )

    1989-06-01

    The three lowest spectral moments of the collision induced absorption (CIA) spectra of H2-He pairs have been computed from first principles for temperatures T from 18 to 7000 K for a number of hydrogen overtone and hot bands involving vibrational quantum numbers nu = 0, 1, 2, 3 yields nu-prime = 0, 1, 2, 3. The data are given in a form suitable for the computation of CIA spectra of H2-He as function of frequency and temperature, using simple computer codes and model line shapes. The work is of interest for the spectroscopy of the atmospheres of the outer planets and of stars that contain neutral molecular hydrogen and helium (late stars, white dwarfs, and Population II stars) in the infrared and visible region of the spectrum. 13 refs.

  2. Collision-Induced Absorption by H2 Pairs in the Second Overtone Band at 298 and 77.5 K: Comparison between Experimental and Theoretical Results

    NASA Technical Reports Server (NTRS)

    Brodbeck, C.; Bouanich, J.-P.; van-Thanh, Nguyen; Fu, Y.; Borysow, A.

    1999-01-01

    The collision-induced spectra of hydrogen in the region of the second overtone at 0.8 microns have been recorded at temperatures of 298 and 77.5 K and for gas densities ranging from 100 to 800 amagats. The spectral profile defined by the absorption coefficient per squared density varies significantly with the density, so that the binary absorption coefficient has been determined by extrapolations to zero density of the measured profiles. Our extrapolated measurements and our recent ab initio quantum calculation are in relatively good agreement with one another. Taking into account the very weak absorption of the second overtone band, the agreement is, however, not as good as it has become (our) standard for strong bands.

  3. Collision-induced Raman scattering by rare-gas atoms: The isotropic spectrum of Ne–Ne and its mean polarizability

    SciTech Connect

    Rachet, Florent; Chrysos, Michael; Dixneuf, Sophie

    2015-05-07

    We report the room-temperature isotropic collision-induced light scattering spectrum of Ne–Ne over a wide interval of Raman shifts, and we compare it with the only available experimental spectrum for that system as well as with spectra calculated quantum-mechanically with the employ of advanced ab initio-computed data for the incremental mean polarizability. The spectral range previously limited to 170 cm{sup −1} is now extended to 485 cm{sup −1} allowing us to successfully solve the inverse-scattering problem toward an analytic model for the mean polarizability that perfectly matches our measurements. We also report the depolarization ratio of the scattering process, lingering over the usefulness of this property for more stringent checks between the various polarizability models.

  4. Photofragment translational spectroscopy of three body dissociations and free radicals

    SciTech Connect

    North, S.W.

    1995-04-01

    This dissertation describes several three-body dissociations and the photodissociation of methyl radicals studied using photofragment translational spectroscopy. The first chapter provides an introduction to three body dissociation, examines current experimental methodology, and includes a discussion on the treatment of photofragment translational spectroscopy data arising from three-body fragmentation. The ultraviolet photodissociation of azomethane into two methyl radicals and nitrogen is discussed in chapter 2. Chapter 3 describes the photodissociation of acetone at 248 nm and 193 nm. At 248 nm the translational energy release from the initial C-C bond cleavage matches the exit barrier height and a comparison with results at 266 nm suggests that is invariant to the available energy. A fraction of the nascent CH{sub 3}CO radicals spontaneously dissociate following rotational averaging. The for the second C-C bond cleavage also matches the exit barrier height. At 193 nm the experimental data can be successfully fit assuming that the dynamics are analogous to those at 248 nm. A simplified model of energy partitioning which adequately describes the experimental results is discussed. Experiments on acetyl halides provide additional evidence to support the proposed acetone dissociation mechanism. A value of 17.0{+-}1.0 kcal/mole for the barrier height, CH{sub 3}CO decomposition has been determined. The photodissociation of methyl radical at 193 nm and 212.8 nm is discussed in the chapter 5. The formation of CH{sub 2} ({sup 1}A{sub l}) and H ({sup 2}S) was the only single photon dissociation pathway observed at both wavelengths.

  5. Hard-X-Ray-Induced Multistep Ultrafast Dissociation

    NASA Astrophysics Data System (ADS)

    Travnikova, Oksana; Marchenko, Tatiana; Goldsztejn, Gildas; Jänkälä, Kari; Sisourat, Nicolas; Carniato, Stéphane; Guillemin, Renaud; Journel, Loïc; Céolin, Denis; Püttner, Ralph; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Simon, Marc

    2016-05-01

    Creation of deep core holes with very short (τ ≤1 fs ) lifetimes triggers a chain of relaxation events leading to extensive nuclear dynamics on a few-femtosecond time scale. Here we demonstrate a general multistep ultrafast dissociation on an example of HCl following Cl 1 s →σ* excitation. Intermediate states with one or multiple holes in the shallower core electron shells are generated in the course of the decay cascades. The repulsive character and large gradients of the potential energy surfaces of these intermediates enable ultrafast fragmentation after the absorption of a hard x-ray photon.

  6. Hard-X-Ray-Induced Multistep Ultrafast Dissociation.

    PubMed

    Travnikova, Oksana; Marchenko, Tatiana; Goldsztejn, Gildas; Jänkälä, Kari; Sisourat, Nicolas; Carniato, Stéphane; Guillemin, Renaud; Journel, Loïc; Céolin, Denis; Püttner, Ralph; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Simon, Marc

    2016-05-27

    Creation of deep core holes with very short (τ≤1  fs) lifetimes triggers a chain of relaxation events leading to extensive nuclear dynamics on a few-femtosecond time scale. Here we demonstrate a general multistep ultrafast dissociation on an example of HCl following Cl 1s→σ^{*} excitation. Intermediate states with one or multiple holes in the shallower core electron shells are generated in the course of the decay cascades. The repulsive character and large gradients of the potential energy surfaces of these intermediates enable ultrafast fragmentation after the absorption of a hard x-ray photon. PMID:27284654

  7. Dissociative Recombination of Molecular Ions for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Novotny, Oldrich; Becker, A.; Buhr, H.; Fleischmann, Andreas; Gamer, Lisa; Geppert, W.; Krantz, C.; Kreckel, H.; Schwalm, D.; Spruck, K.; Wolf, A.; Savin, Daniel Wolf

    2014-06-01

    Dissociative recombination (DR) of molecular ions is a key chemical process in the cold interstellar medium (ISM). DR affects the composition, charge state, and energy balance of such environments. Astrochemical models of the ISM require reliable total DR cross sections as well as knowledge of the chemical composition of the neutral DR products. We have systematically measured DR for many astrophysically relevant molecular ions utilizing the TSR storage ring at the Max-Planck-Institute for Nuclear Physics (MPIK) in Heidelberg, Germany. We used the merged ion-electron beam technique combined with an energy- and position-sensitive imaging detector and are able to study DR down to plasma temperatures as low as 10 K. The DR count rate is used to obtain an absolute merged beams DR rate coefficient from which we can derive a thermal rate coefficient needed for plasma models. Additionally we determine the masses of the DR products by measuring their kinetic energy in the laboratory reference frame. This allows us to assign particular DR fragmentation channels and to obtain their branching ratios. All this information is particularly important for understanding DR of heteronuclear polyatomic ions. We will present DR results for several ions recently investigated at TSR. A new Cryogenic Storage Ring (CSR) is currently being commissioned at MPIK. With the chamber cooled down to ~10 K and a base pressure better than 10-13 mbar, this setup will allow internal cooling of the stored ions down to their rotational ground states, thus opening a new era in DR experiments. New technological challenges arise due to the ultracold, ultra-high vacuum environment of the CSR and thus the detection techniques used at TSR cannot be easily transferred to CSR. We will present new approaches for DR fragment detection in cryogenic environment. This work is supported in part by NASA and the NSF.

  8. Trait dissociation and commission errors in memory reports of emotional events.

    PubMed

    Merckelbach, Harald; Zeles, Gwen; Van Bergen, Saskia; Giesbrecht, Timo

    2007-01-01

    In 2 studies we examined whether trait dissociation is related to spontaneous commission errors (reports of events that did not occur) in free recall of emotional events. We also explored whether the functional locus of the dissociation-commission link is related to repeated retrieval or shallow encoding. In Experiment 1 participants were exposed to a staged incident and were repeatedly asked to add more information to their written accounts of the event. Dissociation levels were related to commission errors, indicating that people who report many dissociative experiences tend to make more commission errors. However, it was not the case that the overall increase in commission errors over successive retrieval attempts was typical for high dissociative participants. In Experiment 2 participants saw a video fragment of a severe car accident. During the video, half the participants performed a dual task, and the other half did not. Participants performing the dual task made more commission errors than controls, but this effect was not more pronounced in those with high trait dissociation scores. These studies show that there is a link between dissociation and spontaneous commission errors in memory reports of emotional events, but the functional locus of this link remains unclear. PMID:17444357

  9. Collision-Induced Absorption Spectra of Binary Mixtures of Molecular Hydrogen with Molecular Deuterium and Argon and of Pure Hydrogen, D

    NASA Astrophysics Data System (ADS)

    Hsieh, Chang-Tsang William

    In the present research project a systematic study of the collision-induced infrared absorption (CIA) spectra of the binary mixtures of H_2 - D_2 in the region of the double fundamental vibrations of H_2 and D_2, and H_2 - Ar in the fundamental band of H_2, and of pure HD in its fundamental and first overtone regions was undertaken. The experiments were carried out with a 2.0 m high-pressure low-temperature transmission-type absorption cell at 77, 201 and 296 K at total gas densities up to 550 amagat. Infrared prism and grating spectrometers equipped with a microprocessor -controlled stepping motor were used to record the spectra. All the experimental results obtained represent first-time observations in collision-induced absorption. Collision-induced infrared absorption spectra of the double transitions of H_2(v=1>=ts 0) and D_2(v=1>=ts 0) have been observed at 77 and 201 K in the spectral region 7000-8000 cm^{-1} for total gas densities up to 550 amagat with a partial gas density ratio of 1:1 of H_2 and D_2. The observed spectra are interpreted in terms of the transitions, Q_1(J) of H_2+Q_1(J) of D _2, Q_1(J) of H_2+S _1(J) of D_2, S_1(J) of H_2 + Q_1(J) of D_2, and S_1(J) of H_2 + S_1(J) of D_2 for J = 0 and 1 for H _2 and J = 0, 1, and 2 for D_2. Analysis of the experimental absorption profiles was carried out using appropriate lineshape functions. The absorption coefficients, lineshape parameters, etc., are obtained from the analysis. Collision-induced enhancement absorption spectra of the fundamental band of H_2 in H_2 - Ar mixtures were recorded at room temperature for a base density of 72 amagat of H_2 for several partial densities of Ar up to 440 amagat. Hexadecapole-induced U transitions, U_1(1), U_1(2), Q_1(0)+U _0(1), and Q_1(1) + U_0(1) have been identified in the spectral region 5400 -6200 cm^{-1}. A "cage" model has been proposed to account for the double transitions of H_2 - H_2 in the H _2 - Ar enhancement spectra. From the analysis of the

  10. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Riley, Nicholas M.; Mullen, Christopher; Weisbrod, Chad R.; Sharma, Seema; Senko, Michael W.; Zabrouskov, Vlad; Westphall, Michael S.; Syka, John E. P.; Coon, Joshua J.

    2016-03-01

    Electron transfer dissociation (ETD) is a valuable tool for protein sequence analysis, especially for the fragmentation of intact proteins. However, low product ion signal-to-noise often requires some degree of signal averaging to achieve high quality MS/MS spectra of intact proteins. Here we describe a new implementation of ETD on the newest generation of quadrupole-Orbitrap-linear ion trap Tribrid, the Orbitrap Fusion Lumos, for improved product ion signal-to-noise via ETD reactions on larger precursor populations. In this new high precursor capacity ETD implementation, precursor cations are accumulated in the center section of the high pressure cell in the dual pressure linear ion trap prior to charge-sign independent trapping, rather than precursor ion sequestration in only the back section as is done for standard ETD. This new scheme increases the charge capacity of the precursor accumulation event, enabling storage of approximately 3-fold more precursor charges. High capacity ETD boosts the number of matching fragments identified in a single MS/MS event, reducing the need for spectral averaging. These improvements in intra-scan dynamic range via reaction of larger precursor populations, which have been previously demonstrated through custom modified hardware, are now available on a commercial platform, offering considerable benefits for intact protein analysis and top down proteomics. In this work, we characterize the advantages of high precursor capacity ETD through studies with myoglobin and carbonic anhydrase.

  11. Universality of fragment shapes.

    PubMed

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  12. Universality of fragment shapes

    PubMed Central

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  13. Universality of fragment shapes

    NASA Astrophysics Data System (ADS)

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-03-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism.

  14. 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.

  15. Two-temperature models for nitrogen dissociation

    NASA Astrophysics Data System (ADS)

    da Silva, M. Lino; Guerra, V.; Loureiro, J.

    2007-12-01

    Accurate sets of nitrogen state-resolved dissociation rates have been reduced to two-temperature (translational T and vibrational Tv) dissociation rates. The analysis of such two-temperature dissociation rates shows evidence of two different dissociation behaviors. For Tv < 0.3 T dissociation proceeds predominantly from the lower-lying vibrational levels, whereas for Tv > 0.3 T dissociation proceeds predominantly form the near-dissociative vibrational levels, with an abrupt change of behavior at Tv = 0.3 T. These two-temperature sets have then been utilized as a benchmark for the comparison against popular multitemperature dissociation models (Park, Hansen, Marrone-Treanor, Hammerling, Losev-Shatalov, Gordiets, Kuznetsov, and Macheret-Fridman). This has allowed verifying the accuracy of each theoretical model, and additionally proposing adequate values for any semi-empirical parameters present in the different theories. The Macheret-Fridman model, who acknowledges the existence of the two aforementioned dissociation regimes, has been found to provide significantly more accurate results than the other models. Although these different theoretical approaches have been tested and validated solely for nitrogen dissociation processes, it is reasonable to expect that the general conclusions of this work, regarding the adequacy of the different dissociation models, could be extended to the description of arbitrary diatomic dissociation processes.

  16. Study of the dissociation of molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Vessot, R. F. C.

    1981-01-01

    Dissociators used to obtain an RF plasma discharge for hydrogen masers and the test system used for operation and evaluation of the dissociators are described. A compact sorption cartridge using a graphite matrix is tested as part of a hydrogen scavenging system. Testing of a vacuum enclosed hydrogen dissociator suitable for long term operation in space is described.

  17. Fragmentation properties of metals

    SciTech Connect

    Grady, D.E.; Kipp, M.E.

    1996-06-01

    In the present study we are developing an experimental fracture material property test method specific to dynamic fragmentation. Spherical test samples of the metals of interest are subjected to controlled impulsive stress loads by acceleration to high velocities with a light-gas launcher facility and subsequent normal impact on thin plates. Motion, deformation and fragmentation of the test samples are diagnosed with multiple flash radiography methods. The impact plate materials are selected to be transparent to the x-ray method so that only test metal material is imaged. Through a systematic series of such tests, both strain-to-failure and fragmentation resistance properties are determined through this experimental method. Fragmentation property data for several steels, copper, aluminum, tantalum and titanium have been obtained to date. Aspects of the dynamic data have been analyzed with computational methods to achieve a better understanding of the processes leading to failure and fragmentation, and to test an existing computational fragmentation model.

  18. Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC4Ym) Monitored with Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Cao, Yanwei; Qin, Yujiao; Bruist, Michael; Gao, Shang; Wang, Bing; Wang, Huixin; Guo, Xinhua

    2015-06-01

    Formation and dissociation of the interstrand i-motifs by DNA with the sequence d(XnC4Ym) (X and Y represent thymine, adenine, or guanine, and n, m range from 0 to 2) are studied with electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and UV spectrophotometry. The ion complexes detected in the gas phase and the melting temperatures (Tm) obtained in solution show that a non-C base residue located at 5' end favors formation of the four-stranded structures, with T > A > G for imparting stability. Comparatively, no rule is found when a non-C base is located at the 3' end. Detection of penta- and hexa-stranded ions indicates the formation of i-motifs with more than four strands. In addition, the i-motifs seen in our mass spectra are accompanied by single-, double-, and triple-stranded ions, and the trimeric ions were always less abundant during annealing and heat-induced dissociation process of the DNA strands in solution (pH = 4.5). This provides a direct evidence of a strand-by-strand formation and dissociation pathway of the interstrand i-motif and formation of the triple strands is the rate-limiting step. In contrast, the trimeric ions are abundant when the tetramolecular ions are subjected to collision-induced dissociation (CID) in the gas phase, suggesting different dissociation behaviors of the interstrand i-motif in the gas phase and in solution. Furthermore, hysteretic UV absorption melting and cooling curves reveal an irreversible dissociation and association kinetic process of the interstrand i-motif in solution.

  19. Overview of nuclear fragmentation models and needs

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.; Cucinotta, F. A.; Wilson, J. W. (Principal Investigator)

    1996-01-01

    It has been known for some time that adequate assessment of spacecraft shield requirements and concomitant estimates of astronauts radiation exposures from galactic cosmic radiation requires accurate, quantitative methods for characterizing these radiation fields as they pass through thick absorbers. The main nuclear interaction processes involved are (1) nuclear elastic and inelastic collisions, and (2) nuclear breakup (fragmentation) and electromagnetic dissociation (EMD). Nuclear fragmentation and EMD are important because they alter the elemental and isotopic composition of the transported radiation fields. At present, there is no suitably accurate theory for predicting nuclear fragmentation cross sections for all collision pairs and energies of interest in space radiation protection. Typical cross-section differences between theory and experiment range from about 25 percent to a factor of two. The resulting errors in transported flux, for high linear energy transfer (LET) particles, are comparble to these cross-section errors. In this overview, theoretical models of heavy ion fragmentation currently used to generate input data bases for cosmic-ray transport and shielding codes are reviewed. Their shortcomings are discussed. Further actions needed to improve their accuracy and generality are presented.

  20. 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.}

  1. 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.

  2. Coulomb dissociation of N,2120

    NASA Astrophysics Data System (ADS)

    Röder, Marko; Adachi, Tatsuya; Aksyutina, Yulia; Alcantara, Juan; Altstadt, Sebastian; Alvarez-Pol, Hector; Ashwood, Nicholas; Atar, Leyla; Aumann, Thomas; Avdeichikov, Vladimir; Barr, M.; Beceiro, Saul; Bemmerer, Daniel; Benlliure, Jose; Bertulani, Carlos; Boretzky, Konstanze; Borge, Maria J. G.; Burgunder, G.; Caamaño, Manuel; Caesar, Christoph; Casarejos, Enrique; Catford, Wilton; Cederkäll, Joakim; Chakraborty, S.; Chartier, Marielle; Chulkov, Leonid; Cortina-Gil, Dolores; Crespo, Raquel; Datta Pramanik, Ushasi; Diaz-Fernandez, Paloma; Dillmann, Iris; Elekes, Zoltan; Enders, Joachim; Ershova, Olga; Estrade, A.; Farinon, F.; Fraile, Luis M.; Freer, Martin; Freudenberger, M.; Fynbo, Hans; Galaviz, Daniel; Geissel, Hans; Gernhäuser, Roman; Göbel, Kathrin; Golubev, Pavel; Gonzalez Diaz, D.; Hagdahl, Julius; Heftrich, Tanja; Heil, Michael; Heine, Marcel; Heinz, Andreas; Henriques, Ana; Holl, Matthias; Ickert, G.; Ignatov, Alexander; Jakobsson, Bo; Johansson, Hâkan; Jonson, Björn; Kalantar-Nayestanaki, Nasser; Kanungo, Rituparna; Kelic-Heil, Aleksandra; Knöbel, Ronja; Kröll, Thorsten; Krücken, Reiner; Kurcewicz, J.; Kurz, Nikolaus; Labiche, Marc; Langer, Christoph; Le Bleis, Tudi; Lemmon, Roy; Lepyoshkina, Olga; Lindberg, Simon; Machado, Jorge; Marganiec, Justyna; Mostazo Caro, Magdalena; Movsesyan, Alina; Najafi, Mohammad Ali; Nilsson, Thomas; Nociforo, Chiara; Panin, Valerii; Paschalis, Stefanos; Perea, Angel; Petri, Marina; Pietri, S.; Plag, Ralf; Prochazka, A.; Rahaman, Md. Anisur; Rastrepina, Ganna; Reifarth, Rene; Ribeiro, Guillermo; Ricciardi, M. Valentina; Rigollet, Catherine; Riisager, Karsten; Rossi, Dominic; Sanchez del Rio Saez, Jose; Savran, Deniz; Scheit, Heiko; Simon, Haik; Sorlin, Olivier; Stoica, V.; Streicher, Branislav; Taylor, Jon; Tengblad, Olof; Terashima, Satoru; Thies, Ronja; Togano, Yasuhiro; Uberseder, Ethan; Van de Walle, J.; Velho, Paulo; Volkov, Vasily; Wagner, Andreas; Wamers, Felix; Weick, Helmut; Weigand, Mario; Wheldon, Carl; Wilson, G.; Wimmer, Christine; Winfield, J. S.; Woods, Philip; Yakorev, Dmitry; Zhukov, Mikhail; Zilges, Andreas; Zuber, Kai; R3B Collaboration

    2016-06-01

    Neutron-rich light nuclei and their reactions play an important role in the creation of chemical elements. Here, data from a Coulomb dissociation experiment on N,2120 are reported. Relativistic N,2120 ions impinged on a lead target and the Coulomb dissociation cross section was determined in a kinematically complete experiment. Using the detailed balance theorem, the 19N (n ,γ )20N and 20N (n ,γ ) 21N excitation functions and thermonuclear reaction rates have been determined. The 19 (n ,γ )20N rate is up to a factor of 5 higher at T <1 GK with respect to previous theoretical calculations, leading to a 10% decrease in the predicted fluorine abundance.

  3. [Prison psychosis and dissociative disorders].

    PubMed

    al Chaabani, S; Bataille, M

    2002-12-01

    Through a few clinical case histories stemming from their daily activities at the psychiatric section of the Lantin Prison, the authors propose to revisit the classic concept of Prison psychosis. They broaden its limits to include other psychotic and dissociative phenomena common to the jail population. This requires a strict differential diagnosis, allowing to eliminate some similar pathologies; nevertheless, some difficulties and imperfections persist. The development of the psychosis, the input from the jail architecture and milieu, the predisposing as well as facilitating factors linked to the personality of the inmate, and triggering phenomena are discussed. Finally, the comorbidity between these psychotic/dissociative phenomena and the borderline & histrionic personality disorders is envisaged. PMID:12632838

  4. [Dis-social personality disorder].

    PubMed

    Habermeyer, E; Herpertz, S C

    2006-05-01

    Deviant behavior is gaining in clinical importance if it is founded on stable, characteristic, and enduring patterns of psychopathologically relevant personality traits which have their onset in childhood or adolescence. The classification of these traits shows variations, so that a distinction between the ICD-10 diagnosis of dis-social personality disorder, DSM-IV diagnosis of antisocial personality disorder, and the concept "psychopathy" is necessary. Our knowledge about the biological basis of antisocial behavior includes neurophysiologic, psychophysiologic, and genetic findings. Also relevant are results of neurotransmitter studies and structural resp. functional neuroimaging findings. Psychosocial risk factors include parental deficits, rejection, disregard, unstable relations, and abuse. Efficient psychotherapeutic treatment is cognitive-behavioral. Pharmacologic treatment is largely "off-label". The diagnosis of antisocial and dis-social personality disorders allows no conclusions on criminal responsibility. In addition to psychiatric diagnostics, considerations on the severity of the disorder and its effects on the ability to inhibit actions are necessary. PMID:16609871

  5. Fast Nitrogen Atoms from Dissociative Excitation of N2 by Electron Impact

    NASA Technical Reports Server (NTRS)

    Ajello, Joseph M.; Ciocca, Marco

    1996-01-01

    The Doppler profiles of one of the fine structure lines of the N I (1200 A) g (sup 4)S(sup 0)-(sup 4)P multiplet and of the N II (1085 A) g (sup 3)p(sup O)-(sup 3)D multiplet have been measured. Excitation of the multiplets is produced by electron impact dissociative excitation of N2. The experimental line profiles are evaluated by fast Fourier transform (FFT) techniques and analysis of the profiles yields the kinetic energy distribution of fragments. The full width at half maximum (FWHM) of N I (1200 A) increases from 27+/-6 mA at 30 eV to 37+/-4 mA at 100 eV as the emission cross section of the dissociative ionization excitation process becomes more important relative to the dissociative excitation process. The FWHM of the N II (1085 A) line is 36+/-4 mA at 100 eV. For each multiplet the kinetic energy distribution function of each of the two fragment N atoms (ions) is much broader than thermal with a mean energy above 1.0 eV. The dissociation process with the largest cross section is predissociation and predominantly produces N atoms with kinetic energy distributions having mean energies above 0.5 eV. Dissociative processes can lead to a substantial escape flux of N I atoms from the satellites, Titan and Triton of the outer planets.

  6. Detection method for dissociation of multiple-charged ions

    DOEpatents

    Smith, Richard D.; Udseth, Harold R.; Rockwood, Alan L.

    1991-01-01

    Dissociations of multiple-charged ions are detected and analyzed by charge-separation tandem mass spectrometry. Analyte molecules are ionized to form multiple-charged parent ions. A particular charge parent ion state is selected in a first-stage mass spectrometer and its mass-to-charge ratio (M/Z) is detected to determine its mass and charge. The selected parent ions are then dissociated, each into a plurality of fragments including a set of daughter ions each having a mass of at least one molecular weight and a charge of at least one. Sets of daughter ions resulting from the dissociation of one parent ion (sibling ions) vary in number but typically include two to four ions, one or more multiply-charged. A second stage mass spectrometer detects mass-to-charge ratio (m/z) of the daughter ions and a temporal or temporo-spatial relationship among them. This relationship is used to correlate the daughter ions to determine which (m/z) ratios belong to a set of sibling ions. Values of mass and charge of each of the sibling ions are determined simultaneously from their respective (m/z) ratios such that the sibling ion charges are integers and sum to the parent ion charge.

  7. Precursor anion states in dissociative electron attachment to chlorophenol isomers

    NASA Astrophysics Data System (ADS)

    Kossoski, F.; Varella, M. T. do N.

    2016-07-01

    We report a theoretical study on low-energy (<10 eV) elastic electron scattering from chlorophenol isomers, namely, para-chlorophenol (pCP), meta-chlorophenol (mCP), and ortho-chlorophenol (oCP). The calculations were performed with the Schwinger multichannel method with pseudopotentials, and analysis of the computed integral cross sections and virtual orbitals revealed one σCCl ∗ , one σOH ∗ , and three π∗ shape resonances. We show that electron capture into the two lower lying π∗ orbitals initiates dissociative processes that lead to the elimination of the chloride ion, accounting for the two overlapping peaks where this fragment was observed. Despite the relatively small differences on the energetics of the π∗ resonances, a major isomeric effect was found on their corresponding autodetachment lifetimes, which accounts for the observed increasing cross sections in the progression pCP < mCP < oCP. In particular, dissociation from the π1 ∗ anion of pCP is largely suppressed because of the unfavorable mixing with the σCCl ∗ state. We found the intramolecular hydrogen bond present in oCP to have the opposite effects of stabilizing the σCCl ∗ resonance and destabilizing the σOH ∗ resonance. We also suggest that the hydrogen abstraction observed in chlorophenols and phenol actually takes place by a mechanism in which the incoming electron is directly attached to the dissociative σOH ∗ orbital.

  8. Multiphoton Dissociation of Electrosprayed MegaDalton-Sized DNA Ions in a Charge-Detection Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Doussineau, Tristan; Paletto, Pierre; Dugourd, Philippe; Antoine, Rodolphe

    2015-01-01

    Charge detection mass spectrometry in combination with a linear electrostatic ion trap coupled to a continuous wavelength infrared CO2 laser has been used to study the multiphoton dissociation of DNA macromolecular ions. Samples, with masses ranging from 2.23 to 31.5 MDa, include single strand circular M13mp18, double strand circular M13mp18, and double strand linear LambdaPhage DNA fragments. Their activation energies for unimolecular dissociation were determined. Activation energy values slightly increase as a function of the molecular weight. The most important result is the difference between the fragmentations observed for hybridized double-strands and dimers of single strands.

  9. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Voinov, Valery G.; Hoffman, Peter D.; Bennett, Samuel E.; Beckman, Joseph S.; Barofsky, Douglas F.

    2015-12-01

    Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer.

  10. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer.

    PubMed

    Voinov, Valery G; Hoffman, Peter D; Bennett, Samuel E; Beckman, Joseph S; Barofsky, Douglas F

    2015-12-01

    Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer. Graphical Abstract ᅟ. PMID:26266643

  11. Mechanistic Study on Electronic Excitation Dissociation of the Cellobiose-Na+ Complex

    NASA Astrophysics Data System (ADS)

    Huang, Yiqun; Pu, Yi; Yu, Xiang; Costello, Catherine E.; Lin, Cheng

    2016-02-01

    The recent development of electron activated dissociation (ExD) techniques has opened the door for high-throughput, detailed glycan structural elucidation. Among them, ExD methods employing higher-energy electrons offer several advantages over low-energy electron capture dissociation (ECD), owing to their applicability towards chromophore-labeled glycans and singly charged ions, and ability to provide more extensive structural information. However, a lack of understanding of these processes has hindered rational optimization of the experimental conditions for more efficient fragmentation as well as the development of informatics tools for interpretation of the complex glycan ExD spectra. Here, cellobiose-Na+ was used as the model system to investigate the fragmentation behavior of metal-adducted glycans under irradiation of electrons with energy exceeding their ionization potential, and served as the basis on which a novel electronic excitation dissociation (EED) mechanism was proposed. It was found that ionization of the glycan produces a mixture of radical cations and ring-opened distonic ions. These distonic ions then capture a low-energy electron to produce diradicals with trivial singlet-triplet splitting, and subsequently undergo radical-induced dissociation to produce a variety of fragment ions, the abundances of which are influenced by the stability of the distonic ions from which they originate.

  12. Water-molecule dissociation by proton and hydrogen impact

    NASA Astrophysics Data System (ADS)

    Luna, H.; de Barros, A. L. F.; Wyer, J. A.; Scully, S. W. J.; Lecointre, J.; Garcia, P. M. Y.; Sigaud, G. M.; Santos, A. C. F.; Senthil, V.; Shah, M. B.; Latimer, C. J.; Montenegro, E. C.

    2007-04-01

    Time-of-flight-based mass analysis of charged water fragments have been used to measure the dissociative and the nondissociative reaction pathways of water formed during collisions with 15to100keV and 500to3500keV H+ projectiles and with 8to100keV H0 projectiles. The fragmentation pathways resulting from the ionization and the electron capture collisions with the incident H+ and H0 projectiles, as well as collisions involving projectile electron loss by the incident H0 projectiles, were separately recorded by detecting the target product ions in coincidence with either the ejected target electrons or the charge-analyzed projectiles. The fragmentation profile shows that at high collision energies the ionization of water arises mainly through outer shell processes. At lower energies valence electron capture and ionization dominate and transfer ionization leads to substantially different fragmentation patterns. H0 and H+ projectiles are found to be equally efficient at ionizing the water molecule. These results are of particular interest to workers in astrophysics and those involved in cancer therapy with heavy particle ion beams.

  13. [Clinical Handling of Patients with Dissociative Disorders].

    PubMed

    Okano, Kenichiro

    2015-01-01

    This paper discusses the way informed psychiatrists are expected to handle dissociative patients in clinical situations, with a specific focus on dissociative identity disorders and dissociative fugue. On the initial interview with dissociative patients, information on their history of trauma and any nascent dissociative symptoms in their childhood should be carefully obtained. Their level of stress in their current life should also be assessed in order to understand their symptomatology, as well as to predict their future clinical course. A psychoeducational approach is crucial; it might be helpful to give information on dissociative disorder to these patients as well as their family members in order to promote their adherence to treatment. Regarding the symptomatology of dissociative disorders, detailed symptoms and the general clinical course are presented. It was stressed that dissociative identity disorder and dissociative fugue, the most high-profile dissociative disorders, are essentially different in their etiology and clinical presentation. Dissociative disorders are often confused with and misdiagnosed as psychotic disorders, such as schizophrenia. Other conditions considered in terms of the differential diagnosis include borderline personality disorder as well as temporal lobe epilepsy. Lastly, the therapeutic approach to dissociative identity disorder is discussed. Each dissociative identity should be understood as potentially representing some traumatically stressful event in the past. The therapist should be careful not to excessively promote the creation or elaboration of any dissociative identities. Three stages are proposed in the individual psychotherapeutic process. In the initial stage, a secure environment and stabilization of symptoms should be sought. The second stage consists of aiding the "host" personality to make use of other more adaptive coping skills in their life. The third stage involves coaching as well as continuous awareness of

  14. 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…

  15. ITMS capabilities in isomer analysis. Part 3. Characterisation of methyl and dimethyl derivatives of 8-desmethylseseline, potential anti-proliferative agents, by tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Kiremire, B.; Traldi, P.; Guiotto, A.; Pastorini, G.; Chilin, A.; Vettori, U.

    1991-05-01

    Two sets of isomeric pyranocoumarins and pyranochromones have been studied by both electron impact and collision-induced dissociation. The daughter spectra were obtained by ion trap mass spectrometry experiments. Characteristic fragments were obtained in electron impact that allowed differentiation between the chromone and the coumarin systems. Distinction between isomers in each set was achieved by collision-induced daughter spectra of selected parent ions.

  16. Fluctuations in nuclear fragmentation

    SciTech Connect

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

    1995-12-01

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

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

    SciTech Connect

    Rajput, Jyoti; Safvan, C. P.

    2011-11-15

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

  18. Dissociative and double photoionization of CO2 from threshold to 90 A

    NASA Technical Reports Server (NTRS)

    Masuoka, T.; Samson, J. A. R.

    1979-01-01

    The molecular photoionization, dissociative photoionization and double photoionization cross sections for CO2 were measured from their onsets down to 90 A by using various combinations of mass spectrometers (a coincidence time-of-flight mass spectrometer and a magnetic mass spectrometer) and light sources (synchrotron radiation, and glow and spark discharge). It is concluded that the one broad peak and the three shoulders in the total adsorption cross section curve between 640 and 90 A are caused completely by dissociative ionization processes. Several peaks observed in the cross section curve for the total fragmentation CO(+)3, O(+) and C(+) are compared with those in the photoelectron spectrum reported for CO2.

  19. Modelling of Collision Induced Absorption Spectra Of H2-H2 Pairs for the Planetary Atmospheres Structure: The Second Overtone Band

    NASA Technical Reports Server (NTRS)

    Borysow, Aleksandra; Borysow, Jacek I.

    1998-01-01

    The main objective of the proposal was to model the collision induced, second overtone band of gaseous hydrogen at low temperatures. The aim of this work is to assist planetary scientists in their investigation of planetary atmospheres, mainly those of Uranus and Neptune. The recently completed extended database of collision induced dipole moments of hydrogen pairs allowed us, for the first time, to obtain dipole moment matrix elements responsible for the roto-vibrational collision induced absorption spectra of H2-H2 in the second overtone band. Despite our numerous attempts to publish those data, the enormous volume of the database did not allow us to do this. Instead, we deposited the data on a www site. The final part of this work has been partially supported by NASA, Division for Planetary Atmospheres. In order to use our new data for modelling purpose, we first needed to test how well we can reproduce the existing experimental data from theory, when using our new input data. Two papers resulted from this work. The obtained agreement between theoretical results and the measurements appeared to be within 10-30%. The obviously poorer agreement than observed for the first H2 overtone, the fundamental, and the rototranslational bands can be attributed to the fact that dipole moments responsible for the second overtone are much weaker, therefore susceptible to larger numerical uncertainties. At the same time, the intensity of the second overtone band is much weaker and therefore it is much harder to be measured accurately in the laboratory. We need to point out that until now, no dependable model of the 2nd overtone band was available for modelling of the planetary atmospheres. The only one, often referred to in previous works on Uranian and Neptune's atmospheres, uses only one lineshape, with one (or two) parameter(s) deduced at the effective temperature of Uranus (by fitting the planetary observation). After that, the parameter(s) was(were) made temperature

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

    NASA Astrophysics Data System (ADS)

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

    1993-09-01

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

  1. 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.

  2. COLLISIONS OF POROUS CLUSTERS: A GRANULAR-MECHANICS STUDY OF COMPACTION AND FRAGMENTATION

    SciTech Connect

    Ringl, Christian; Urbassek, Herbert M.; Bringa, Eduardo M.; Bertoldi, Dalia S.

    2012-06-20

    The collision of granular clusters can result in a number of complex outcomes from sticking to partial or full destruction of the clusters. These outcomes will contribute to the size distribution of dust aggregates, changing their optical properties and their capability to contribute to solid-state astrochemistry. We study the collision of two clusters of equal size, formed by approximately 7000 sub-{mu}m grains each, with a mass and velocity range that is difficult to sample in experiments. We obtain the outcome of the collision: compaction, fragmentation, and size distribution of ejecta, and type of outcome, as a function of velocity and impact parameter. We compare our results to other models and simulations, at both atomistic and continuum scales, and find some agreement together with some discrepancies. We also study collision-induced compaction as a function of cluster size, up to sizes of N = 250, 000, and find that for large clusters considerably higher compactions result at higher velocities.

  3. Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When collision induced dissociation is used to fragment phosphorylated peptides during tandem mass spectrometry (MS2), an ion exhibiting the neutral loss of phosphoric acid can be the major product. The neutral loss ion can then be fragmented during MS3 for additional resolution of the peptide sequ...

  4. Observation of the Hydrogen Migration in the Cation-Induced Fragmentation of the Pyridine Molecules.

    PubMed

    Wasowicz, Tomasz J; Pranszke, Bogusław

    2016-02-25

    The ability to selectively control chemical reactions related to biology, combustion, and catalysis has recently attracted much attention. In particular, the hydrogen atom relocation may be used to manipulate bond-breaking and new bond-forming processes and may hold promise for far-reaching applications. Thus, the hydrogen atom migration preceding fragmentation of the gas-phase pyridine molecules by the H(+), H2(+), He(+), He(2+), and O(+) impact has been studied experimentally in the energy range of 5-2000 eV using collision-induced luminescence spectroscopy. Formation of the excited NH(A(3)Π) radicals was observed among the atomic and diatomic fragments. The structure of the pyridine molecule is lacking of the NH group, therefore observation of its A(3)Π → X(3)Σ(-) emission bands is an evidence of the hydrogen atom relocation prior to the cation-induced fragmentation. The NH(A(3)Π) emission yields indicate that formation of the NH radicals depends on the type of selected projectile and can be controlled by tuning its velocity. The plausible collisional mechanisms as well as fragmentation channels for NH formation in pyridine are discussed. PMID:26837458

  5. Rotamers and Migration: Investigating the Dissociative Photoionization of Ethylenediamine.

    PubMed

    Muller, Giel; Voronova, Krisztina; Sztáray, Bálint; Meloni, Giovanni

    2016-06-01

    The unimolecular dissociation of energy-selected ethylenediamine cations was studied by threshold photoelectron photoion coincidence spectroscopy (TPEPICO) in the photon energy range of 8.60-12.50 eV. Modeling the breakdown diagram and time-of-flight distributions with rigid activated complex RRKM theory yielded 0 K appearance energies for eight dissociation channels, leading to NH2CHCH2(+)(•) at 9.120 ± 0.010 eV, CH3C(NH2)2(+) at 9.200 ± 0.012 eV, NH2CHCH3(+) at 9.34 ± 0.08 eV, CH2NH2(+) at 9.449 ± 0.025 eV, CH2NH3(+) at 9.8 ± 0.1 eV, c-C2H4NH2(+) at 10.1 ± 0.1 eV, CH3NHCHCH2(+) at 10.2 ± 0.1 eV, and the reappearance of CH2NH2(+) at 10.2 ± 0.1 eV. The CBS-QB3-calculated pathways highlighted the influence of intramolecular hydrogen attractions on the dissociation processes, presenting novel isomers and low-energy van der Waals intermediates that led to fragments in good agreement with experimental results. While most of the dissociation channels take place through reverse barriers, the 0 K heat of formation of (•)CH2NH2 was determined to be 147.6 ± 3.7 kJ mol(-1), in excellent agreement with literature, and the 0 K heat of formation of CH2NH3(+) at 844 ± 10 kJ mol(-1) is the first experimentally measured value available and is in good agreement with theory. PMID:27177327

  6. Comparison of sustained off-resonance irradiation collisionally activated dissociation and multipole storage-assisted dissociation for top-down protein analysis

    SciTech Connect

    Keller, Karin M; Brodbelt, Jennifer S; Hettich, Robert {Bob} L; Van Berkel, Gary J

    2004-01-01

    Tandem mass spectrometric data acquired for small (8--18 kDa) intact proteins by sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD) and multipole storage-assisted dissociation (MSAD) were compared, and the results indicate that the two activation methods do not always provide the same fragmentation patterns. In MSAD experiments, the charge state distribution made available by the ionization conditions may dictate the range of fragment ions that can be generated. In addition, conditions of high space charge within the hexapole impair transmission and/or trapping of high m/z species, which can result in loss of important precursor and product ions. Finally, the non-resonant nature of activation in MSAD can provide access to secondary dissociation processes that are not available by SORI. Because of these considerations, MSAD is less reliable than SORI for generating sequence tag data. However, it appears that MSAD samples 'preferred' cleavage processes (i.e. those occurring at D and P residues) just as well as SORI, which implies that MSAD data may be somewhat more compatible with search algorithms that utilize unprocessed fragment ion masses.

  7. High-energy collision-activated and electron-transfer dissociation of gas-phase complexes of tryptophan with Na+, K+, and Ca2+

    NASA Astrophysics Data System (ADS)

    Fujihara, Akimasa; Sha, Yuki; Matsuo, Sou; Toyoda, Michisato; Hayakawa, Shigeo

    2014-10-01

    The structure and reactivity of gas-phase complexes of tryptophan (Trp) with Na+, K+, and Ca2+ were examined by high-energy collision-activated dissociation (CAD) and electron transfer dissociation (ETD) using alkali metal targets. In the CAD spectra of M+Trp (M = Na and K), neutral Trp loss was the primary dissociation pathway, and the product ion of collision-induced intracomplex electron transfer from the indole π ring of Trp to the alkali metal ion was observed, indicating a charge-solvated structure in which Trp is non-zwitterionic. The NH3 loss observed in the CAD spectrum of Ca2+Trp2 is ascribed to a CZ (mixed charge-solvated/zwitterionic)-type structure, in which one Trp is non-zwitterionic and the other Trp adopts a zwitterionic structure with an NH3+ moiety. The H atom and NH3 losses observed in the ETD spectrum of Ca2+Trp2 indicate the formation of a hypervalent radical in the complex, R-NH3, via electron transfer from the alkali metal target to the NH3+ group of the CZ-type structure. Ca2+ attachment to Trp cluster induces the zwitterionic structure of Trp in the gas phase, and an electron transfer to the zwitterionic Trp forms the hypervalent radical as a reaction intermediate.

  8. Characterization of oligodeoxynucleotides by electron detachment dissociation fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Yang, Jiong; Mo, Jingjie; Adamson, Julie T; Håkansson, Kristina

    2005-03-15

    Electron detachment dissociation (EDD), recently introduced by Zubarev and co-workers for the dissociation of multiply charged biomolecular anions via a radical ion intermediate, has been shown to be analogous to electron capture dissociation (ECD) in several respects, including more random peptide fragmentation and retention of labile posttranslational modifications. We have previously demonstrated unique fragmentation behavior in ECD compared to vibrational excitation for oligodeoxynucleotide cations. However, that approach is limited by the poor sensitivity for oligonucleotide ionization in positive ion mode. Here, we show implementation of EDD on a commercial Fourier transform ion cyclotron resonance mass spectrometer utilizing two different configurations: a heated filament electron source and an indirectly heated hollow dispenser cathode electron source. The dispenser cathode configuration provides higher EDD efficiency and additional fragmentation channels for hexamer oligodeoxynucleotides. As in ECD, even-electron d/w ion series dominate the spectra, but we also detect numerous a/z (both even-electron and radical species), (a/z - B), c/x, (c/x - B), and (d/w - B) ions with minimal nucleobase loss from the precursor ions. In contrast to previous high-energy collision-activated dissociation (CAD) and ion trap CAD of radical oligonucleotide anions, we only observe minimum sugar cross-ring cleavage, possibly due to the short time scale of EDD, which limits secondary fragmentation. Thus, EDD provides fragmentation similar to ECD for oligodeoxynucleotides but at enhanced sensitivity. Finally, we show that noncovalent bonding in a DNA duplex can be preserved following EDD, illustrating another analogy with ECD. We believe the latter finding implies EDD has promise for characterization of nucleic acid structure and folding. PMID:15762599

  9. Fragmentation network of doubly charged methionine: Interpretation using graph theory.

    PubMed

    Ha, D T; Yamazaki, K; Wang, Y; Alcamí, M; Maeda, S; Kono, H; Martín, F; Kukk, E

    2016-09-01

    The fragmentation of doubly charged gas-phase methionine (HO2CCH(NH2)CH2CH2SCH3) is systematically studied using the self-consistent charge density functional tight-binding molecular dynamics (MD) simulation method. We applied graph theory to analyze the large number of the calculated MD trajectories, which appears to be a highly effective and convenient means of extracting versatile information from the large data. The present theoretical results strongly concur with the earlier studied experimental ones. Essentially, the dication dissociates into acidic group CO2H and basic group C4NSH10. The former may carry a single or no charge and stays intact in most cases, whereas the latter may hold either a single or a double charge and tends to dissociate into smaller fragments. The decay of the basic group is observed to follow the Arrhenius law. The dissociation pathways to CO2H and C4NSH10 and subsequent fragmentations are also supported by ab initio calculations. PMID:27608997

  10. 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.

  11. Selectable fragmentation warhead

    SciTech Connect

    Bryan, C.S.; Paisley, D.L.; Montoya, N.I.; Stahl, D.B.

    1993-07-20

    A selectable fragmentation warhead is described comprising: a case having proximal and distal ends; a fragmenting plate mounted in said distal end of said casing; first explosive means cast adjacent to said fragmenting plate for creating a predetermined number of fragments from said fragmenting plate; three or more first laser-driven slapper detonators located adjacent to said first explosive means for detonating said first explosive means in a predetermined pattern; smoother-disk means located adjacent to said first means for accelerating said fragments; second explosive means cast adjacent to said smoother-disk means for further accelerating said fragments; at least one laser-driven slapper detonators located in said second explosive means; a laser located in said proximal end of said casing; optical fibers connecting said laser to said first and second laser-driven slapper detonators; and optical switch means located in series with said optical fibers connected to said plurality of first laser-driven slapper detonators for blocking or passing light from said laser to said plurality of first laser-driven slapper detonators.

  12. Stratification of gallstone fragments: the key to more effective fragmentation.

    PubMed

    Alderfer, J T; Laufer, I; Wisniewski, F; Malet, P F

    1992-04-01

    During previous experiments with in vitro fragmentation in a simulated gallbladder, we noticed that stone fragments tended to stratify with the dust and smaller fragments settled to the dependent portion, while the larger fragments settled on top. We reviewed the oral cholecystogram (OCG) of 10 patients examined 6 months following gallstone lithotripsy. In all cases with adequate visualization of stone fragments, the stratification phenomenon was observed. We hypothesized that adjusting the shock wave focus to target on these large fragments would improve the efficiency of fragmentation. To test this hypothesis, we fragmented three matched pairs of gallstones in vitro. For each pair, the stones were removed from the same gallbladder and the stone weights of the two stones were within 10%. The smaller member of each pair was fragmented using the "old method" with the focus on the fragment line. The larger stone was fragmented with the "new method" with the focus in the acoustic shadow deep to the echogenic line caused by the dust and small fragments in the dependent portion. The distribution of fragments was analyzed by passing the fragments through a series of filters. With the new method of targeting, the proportion of fragments less than 1.5 mm was doubled while the fragments greater than 5 mm were eliminated. The new method of targeting, taking into account the stratification of stone fragments, produces more effective fragmentation and should lead to more rapid clearance of fragments from the gallbladder. PMID:10149180

  13. Quantum control of molecular fragmentation in strong laser fields

    NASA Astrophysics Data System (ADS)

    Zohrabi, Mohammad

    Present advances in laser technology allow the production of ultrashort (<˜5 fs, approaching single cycle at 800 nm), intense tabletop laser pulses. At these high intensities laser-matter interactions cannot be described with perturbation theory since multiphoton processes are involved. This is in contrast to photodissociation by the absorption of a single photon, which is well described by perturbation theory. For example, at high intensities (<˜5x1013 W/cm2) the fragmentation of molecular hydrogen ions has been observed via the absorption of three or more photons. In another example, an intriguing dissociation mechanism has been observed where molecular hydrogen ions seem to fragment by apparently absorbing no photons. This is actually a two photon process, photoabsorption followed by stimulated emission, resulting in low energy fragments. We are interested in exploring these kinds of multiphoton processes. Our research group has studied the dynamics and control of fragmentation induced by strong laser fields in a variety of molecular targets. The main goal is to provide a basic understanding of fragmentation mechanisms and possible control schemes of benchmark systems such as H2+. This knowledge is further extended to more complex systems like the benchmark H3+ polyatomic and other molecules. In this dissertation, we report research based on two types of experiments. In the first part, we describe laser-induced fragmentation of molecular ion-beam targets. In the latter part, we discuss the formation of highly-excited neutral fragments from hydrogen molecules using ultrashort laser pulses. In carrying out these experiments, we have also extended experimental techniques beyond their previous capabilities. We have performed a few experiments to advance our understanding of laser-induced fragmentation of molecular-ion beams. For instance, we explored vibrationally resolved spectra of O2+ dissociation using various wavelengths. We observed a vibrational suppression

  14. Religious Dissociation and Economic Appraisal in Brazil.

    PubMed

    François Dengah, H J

    2016-04-01

    Research on the association between religion and health often neglects to provide an explicit theoretical mechanism of influence between faith and well-being. This research posits that dissociative behaviors, such as glossolalia, may provide a biological pathway that influences both physiological and psychological health. This paper argues that religious dissociation acts as a moderator between economic stressors and psychobiological appraisal. Brazil, with its economic inequality and preponderance of religious dissociative rituals, provides an ideal context to examine religious dissociation as a moderator of stress. Utilizing data from a cross section of Brazilian faiths, this paper examines: (1) Whether individuals with low socioeconomic status preferentially participate and experience religious dissociative states and (2) whether dissociative states are correlated with greater psychological appraisal of status. PMID:25687180

  15. Dissociative Tendencies and Facilitated Emotional Processing

    PubMed Central

    Oathes, Desmond J.; Ray, William J.

    2009-01-01

    Dissociation is a process linked to lapses of attention, history of abuse or trauma, compromised emotional memory, and a disintegrated sense of self. It is theorized that dissociation stems from avoiding emotional information, especially negative emotion, to protect a fragile psyche. The present study tested whether or not dissociaters do actually avoid processing emotion by asking groups scoring high or low on the Dissociative Experiences Scale to judge the affective valence of several types of emotional stimuli. Manipulations of valence, modality (pictures or words), task complexity, and personal relevance lead to results suggesting that dissociation is linked to facilitated rather than deficient emotional processing. Our results are consistent with a theory that sensitivity to emotional material may be a contributing factor in subsequent dissociation to avoid further elaboration of upsetting emotion in these individuals. The findings for dissociation further exemplify the influence of individual differences in the link between cognition and emotion. PMID:18837615

  16. Stability and Degradation of Caffeoylquinic Acids under Different Storage Conditions Studied by High-Performance Liquid Chromatography with Photo Diode Array Detection and High-Performance Liquid Chromatography with Electrospray Ionization Collision-Induced Dissociation Tandem Mass Spectrometry.

    PubMed

    Xue, Meng; Shi, Hang; Zhang, Jiao; Liu, Qing-Quan; Guan, Jun; Zhang, Jia-Yu; Ma, Qun

    2016-01-01

    Caffeoylquinic acids (CQAs) are main constituents in many herbal medicines with various biological and pharmacological effects. However, CQAs will degrade or isomerize when affected by temperature, pH, light, etc. In this study, high-performance liquid chromatography with photodiode array detection (HPLC-PDA) and high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) was utilized to study the stability and degradation of CQAs (three mono-acyl CQAs and four di-acyl CQAs) under various ordinary storage conditions (involving different temperatures, solvents, and light irradiation). The results indicated that the stability of CQAs was mainly affected by temperature and light irradiation, while solvents did not affect it in any obvious way under the conditions studied. Mono-acyl CQAs were generally much more stable than di-acyl CQAs under the same conditions. Meanwhile, the chemical structures of 30 degradation products were also characterized by HPLC-MS(n), inferring that isomerization, methylation, and hydrolysis were three major degradation pathways. The result provides a meaningful clue for the storage conditions of CQAs standard substances and samples. PMID:27455213

  17. Dissociation of internal energy-selected methyl bromide ion revealed from threshold photoelectron-photoion coincidence velocity imaging

    NASA Astrophysics Data System (ADS)

    Tang, Xiaofeng; Zhou, Xiaoguo; Sun, Zhongfa; Liu, Shilin; Liu, Fuyi; Sheng, Liusi; Yan, Bing

    2014-01-01

    Dissociative photoionization of methyl bromide (CH3Br) in an excitation energy range of 10.45-16.90 eV has been investigated by using threshold photoelectron-photoion coincidence (TPEPICO) velocity imaging. The coincident time-of-flight mass spectra indicate that the ground state X2E of CH3Br+ is stable, and both A2A1 and B2E ionic excited states are fully dissociative to produce the unique fragment ion of CH3+. From TPEPICO 3D time-sliced velocity images of CH3+ dissociated from specific state-selected CH3Br+ ion, kinetic energy release distribution (KERD) and angular distribution of CH3+ fragment ion are directly obtained. Both spin-orbit states of Br(2P) atom can be clearly observed in fast dissociation of CH3Br+(A2A1) ion along C-Br rupture, while a KERD of Maxwell-Boltzmann profile is obtained in dissociation of CH3Br+(B2E) ion. With the aid of the re-calculated potential energy curves of CH3Br+ including spin-orbit coupling, dissociation mechanisms of CH3Br+ ion in A2A1 and B2E states along C-Br rupture are revealed. For CH3Br+(A2A1) ion, the CH3+ + Br(2P1/2) channel is occurred via an adiabatic dissociation by vibration, while the Br(2P3/2) formation is through vibronic coupling to the high vibrational level of X2E state followed by rapid dissociation. C-Br bond breaking of CH3Br+(B2E) ion can occur via slow internal conversion to the excited vibrational level of the lower electronic states and then dissociation.

  18. Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes.

    PubMed

    Quintyn, Royston S; Zhou, Mowei; Yan, Jing; Wysocki, Vicki H

    2015-12-01

    One attractive feature of ion mobility mass spectrometry (IM-MS) lies in its ability to provide experimental collision cross section (CCS) measurements, which can be used to distinguish different conformations that a protein complex may adopt during its gas-phase unfolding. However, CCS values alone give no detailed information on subunit structure within the complex. Consequently, structural characterization typically requires molecular modeling, which can have uncertainties without experimental support. One method of obtaining direct experimental evidence on the structures of these intermediates is utilizing gas-phase activation techniques that can effectively dissociate the complexes into substructures while preserving the native topological information. The most commonly used activation method, collision-induced dissociation (CID) with low-mass target gases, typically leads to unfolding of monomers of a protein complex. Here, we describe a method that couples IM-MS and surface-induced dissociation (SID) to dissociate the source-activated precursors of three model protein complexes: C-reactive protein (CRP), transthyretin (TTR), and concanavalin A (Con A). The results of this study confirm that CID involves the unfolding of the protein complex via several intermediates. More importantly, our experiments also indicate that retention of similar CCS between different intermediates does not guarantee retention of structure. Although CID spectra (at a given collision energy) of source-activated, mass-selected precursors do not distinguish between native-like, collapsed, and expanded forms of a protein complex, dissociation patterns and/or average charge states of monomer products in SID of each of these forms are unique. PMID:26499904

  19. NEW H{sub 2} COLLISION-INDUCED ABSORPTION AND NH{sub 3} OPACITY AND THE SPECTRA OF THE COOLEST BROWN DWARFS

    SciTech Connect

    Saumon, Didier; Marley, Mark S.; Abel, Martin; Frommhold, Lothar; Freedman, Richard S. E-mail: Mark.S.Marley@nasa.gov E-mail: frommhold@physics.utexas.edu

    2012-05-01

    We present new cloudy and cloudless model atmospheres for brown dwarfs using recent ab initio calculations of the line list of ammonia (NH{sub 3}) and of the collision-induced absorption of molecular hydrogen (H{sub 2}). We compare the new synthetic spectra with models based on an earlier description of the H{sub 2} and NH{sub 3} opacities. We find a significant improvement in fitting the nearly complete spectral energy distribution of the T7p dwarf Gliese 570D and in near-infrared color-magnitude diagrams of field brown dwarfs. We apply these new models to the identification of NH{sub 3} absorption in the H-band peak of very late T dwarfs and the new Y dwarfs and discuss the observed trend in the NH{sub 3}-H spectral index. The new NH{sub 3} line list also allows a detailed study of the medium-resolution spectrum of the T9/T10 dwarf UGPS J072227.51-054031.2 where we identify several specific features caused by NH{sub 3}.

  20. Modeling of collision-induced infrared absorption spectra of H2 pairs in the first overtone band at temperatures from 20 to 500 K

    NASA Technical Reports Server (NTRS)

    Zheng, Chunguang; Borysow, Aleksandra

    1995-01-01

    A simple formalism is presented that permits quick computations of the low-resolution, rotovibrational collision-induced absorption (RV CIA) spectra of H2 pairs in the first overtone band of hydrogen, at temperatures from 20 to 500 K. These spectra account for the free-free transitions. The sharp dimer features, originating from the bound-free, free-bound, and bound-bound transitions are ignored, though their integrated intensities are properly accounted for. The method employs spectral model line- shapes with parameters computed from the three lowest spectral moments. The moments are obtained from first principles expressed as analytical functions of temperature. Except for the sharp dimer features, which are absent in this model, the computed spectra reproduce closely the results of exact quantum mechanical lineshape computations. Comparisons of the computed spectra with existing experimental data also show good agreement. The work interest for the modeling of the atmospheres of the outer planets in the near-infrared region of the spectrum. The user-friendly Fortran program developed here is available on request from the authors.

  1. Ab initio 3D potential energy and dipole moment surfaces for the CH4-Ar complex: Collision-induced intensity and dimer content

    NASA Astrophysics Data System (ADS)

    Kalugina, Yulia N.; Lokshtanov, Sergei E.; Cherepanov, Victor N.; Vigasin, Andrey A.

    2016-02-01

    We present new three-dimensional potential energy surface (PES) and dipole moment surfaces (DMSs) for the CH4-Ar van der Waals system. Ab initio calculations of the PES and DMS were carried out using the closed-shell single- and double-excitation coupled cluster approach with non-iterative perturbative treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = D,T,Q) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. The dipole moment surface was obtained using aug-cc-pVTZ basis set augmented with mid-bond functions for better description of exchange interactions. The second mixed virial coefficient was calculated and compared to available experimental data. The equilibrium constant for true dimer formation was calculated using classical partition function based on the knowledge of ab initio PES. Temperature variations of the zeroth spectral moment of the rototranslational collision-induced band as well as its true dimer constituent were traced with the use of the Boltzmann-weighted squared induced dipole properly integrated over respective phase space domains. Height profiles for N2-N2, N2-H2, CH4-N2, (CH4)2, and CH4-Ar true bound dimers in Titan's atmosphere were calculated with the use of reliable ab initio PESs.

  2. The HD spectrum near 2.3 μm by CRDS-VECSEL: Electric quadrupole transition and collision-induced absorption

    NASA Astrophysics Data System (ADS)

    Vasilchenko, S.; Mondelain, D.; Kassi, S.; Čermák, P.; Chomet, B.; Garnache, A.; Denet, S.; Lecocq, V.; Campargue, A.

    2016-08-01

    The HD absorption spectrum is investigated near 2.3 μm with the help of a newly developed Cavity Ring Down Spectrometer (CRDS) using a VECSEL (Vertical External Cavity Surface Emitting Laser) as light source. The HD CRDS spectra were recorded for a series of ten pressure values in the range 50-650 Torr. The sensitivity of the recordings - noise equivalent absorption of the spectra on the order of αmin ≈ 5 × 10-10 cm-1 - has allowed for the first detection of the S(3) quadrupole electric transition of the HD fundamental band, at 4359.940 cm-1. The line center determined with an uncertainty of 0.002 cm-1 agrees with the most recent theoretical calculations. The retrieved value of the line intensity (2.5 × 10-27 cm/molecule at 296 K) agrees within 12% with the ab initio values included in the HITRAN spectroscopic database. We take the opportunity of this contribution to provide an exhaustive review of seventy-three HD absorption lines previously detected up to 20,000 cm-1. From the pressure dependence of the baseline of the CRDS spectra, the binary absorption coefficient of the HD collision induced absorption band is determined to be 1.17(4) × 10-6 cm-1amagat-2 at 4360 cm-1.

  3. Ab initio 3D potential energy and dipole moment surfaces for the CH4-Ar complex: Collision-induced intensity and dimer content.

    PubMed

    Kalugina, Yulia N; Lokshtanov, Sergei E; Cherepanov, Victor N; Vigasin, Andrey A

    2016-02-01

    We present new three-dimensional potential energy surface (PES) and dipole moment surfaces (DMSs) for the CH4-Ar van der Waals system. Ab initio calculations of the PES and DMS were carried out using the closed-shell single- and double-excitation coupled cluster approach with non-iterative perturbative treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = D,T,Q) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. The dipole moment surface was obtained using aug-cc-pVTZ basis set augmented with mid-bond functions for better description of exchange interactions. The second mixed virial coefficient was calculated and compared to available experimental data. The equilibrium constant for true dimer formation was calculated using classical partition function based on the knowledge of ab initio PES. Temperature variations of the zeroth spectral moment of the rototranslational collision-induced band as well as its true dimer constituent were traced with the use of the Boltzmann-weighted squared induced dipole properly integrated over respective phase space domains. Height profiles for N2-N2, N2-H2, CH4-N2, (CH4)2, and CH4-Ar true bound dimers in Titan's atmosphere were calculated with the use of reliable ab initio  PESs. PMID:26851918

  4. Double vibrational collision-induced Raman scattering by SF{sub 6}-N{sub 2}: Beyond the point-polarizable molecule model

    SciTech Connect

    Verzhbitskiy, I. A.; Chrysos, M.; Kouzov, A. P.

    2010-11-15

    Collision-induced Raman bandshapes and zeroth-order spectral moments are calculated both for the depolarized spectrum and for the extremely weak isotropic spectrum of the SF{sub 6}({nu}{sub 1}) +N{sub 2}({nu}{sub 1}) double-Raman-scattering band. A critical comparison is made with experiments conducted recently by the authors [Phys. Rev. A 81, 012702 (2010); 81, 042705 (2010)]. The study of this transition, hitherto restricted to the model framework of two point-polarizable molecules, is now completed to incorporate effects beyond the point-molecule approximation. Whereas the extended model offers a few percent improvement in the depolarized spectrum, it reveals a huge 80% increase in the isotropic spectrum and its moment, owing essentially to the polarizability anisotropy of N{sub 2}. For both spectra, agreement between quantum-mechanical calculations and our experiments is found, provided that the best ab initio data for the (hyper)polarizability parameters are used. This refined study shows clearly the need to include all mechanisms and data to a high level of accuracy and allows one to decide between alternatives about difficult and controversial issues such as the intermolecular potential or the sensitive Hamaker force constants.

  5. Electromagnetic Dissociation and Spacecraft Electronics Damage

    NASA Technical Reports Server (NTRS)

    Norbury, John W.

    2016-01-01

    When protons or heavy ions from galactic cosmic rays (GCR) or solar particle events (SPE) interact with target nuclei in spacecraft, there can be two different types of interactions. The more familiar strong nuclear interaction often dominates and is responsible for nuclear fragmentation in either the GCR or SPE projectile nucleus or the spacecraft target nucleus. (Of course, the proton does not break up, except possibly to produce pions or other hadrons.) The less familiar, second type of interaction is due to the very strong electromagnetic fields that exist when two charged nuclei pass very close to each other. This process is called electromagnetic dissociation (EMD) and primarily results in the emission of neutrons, protons and light ions (isotopes of hydrogen and helium). The cross section for particle production is approximately defined as the number of particles produced in nucleus-nucleus collisions or other types of reactions. (There are various kinematic and other factors which multiply the particle number to arrive at the cross section.) Strong, nuclear interactions usually dominate the nuclear reactions of most interest that occur between GCR and target nuclei. However, for heavy nuclei (near Fe and beyond) at high energy the EMD cross section can be much larger than the strong nuclear interaction cross section. This paper poses a question: Are there projectile or target nuclei combinations in the interaction of GCR or SPE where the EMD reaction cross section plays a dominant role? If the answer is affirmative, then EMD mechanisms should be an integral part of codes that are used to predict damage to spacecraft electronics. The question can become more fine-tuned and one can ask about total reaction cross sections as compared to double differential cross sections. These issues will be addressed in the present paper.

  6. Coulomb Dissociation of 27P

    NASA Astrophysics Data System (ADS)

    Beceiro Novo, S.; Sümmerer, K.; Cortina-Gil, D.; Wimmer, C.; Plag, R.; Alvarez-Pol, H.; Aumann, T.; Behr, K.; Boretzky, K.; Casarejos, E.; Chatillon, A.; Datta-Pramanik, U.; Elekes, Z.; Fulop, Z.; Galaviz, D.; Geissel, H.; Giron, S.; Greife, U.; Hammache, F.; Heil, M.; Hoffman, J.; Johansson, H.; Karagiannis, C.; Kiselev, O.; Kurz, N.; Larsson, K.; Le Bleis, T.; Litvinov, Y.; Mahata, K.; Muentz, C.; Nociforo, C.; Ott, W.; Paschalis, S.; Prokopowicz, W.; Rodriguez-Tajes, C.; Rossi, D.; Simon, H.; Stanoiu, M.; Stroth, J.; Typel, S.; Wagner, A.; Wamers, F.; Weick, H.

    2012-09-01

    In this work the astrophysical 26Si(p,γ)27P reaction is studied using the Coulomb dissociation technique. We performed a 27P Coulomb Dissociation experiment at GSI, Darmstadt (28 May-5 June 2007) using the ALADIN-LAND setup which allows complete-kinematic studies. A secondary 27P beam at 498 AMeV impinging a 515mg/cm2 Pb target was used. The relative energy of the outgoing system (26Si+p) is measured obtaining the resonant states of the 27P. Preliminary results show four resonant states measured at 0.36±0.07, 0.88±0.09, 1.5±0.2, 2.3±0.3 MeV and evidence of a higher state at around 3.1 MeV. The preliminary total cross section obtained for relative energies between 0 and 3 MeV has been measured and yields 55±7 mb.

  7. Fragment capture device

    DOEpatents

    Payne, Lloyd R.; Cole, David L.

    2010-03-30

    A fragment capture device for use in explosive containment. The device comprises an assembly of at least two rows of bars positioned to eliminate line-of-sight trajectories between the generation point of fragments and a surrounding containment vessel or asset. The device comprises an array of at least two rows of bars, wherein each row is staggered with respect to the adjacent row, and wherein a lateral dimension of each bar and a relative position of each bar in combination provides blockage of a straight-line passage of a solid fragment through the adjacent rows of bars, wherein a generation point of the solid fragment is located within a cavity at least partially enclosed by the array of bars.

  8. Dissociative Recombination without a Curve Crossing

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.

    1994-01-01

    Ab initio calculations show that a curve crossing is not always needed for a high dissociative- recombination cross section. For HeH(+), in which no neutral states cross the ion potential curve, dissociative recombination is driven by the nuclear kinetic-energy operator on adiabatic potential curves. The kinetic-energy derivative operator allows for capture into repulsive curves that are outside of the classical turning points for the nuclear motion. The dominant dissociative route is the C (2)Sigma(+) state leading to H(n = 2) atoms. An analogous mechanism is proposed for the dissociative recombination of H3(+).

  9. Degree of somatoform and psychological dissociation in dissociative disorder is correlated with reported trauma.

    PubMed

    Nijenhuis, E R; Spinhoven, P; van Dyck, R; van der Hart, O; Vanderlinden, J

    1998-10-01

    In this study, the prevalence and severity of traumatic experiences as reported by patients with dissociative disorders and with other DSM-IV psychiatric diagnoses were compared. Furthermore, the predictive value of emotional, physical, and sexual trauma with respect to somatoform and psychological dissociation was analyzed. In contrast with comparison patients, dissociative disorder patients reported severe and multifaceted traumatization. Physical and sexual trauma predicted somatoform dissociation, sexual trauma predicted psychological dissociation as well. According to the memories of the dissociative disorder patients, this abuse occurred in an emotionally neglectful and abusive social context. Pathological dissociation was best predicted by early onset of reported intense, chronic and multiple traumatization. Methodological limitations restricting causal inferences between reported trauma and dissociation are discussed. PMID:9870223

  10. Fracture tooth fragment reattachment

    PubMed Central

    Maitin, Nitin; Maitin, Shipra Nangalia; Rastogi, Khushboo; Bhushan, Rajarshi

    2013-01-01

    Coronal fractures of the anterior teeth are a common form of dental trauma and its sequelae may impair the establishment and accomplishment of an adequate treatment plan. Among the various treatment options, reattachment of a crown fragment is a conservative treatment that should be considered for crown fractures of anterior teeth. This clinical case reports the management of two coronal tooth fracture cases that were successfully treated using tooth fragment reattachment using glass-fibre-reinforced composite post. PMID:23853012

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

    NASA Astrophysics Data System (ADS)

    Summerfield, Scott G.; Gaskell, Simon J.

    1997-11-01

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

  12. Dissociative symptoms and dissociative disorder comorbidity in patients with obsessive-compulsive disorder.

    PubMed

    Belli, Hasan; Ural, Cenk; Vardar, Melek Kanarya; Yesılyurt, Sema; Oncu, Fatıh

    2012-10-01

    The present study attempted to assess the dissociative symptoms and overall dissociative disorder comorbidity in patients with obsessive-compulsive disorder (OCD). In addition, we examined the relationship between the severity of obsessive-compulsive symptoms and dissociative symptoms. All patients admitted for the first time to the psychiatric outpatient unit were included in the study. Seventy-eight patients had been diagnosed as having OCD during the 2-year study period. Patients had to meet the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for OCD. Most (76.9%; n = 60) of the patients were female, and 23.1% (n = 18) of the patients were male. Dissociation Questionnaire was used to measure dissociative symptoms. The Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Dissociative Disorders interviews and Yale-Brown Obsessive Compulsive Checklist and Severity Scale were used. Eleven (14%) of the patients with OCD had comorbid dissociative disorder. The most prevalent disorder in our study was dissociative depersonalization disorder. Dissociative amnesia and dissociative identity disorder were common as well. The mean Yale-Brown score was 23.37 ± 7.27 points. Dissociation Questionnaire scores were between 0.40 and 3.87 points, and the mean was 2.23 ± 0.76 points. There was a statistically significant positive correlation between Yale-Brown points and Dissociation Questionnaire points. We conclude that dissociative symptoms among patients with OCD should alert clinicians for the presence of a chronic and complex dissociative disorder. Clinicians may overlook an underlying dissociative process in patients who have severe symptoms of OCD. However, a lack of adequate response to cognitive-behavioral and drug therapy may be a consequence of dissociative process. PMID:22425531

  13. DNA Concentration-Dependent Dissociation of EcoRI: Direct Transfer or Reaction during Hopping

    PubMed Central

    Sidorova, Nina Y.; Scott, Thomas; Rau, Donald C.

    2013-01-01

    Direct transfer of proteins between DNA helices is a recognized important feature of the recognition site search process. Direct transfer is characterized by a dissociation rate that depends on total DNA concentration. This is taken as evidence for the formation of an intermediate DNA-protein-DNA ternary complex. We find that the dissociation rate of EcoRI-DNA-specific complexes at 80 mM NaCl depends on the concentration of competitor oligonucleotide suggesting that direct transfer contributes to EcoRI dissociation. This dependence on competitor DNA concentration is not seen at 180 mM salt. A careful examination of the salt concentration dependence of the dissociation rate, however, shows that the predictions for the formation of a ternary complex are not observed experimentally. The findings can be rationalized by considering that just after dissociating from a DNA fragment the protein remains in close proximity to that fragment, can reassociate with it, and diffuse back to the recognition site rather than bind to an oligonucleotide in solution, a hopping excursion. The probability that a protein will bind to an oligonucleotide during a hop can be approximately calculated and shown to explain the data. A dependence of the dissociation rate of a DNA-protein complex on competitor DNA concentration does not necessarily mean direct transfer. PMID:23528089

  14. 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

  15. Signatures of bond formation and bond scission dynamics in dissociative electron attachment to methane.

    PubMed

    Douguet, N; Slaughter, D S; Adaniya, H; Belkacem, A; Orel, A E; Rescigno, T N

    2015-10-14

    We present a combined experimental and theoretical investigation of the dynamics and angular dependence of dissociative electron attachment to methane. We show that a triply degenerate (T2) Feshbach resonance is responsible for the broad 10 eV dissociation peak in methane. This resonance alone is shown to correlate asymptotically to the various dissociation channels observed experimentally. The molecular-frame entrance amplitude for electron attachment is calculated for each component of the threefold degenerate resonance. By investigating the topology of the anion potential energy surfaces, we deduce the main pathways to two- and three-body breakup channels involving both bond scission and bond formation. The computed fragment angular distributions reproduce the main trends of the experimental measurements. PMID:26371546

  16. Carrier-envelope phase control over the branching ratios in strong-field dissociation of HD+

    NASA Astrophysics Data System (ADS)

    Rigsbee, Brandon; Wang, Yujun; Esry, Brett

    2014-05-01

    We have theoretically explored the carrier-envelope phase (CEP) effect on the dissociation of HD+ with short, intense laser pulses. The branching ratios (BR) of the dissociating fragments are calculated for several laser wavelengths ranging from 800 nm to 4000 nm with two-cycle pulse durations. The CEP dependence of the BR is shown to be stronger with increasing wavelength. In addition, we explore the feasibility of CEP control over the BR with relatively long pulses by exploiting the dynamics of the nonadiabatic coupling which has a strong dependence on the internuclear distance and energy of the dissociating wave packet. J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA.

  17. The Dissociation Energies of CH4 and C2H2 Revisited

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The bond dissociation energies of CH4 and C2H2 and their fragments are investigated using basis set extrapolations and high levels of correlation. The computed bond dissociation energies (D(sub e)) are accurate to within 0.2 kcal/mol. The agreement with the experimental (D(sub 0)) values is excellent if we assume that the zero-point energy of C2H is 9.18 kcal/mol. The effect of core (1s) correlation on the bond dissociation energies of C-H bonds is shown to vary from 0.2 to 0.7 kcal/mol and that for C-C bonds varies from 0.4 to 2.2 kcal/mol.

  18. Shattering of SiMe3+ during surface-induced dissociation

    NASA Astrophysics Data System (ADS)

    Schultz, David G.; Hanley, Luke

    1998-12-01

    We provide experimental evidence that upon hyperthermal impact of Si(CD3)3+ ions with an organic surface, a portion of the ions undergo dissociation while still in contact with the surface. We use a tandem configuration of quadrupole mass spectrometers along with an energy analyzer to measure the kinetic energy distributions of the fragments that form as a result of the surface scattering of 25 eV Si(CD3)3+. These distributions are different for scattering from a clean Au(111) surface versus scattering from an organic surface composed of a self-assembled monolayer of hexanethiolate on Au(111). Parent and fragment ions recoil from the clean Au(111) surface with the same velocity, as is expected for fragmentation away from the surface. However, the same scattering products recoil from the organic surface with different velocities but similar energies, suggesting that the fragmentation dynamics are modified by surface interactions. We perform molecular dynamics simulations which predict residence times of ˜210 fs at the organic surface and ˜20 fs at the Au surface. The simulations also predict that 13% and 31% of the ions fragment within 1.1 ps of surface impact at the organic and Au surfaces, respectively. Thus, the experimental observation of dissociation at only the organic surface results from its longer ion-surface interaction time. The fragmentation time scale predicted by Rice-Ramsperger-Kassel-Marcus calculations is yet longer, suggesting that at least a portion of the surface-induced dissociation of Si(CD3)3+ may occur via a nonstatistical mechanism. Our interpretation draws heavily from an analogous "shattering" mechanism previously proposed for cluster-surface scattering [E. Hendell, U. Even, T. Raz, and R. D. Levine, Phys. Rev. Lett. 75, 2670 (1995)].

  19. Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits to promote a comprehensive portrait of protein characterization.

  20. Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization.

    PubMed

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

    2016-09-01

    Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits to promote a comprehensive portrait of protein characterization. Graphical Abstract ᅟ. PMID:27287047