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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. Evidence for Sequence Scrambling in Collision-Induced Dissociation of y-Type Fragment Ions

    NASA Astrophysics Data System (ADS)

    Miladi, Mahsan; Harper, Brett; Solouki, Touradj

    2013-11-01

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

  3. 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

  4. 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.

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  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. Rearrangements Leading to Fragmentations of Hydrocinnamate and Analogous Nitrogen-Containing Anions Upon Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Gillis, Elizabeth A. L.; Grossert, J. Stuart; White, Robert L.

    2014-03-01

    Tandem mass spectrometry (MS/MS) confirmed decarboxylation as the major collision-induced dissociation (CID) pathway of deprotonated hydrocinnamic acid (C6H5CH2CH2CO2H), N-phenylglycine (C6H5NHCH2CO2H) and 3-pyridin-2-ylpropanoic acid (C5H4NCH2CH2CO2H). The structure and stability of isomeric precursor and product anions were examined using density functional theory and ab initio methods. Geometry optimizations and frequency calculations were performed using the B3LYP/6-31++G(2d,p) level of theory and basis set with additional single point energies calculated at the MP2/6-311++G(2d,p) level. The formation of a delocalized product anion by carboxyl group-mediated migration of a benzylic proton to the ortho position of the ring and subsequent Cα-CO2 - bond cleavage was energetically more favorable than direct decarboxylation and rearrangements of anions within ion-neutral complexes with carbon dioxide. The energy barrier for rearrangement of the delocalized product anion to the more stable benzylic anion was lowest in the fragmentation pathway of 3-pyridin-2-ylpropanoate. More energetically demanding fragmentation processes were indicated by the formation of other product anions at higher collision energy. Computations supported the feasibility of the formation of hydroxycarbonyl, styrene, and phenide ions from the benzylic anion of hydrocinnamate and the corresponding product anions from the nitrogen-containing analogues. The loss of dihydrogen from decarboxylated 3-pyridin-2-ylpropanoate was characterized computationally as hydride abstraction of an aryl proton. Overall, the results highlight the importance of exploring rearrangements in the fragmentation pathways of ions formed by electrospray ionization (ESI).

  10. Differentiating chondroitin sulfate glycosaminoglycans using collision-induced dissociation; uronic acid cross-ring diagnostic fragments in a single stage of tandem mass spectrometry.

    PubMed

    Kailemia, Muchena J; Patel, Anish B; Johnson, Dane T; Li, Lingyun; Linhardt, Robert J; Amster, I Jonathan

    2015-01-01

    The stereochemistry of the hexuronic acid residues of the structure of glycosaminoglycans (GAGs) is a key feature that affects their interactions with proteins and other biological functions. Electron based tandem mass spectrometry methods, in particular electron detachment dissociation (EDD), have been able to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) residues in some heparan sulfate tetrasaccharides by producing epimer-specific fragments. Similarly, the relative abundance of glycosidic fragment ions produced by collision-induced dissociation (CID) or EDD has been shown to correlate with the type of hexuronic acid present in chondroitin sulfate GAGs. The present work examines the effect of charge state and degree of sodium cationization on the CID fragmentation products that can be used to distinguish GlcA and IdoA containing chondroitin sulfate A and dermatan sulfate chains. The cross-ring fragments (2,4)A(n) and (0,2)X(n) formed within the hexuronic acid residues are highly preferential for chains containing GlcA, distinguishing it from IdoA. The diagnostic capability of the fragments requires the selection of a molecular ion and fragment ions with specific ionization characteristics, namely charge state and number of ionizable protons. The ions with the appropriate characteristics display diagnostic properties for all the chondroitin sulfate and dermatan sulfate chains (degree of polymerization of 4-10) studied.

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

    PubMed

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

    2014-11-01

    The collision-induced dissociation (CID) of cationic fatty acid-metal ion complexes has been extensively studied and, in general, provides rich structural information. In particular, charge-remote fragmentation processes are commonly observed allowing the assignment of double bond position. In a previous manuscript, we presented two methods to doubly deprotonate polyunsaturated fatty acids to form anionic fatty acid-sodium ion complexes, referred to as [M - 2H + Na] (-) ions. In the current manuscript, the CID behavior of these [M - 2H + Na] (-) ions is investigated for the first time. Significantly, we also present a deuterium-labeling experiment, which excludes the possibility that deprotonation occurs predominately at the α-carbon in the formation of fatty acid [M - H + NaF](-) ions. This supports our original proposal where deprotonation occurs at the bis-allylic positions of polyunsaturated fatty acids. CID spectra of polyunsaturated fatty acid [M - 2H + Na](-) ions display abundant product ions arising from acyl chain cleavages. Through the examination of fatty acid isomers, it is demonstrated that double bond position may be unequivocally determined for methylene-interrupted polyunsaturated fatty acids with three or more carbon-carbon double bonds. In addition, CID of [M - 2H + Na](-) ions was applied to 18:3 isomers of Nannochloropsis oculata and three isomers were tentatively identified: ∆(9,12,15)18:3, ∆(6,9,12)18:3, and ∆(5,8,11)18:3. We propose that structurally-informative product ions are formed via charge-driven fragmentation processes at the site of the resonance-stabilized carbanion as opposed to charge-remote fragmentation processes, which could be inferred if deprotonation occurred predominately at the α-carbon.

  12. 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.

  13. Collision-induced dissociation of fluoropyridinide anions

    NASA Astrophysics Data System (ADS)

    Kato, Shuji; Lineberger, W. Carl; Bierbaum, Veronica M.

    2007-10-01

    Collision-induced dissociation of ortho-fluoro, meta-fluoro, and 2,6-difluoropyridinide anions are studied using the selected ion flow tube technique. Structures and energetics of the reactants, transition states, and products are calculated at the MP4(SDQ)/6-31 + G(d) level of theory based on the B3LYP/6-311++G(d,p) and/or MP2/6-31 + G(d) optimized geometries. The monofluoropyridinide anions (C5NH3F-) dissociate almost exclusively via loss of an HF molecule, i.e., C5NH2- + HF at low collision energies, in addition to loss of F- at higher energies. 2,6-Difluoropyridinide anions (C5NH2F2-) dissociate via successive loss of HF molecules to form C5NHF- then C5N- depending on the collision energy. The CID results strongly suggest formation of ring-intact pyridynide structures (C5NH2-, C5NHF-) with a bent triple bond embedded in the azine ring systems. Calculated reaction energy diagrams are totally consistent with the experimental observations. Didehydropyridynides C5NH2- and C5NHF- have substantial barriers to decomposition. Tetradehydropyridynide C5N- is a highly strained ring system and metastable with a predicted barrier of about 5 kcal mol-1 (20 kJ mol-1) toward ring-opening to a linear NCCCCC- structure. The observed C5N- species is most likely the linear anion under experimental conditions; however, the ring-intact C5N- pyridynide is a highly energetic species releasing about 80 kcal mol-1 (340 kJ mol-1) of energy upon the ring-opening.

  14. 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.

  15. 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.

  16. Ion trap collision-induced dissociation of locked nucleic acids.

    PubMed

    Huang, Teng-yi; Kharlamova, Anastasia; McLuckey, Scott A

    2010-01-01

    Gas-phase dissociation of model locked nucleic acid (LNA) oligonucleotides and functional LNA-DNA chimeras have been investigated as a function of precursor ion charge state using ion trap collision-induced dissociation (CID). For the model LNA 5 and 8 mer, containing all four LNA monomers in the sequence, cleavage of all backbone bonds, generating a/w-, b/x-, c/y-, and d/z-ions, was observed with no significant preference at lower charge states. Base loss ions, except loss of thymine, from the cleavage of N-glycosidic bonds were also present. In general, complete sequence coverage was achieved in all charge states. For the two LNA-DNA chimeras, however, dramatic differences in the relative contributions of the competing dissociation channels were observed among different precursor ion charge states. At lower charge states, sequence information limited to the a-Base/w-fragment ions from cleavage of the 3'C-O bond of DNA nucleotides, except thymidine (dT), was acquired from CID of both the LNA gapmer and mixmer ions. On the other hand, extensive fragmentation from various dissociation channels was observed from post-ion/ion ion trap CID of the higher charge state ions of both LNA-DNA chimeras. This report demonstrates that tandem mass spectrometry is effective in the sequence characterization of LNA oligonucleotides and LNA-DNA chimeric therapeutics.

  17. Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation.

    PubMed

    Johnson, Andrew R; Carlson, Erin E

    2015-11-01

    Mass spectrometry is a powerful tool in natural product structure elucidation, but our ability to directly correlate fragmentation spectra to these structures lags far behind similar efforts in peptide sequencing and proteomics. Often, manual data interpretation is required and our knowledge of the expected fragmentation patterns for many scaffolds is limited, further complicating analysis. Here, we summarize advances in natural product structure elucidation based upon the application of collision induced dissociation fragmentation mechanisms.

  18. 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.

  19. Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization

    NASA Astrophysics Data System (ADS)

    Ropartz, David; Li, Pengfei; Fanuel, Mathieu; Giuliani, Alexandre; Rogniaux, Hélène; Jackson, Glen P.

    2016-08-01

    The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting.

  20. Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization.

    PubMed

    Ropartz, David; Li, Pengfei; Fanuel, Mathieu; Giuliani, Alexandre; Rogniaux, Hélène; Jackson, Glen P

    2016-10-01

    The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting. Graphical Abstract ᅟ. PMID:27582116

  1. Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization

    NASA Astrophysics Data System (ADS)

    Ropartz, David; Li, Pengfei; Fanuel, Mathieu; Giuliani, Alexandre; Rogniaux, Hélène; Jackson, Glen P.

    2016-10-01

    The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting.

  2. Infrared and collision-induced fragmentation of iron ethoxide cations

    NASA Astrophysics Data System (ADS)

    Kirkwood, D. A.; Stace, A. J.

    1997-12-01

    The multi-photon infrared photo-dissociation (MPD) of iron ethoxide cations of the general form Fe+(EtOH)m(EtO)n has been studied in an ion trap using a line tuneable CO2 laser. The ions exhibit very characteristic infrared absorption profiles which are shown to be quite different from those recorded for Fe+(EtOH)n cluster ions. From a comparison with solid state data, it is suggested that the mode responsible for absorption is a C---O stretch in the ethoxide group. To complement the interpretation of the MPD data, the collision-induced dissociation (CID) of the same series of ions was promoted by the application of a tickle voltage to the end caps of the ion trap. Both MPD and CID generate the same fragment ions, but the relative intensities are different. A detailed study of Fe+(EtOH)(EtO) using isotopes reveals fragmentation pathways leading primarily to the loss of H2, CH2O and CH3CHO, all of which can be accounted for via a series of insertion and radical transfer steps. Central to many of the reactions is an initial insertion step which results in the formation of HFe+(EtO)2.

  3. Photo- and collision-induced dissociation of Ar cluster ions

    NASA Astrophysics Data System (ADS)

    Kondow, Tamotsu; Nagata, Takeshi; Nonose, Shinji

    1992-04-01

    Photo- and collision- induced dissociation of an argon cluster ion, Arn+, were investigated by use of mass spectrometry. The kinetic and angular distributions of the ionic and neutral photofragments revealed two reaction pathways; dissociation of the trimeric core ion and evaporation from its solvation shell. In the Kr and Ne collisions with Arn+, the size- and collision energy- dependences of the dissociation cross sections were explained in the scheme of the charge - induced dipole, and induced dipole - induced dipole scatterings. Conversion efficiency of the collision energy into the internal energy of Arn+ was found to be proportional to the internal degrees of freedom. The upper limit of the conversion efficiency was estimated to be about 60 % in the collision energy of 0.2 eV.

  4. Collision induced fragmentation of small ionic argon clusters

    NASA Astrophysics Data System (ADS)

    Barat, M.; Brenot, J. C.; Fayeton, J. A.; Picard, Y. J.

    2002-07-01

    The mechanisms of collision induced fragmentation of small Arn+ (n=2-9) clusters are investigated in the 100 eV center-of-mass energy range. The velocity vectors of the fragments are measured in a multicoincidence experiment for two- and three-body fragmentation. The relative role of the two basic dynamics, electronic transitions, and momentum transfer in binary collisions is evaluated. The structure of the clusters deeply influences the type of mechanism. This is clearly the case of Ar3+ for which a specific impulsive process called "diatom" mechanism plays an important part in the fragmentation of one isomer.

  5. 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.

  6. Tandem Mass Spectrometry of Bilin Tetrapyrroles by Electrospray Ionization and Collision Induced Dissociation

    PubMed Central

    Quinn, Kevin D.; Nguyen, Nhu Q. T.; Wach, Michael M.; Wood, Troy D.

    2012-01-01

    Rationale Bilins are metabolic products of hosts and bacteria on porphyrins, and are markers of health state and human waste contamination. Although bilin tandem mass spectrometry reports exist, their fragmentation behavior as a function of structure has not been compared, nor has fragmentation been examined as a function of collision energy. Methods: The fragmentation of bilins generated by positive ion mode electrospray ionization is examined by collision induced dissociation (CID). CID on a quadrupole ion trap and on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer as a function of collision energy is compared. Methyl esterification was used to deduce which product ions contain the inner pyrrole rings. FT-ICR high mass accuracy measurements were used to determine the formulas of the resultant product ions. Results The central carbon’s bonding to the inner pyrrole rings influences fragmentation. Bilirubin is unique because fragmentation adjacent to the central methylene group between innermost rings predominates, and loss of a terminal pyrrole is observed only with helium collision gas. The other bilins lose the terminal pyrroles first; as CID energy is increased, additional fragmentation due to neutral losses of small molecules such as H2O, CO, CO2, and methanol occurs. Conclusions Based on these observations, fragmentation schemes for the bilins are proposed that are strongly dependent on the molecular structure and collision energy; only bilirubin fragmentation is influenced significantly by the collision gas used. This report should have value in identification of this class of molecules for biomarker detection. PMID:22777778

  7. Collision-induced dissociation of intact duplex and single-stranded siRNA anions.

    PubMed

    Huang, Teng-Yi; Liu, Jian; Liang, Xiaorong; Hodges, Brittany D M; McLuckey, Scott A

    2008-11-15

    A tandem mass spectrometry approach is demonstrated for complete sequencing of a model small interfering RNA (siRNA) based on ion trap collisional activation of intact single-stranded anions. Various charge states of the siRNA duplex and the individual strands were generated by nanoelectrospray (nano-ESI). The siRNA duplex anions were predominantly dissociated into the sense and antisense strands by collisional activation. The characteristic fragment ions (c/y- and a-B/w-ion series) from both strands were observed when higher activation amplitude was applied and when beam-type collisional activation was examined; however, the coexistence of fragment ions from both strands complicated spectral interpretation. The effect of precursor ion charge state on the dissociation of the individual sense and antisense strand siRNA anions was studied using ion trap collision-induced dissociation under various activation amplitudes. Through the activation of relatively low charge state precursor ions at relatively low excitation energy, selective backbone dissociation predominantly via the c/y channels was achieved. By applying relatively high excitation energy, the a-B/w channels also became prominent; however, the increase in spectral complexity made complete peak assignment difficult. In order to simplify the product ion spectra, proton-transfer reactions were applied, and complete sequencing of each strand was achieved. The application of tandem mass spectrometry to intact single-stranded anions demonstrated in this study can be adapted for the rapid identification of other noncoding RNAs in RNomics studies.

  8. 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.

  9. 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.

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Snyder, Dalton T.; Cooks, R. Graham

    2016-09-01

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

  13. 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.

  14. 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

  15. 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

  16. Electrospray ionization and collision induced dissociation mass spectrometry of primary fatty acid amides.

    PubMed

    Divito, Erin B; Davic, Andrew P; Johnson, Mitchell E; Cascio, Michael

    2012-03-01

    Primary fatty acid amides are a group of bioactive lipids that have been linked with a variety of biological processes such as sleep regulation and modulation of monoaminergic systems. As novel forms of these molecules continue to be discovered, more emphasis will be placed on selective, trace detection. Currently, there is no published experimental determination of collision induced dissociation of PFAMs. A select group of PFAM standards, 12 to 22 length carbon chains, were directly infused into an electrospray ionization source Quadrupole Time of Flight Mass Spectrometer. All standards were monitored in positive mode using the [M + H](+) peak. Mass Hunter Qualitative Analysis software was used to calculate empirical formulas of the product ions. All PFAMs showed losses of 14 m/z indicative of an acyl chain, while the monounsaturated group displayed neutral losses corresponding to H(2)O and NH(3). The resulting spectra were used to propose fragmentation mechanisms. Isotopically labeled PFAMs were used to validate the proposed mechanisms. Patterns of saturated versus unsaturated standards were distinctive, allowing for simple differentiation. This determination will allow for fast, qualitative identification of PFAMs. Additionally, it will provide a method development tool for selection of unique product ions when analyzed in multiple reaction monitoring mode.

  17. Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculation.

    PubMed

    Pak, Alireza; Lesage, Denis; Gimbert, Yves; Vékey, Károly; Tabet, Jean-Claude

    2008-04-01

    The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values () carried by desolvated ions. These mean internal energy values seem to be slightly dependent on the size of the studied ion. ESI mass spectra and CID spectra were then simulated using the MassKinetics software to propose an empirical equation for the mean internal energy () versus cone voltage (V(c)) for different source temperatures (T): < E(int) > = [405 x 10(-6) - 480 x 10(-9) (DOF)] V(c)T + E(therm)(T). In this equation, the E(therm)(T) parameter is the mean internal energy due to the source temperature at 0 V(c).

  18. 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.

  19. Electron Transfer and Collision Induced Dissociation of Non-Derivatized and Derivatized Desmosine and Isodesmosine

    NASA Astrophysics Data System (ADS)

    Ongay, Sara; Hermans, Jos; Bruins, Andries P.; Nieuwendijk, Adrianus M. C. H.; Overkleeft, Hermen; Bischoff, Rainer

    2013-01-01

    Electron transfer dissociation (ETD) has attracted increasing interest due to its complementarity to collision-induced dissociation (CID). ETD allows the direct localization of labile post-translational modifications, which is of main interest in proteomics where differences and similarities between ETD and CID have been widely studied. However, due to the fact that ETD requires precursor ions to carry at least two charges, little is known about differences in ETD and CID of small molecules such as metabolites. In this work, ETD and CID of desmosine (DES) and isodesmosine (IDS), two isomers that due to the presence of a pyridinium group can carry two charges after protonation, are studied and compared. In addition, the influence of DES/IDS derivatization with propionic anhydride and polyethyleneglycol (PEG) reagents on ETD and CID was studied, since this is a common strategy to increase sensitivity and to facilitate the analysis by reversed-phase chromatography. Clear differences between ETD and CID of non-derivatized and derivatized-DES/IDS were observed. While CID is mainly attributable to charge-directed fragmentation, ETD is initiated by the generation of a hydrogen atom at the initial protonation site and its subsequent transfer to the pyridinium ring of DES/IDS. These differences are reflected in the generation of complex CID spectra dominated by the loss of small, noninformative molecules (NH3, CO, H2O), while ETD spectra are simpler and dominated by characteristic side-chain losses. This constitutes a potential advantage of ETD in comparison to CID when employed for the targeted analysis of DES/IDS in biological samples.

  20. 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).

  1. Matrix-assisted laser desorption/ionization mass spectrometry of neutral and acidic oligosaccharides with collision-induced dissociation.

    PubMed

    Mechref, Y; Baker, A G; Novotny, M V

    1998-12-15

    Using ribonuclease B and human alpha 1-acid glycoprotein (AGP) as model glycoproteins, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry with collision-induced dissociation (CID) is validated here as an effective tool for oligosaccharide sequencing. The spectra acquired for high-mannose and complex oligosaccharide structures show characteristic fragments resulting from cleavages of the glycosidic bonds and a few cross-ring cleavages. Esterification of the sialic acid residues is essential in stabilizing the acidic N-linked oligosaccharides. An important analytical feature observed in all acquired spectra is the occurrence of cleavages on the same antenna up to the branching point, as deduced from the absence of fragmentation due to the simultaneous cleavages on two or more antennas.

  2. Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments.

    PubMed

    Molina, Estefanía Rossich; Ortiz, Daniel; Salpin, Jean-Yves; Spezia, Riccardo

    2015-12-01

    In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

  3. 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.

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

    SciTech Connect

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

    2010-06-01

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

  5. Chiral Differentiation of Amino Acids by In-Source Collision-Induced Dissociation Mass Spectrometry.

    PubMed

    Kong, Xianglei; Huo, Zhaiyi; Zhai, Wei

    2014-01-01

    Chiral recognition of d- and l-amino acids is achieved by a method combining electrospray ionization (ESI) and in-source collision-induced dissociation (CID) mass spectrometry (MS). Trimeric cluster ions [Cu(II)(A)(ref)2-H](+) are formed by ESI of mixtures of d- or l-analyte amino acid (A), chiral reference (ref) and CuSO4. By increasing the applied voltage in the ESI source region, the trimeric ions become unstable and dissociate progressively. Thus chiral differentiation of the analyte can be achieved by comparing the dependence of their relative intensities to a reference ion on applied voltages. The method does not need MS/MS technique, thus can be readily performed on single-stage MS instruments by turning the voltage of sampling cone.

  6. Collision-induced dissociation (CID) of guanine radical cation in the gas phase: an experimental and computational study.

    PubMed

    Cheng, Ping; Li, Yanni; Li, Shuqi; Zhang, Mingtao; Zhou, Zhen

    2010-05-14

    Gas-phase guanine (G) radical cations were generated by electrospraying a solution of guanosine (L) and Cu(NO(3))(2). Collision-induced dissociation (CID) for guanine radical cations yielded five competing dissociation channels, corresponding to the elimination neutral molecules of NH(3), HCN, H(2)NC[triple bond]N (HN=C=NH), HNCO and the neutral radical N=C=NH, respectively. The primary product ions were further characterized by their relevant fragmentions. Ab initio and density functional theory (DFT) calculations were employed to explain the experimental observations. Ten stable radical cation isomers were optimized and the potential energy surfaces (PESs) for the isomerization processes were explored in detail. Starting with the most stable isomer, the primary dissociation channels of guanine radical cations were theoretically investigated. DFT calculations show that the energy barriers for the eliminations of NH(3), HCN, H(2)NC[triple bond]N (HN=C=NH), HNCO and N=C=NH are 397 kJ mol(-1), 479 kJ mol(-1), 294 kJ mol(-1) (298 kJ mol(-1)), 306 kJ mol(-1), and 275 kJ mol(-1), respectively. The results are consistent with the energy-resolved CID of guanine radical cation, in which the eliminations of NH(3) and HCN are less abundant than the other channels. PMID:20428546

  7. Threshold collision-induced dissociation of hydrogen-bonded dimers of carboxylic acids.

    PubMed

    Jia, Beike; Angel, Laurence A; Ervin, Kent M

    2008-02-28

    Energy-resolved competitive collision-induced dissociation is used to investigate the proton-bound heterodimer anions of a series of carboxylic acids (formic, acetic, and benzoic acid) and nitrous acid with their conjugate bases. The dissociation reactions of the complexes [CH3COO.H.OOCH]-, [CH3COO.H.ONO]-, [HCOO.H. ONO]-, [C6H5COO.H.OOCH]-, and [C6H5COO.H.ONO]- are investigated using a guided ion beam tandem mass spectrometer. Cross sections of the two dissociation channels are measured as a function of the collision energy between the complex ions and xenon target gas. Apparent relative gas-phase acidities are found by modeling the cross sections near the dissociation thresholds using statistical rate theory. Internal inconsistencies are found in the resulting relative acidities. These deviations apparently result from the formation of higher-energy conformers of the acids within the complex ions induced by double hydrogen bonding, which impedes the kinetics of dissociation to ground-state product acid conformations.

  8. 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.

  9. Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

    NASA Astrophysics Data System (ADS)

    Beach, Daniel G.; Gabryelski, Wojciech

    2012-05-01

    In our recent work towards the nontarget identification of products of nucleic acid (NA) damage in urine, we have found previous work describing the dissociation of NA bases not adequate to fully explain their observed reactivity. Here we revisit the gas-phase chemistry of protonated uracil (U) during collision induced dissociation (CID) using two modern tandem mass spectrometry techniques; quadrupole ion trap (QIT) and quadrupole time of flight (Q-TOF). We present detailed mechanistic proposals that account for all observed products of our experiments and from previous isotope labeling data, and that are supported by previous ion spectroscopy results and theoretical work. The diverse product-ions of U cannot be explained adequately by only considering the lowest energy form of protonated U as a precursor. The tautomers adopted by U during collisional excitation make it possible to relate the complex reactivity observed to reasonable mechanistic proposals and feasible product-ion structures for this small highly conjugated heterocycle. These reactions proceed from four different stable tautomers, which are excited to a specific activated precursor from which dissociation can occur via a charge-directed process through a favorable transition state to give a stabilized product. Understanding the chemistry of uracil at this level will facilitate the identification of new modified uracil derivatives in biological samples based solely on their reactivity during CID. Our integrated approach to describing ion dissociation is widely applicable to other NA bases and similar classes of biomolecules.

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

    PubMed Central

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

    2014-01-01

    An ion mobility/time-of-flight mass spectrometer (IMS/TOF MS) platform that allows for resonant excitation collision induced dissociation (CID) is presented. Highly efficient, mass-resolved fragmentation without additional excitation of product ions was accomplished and over-fragmentation common in beam-type CID experiments was alleviated. A quadrupole ion guide was modified to apply a dipolar AC signal across a pair of rods for resonant excitation. The method was characterized with singly protonated methionine enkephalin and triply protonated peptide angiotensin I, yielding maximum CID efficiencies of 44% and 84%, respectively. The Mathieu qx,y parameter was set at 0.707 for these experiments to maximize pseudopotential well depths and CID efficiencies. Resonant excitation CID was compared to beam-type CID for the peptide mixture. The ability to apply resonant waveforms in mobility-resolved windows is demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS-MS analysis. PMID:24470195

  11. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    An ion mobility/time-of-flight mass spectrometer (IMS/TOF MS) platform that allows for resonant excitation collision induced dissociation (CID) is presented. Highly efficient, mass-resolved fragmentation without additional excitation of product ions was accomplished and over-fragmentation common in beam-type CID experiments was alleviated. A quadrupole ion guide was modified to apply a dipolar AC signal across a pair of rods for resonant excitation. The method was characterized with singly protonated methionine enkephalin and triply protonated peptide angiotensin I, yielding maximum CID efficiencies of 44 % and 84 %, respectively. The Mathieu qx,y parameter was set at 0.707 for these experiments to maximize pseudopotential well depths and CID efficiencies. Resonant excitation CID was compared with beam-type CID for the peptide mixture. The ability to apply resonant waveforms in mobility-resolved windows is demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge ( m/ z) ratios within a single IMS-MS analysis.

  13. Collision induced dissociation study of azobenzene and its derivatives: computational and experimental results

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    2015-03-01

    Experimental and computational investigation have been performed in order to study the bond dissociation energy of azobenzene and its derivatives using collision induced dissociation method as well as other energy and structural characteristics. The results have been verified by comparing with results obtained from computational quantum chemistry. We used different density functional methods as well as the Möller-Plesset perturbation theory and the coupled cluster methods to explore geometric, electronic and the spectral properties of the sample molecules. Geometries were calculated and optimized using the 6-311 + + G(2d,2p) basis set and the B3LYP level of theory and these optimized structures have been subjected to the frequency calculations to obtain thermochemical properties by means of different density functional, Möller-Plesset, and coupled cluster theories to obtain a high accuracy estimation of the bond dissociation energy value. The results from experiments and the results obtained from computational thermochemistry are in close agreement. Physics and Astronomy Department

  14. Resonance activation and collision-induced-dissociation of ions using rectangular wave dipolar potentials in a digital ion trap mass spectrometer.

    PubMed

    Xu, Fuxing; Wang, Liang; Dai, Xinhua; Fang, Xiang; Ding, Chuan-Fan

    2014-04-01

    Collision-induced dissociation (CID) of ions by resonance activation in a quadrupole ion trap is usually accomplished by resonance exciting the ions to higher kinetic energy, whereby the high kinetic energy ions collide with a bath gas, such as helium or argon, inside the trap and dissociate to fragments. A new ion activation method using a well-defined rectangular wave dipolar potential formed by dividing down the trapping rectangular waveform is developed and examined herein. The mass-selected parent ions are resonance excited to high kinetic energies by simply changing the frequency of the rectangular wave dipolar potential and dissociation proceeds. A relationship between the ion mass and the activation waveform frequency is also identified and described. This highly efficient (CID) procedure can be realized by simply changing the waveform frequency of the dipolar potential, which could certainly simplify tandem mass spectrometry analysis methods.

  15. Electrospray ionization collision-induced dissociation mass spectrometry: a tool to characterize synthetic polyaminocarboxylate ferric chelates used as fertilizers.

    PubMed

    Orera, Irene; Orduna, Jesús; Abadía, Javier; Alvarez-Fernández, Ana

    2010-01-01

    Fertilizers based on synthetic polyaminocarboxylate ferric chelates have been known since the 1950s to be successful in supplying Fe to plants. In commercial Fe(III)-chelate fertilizers, a significant part of the water-soluble Fe-fraction consists of still uncharacterized Fe byproducts, whose agronomical value is unknown. Although collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) is a valuable tool for the identification of such compounds, no fragmentation data have been reported for most Fe(III)-chelate fertilizers. The aim of this study was to characterize the CID-MS(2) fragmentation patterns of the major synthetic Fe(III)-chelates used as Fe-fertilizers, and subsequently use this technique for the characterization of commercial fertilizers. Quadrupole-time-of-flight (QTOF) and spherical ion trap mass analyzers equipped with an electrospray ionization (ESI) source were used. ESI-CID-MS(2) spectra obtained were richer when using the QTOF device. Specific differences were found among Fe(III)-chelate fragmentation patterns, even in the case of positional isomers. The analysis of a commercial Fe(III)-chelate fertilizer by high-performance liquid chromatography (HPLC) coupled to ESI-MS(QTOF) revealed two previously unknown, Fe-containing compounds, that were successfully identified by a comprehensive comparison of the ESI-CID-MS(2)(QTOF) spectra with those of pure chelates. This shows that HPLC/ESI-CID-MS(2)(QTOF), along with the Fe(III)-chelate fragmentation patterns, could be a highly valuable tool to directly characterize the water-soluble Fe fraction in Fe(III)-chelate fertilizers. This could be of great importance in issues related to crop Fe-fertilization, both from an agricultural and an environmental point of view.

  16. Strategy to improve the quantitative LC-MS analysis of molecular ions resistant to gas-phase collision induced dissociation: application to disulfide-rich cyclic peptides.

    PubMed

    Ciccimaro, Eugene; Ranasinghe, Asoka; D'Arienzo, Celia; Xu, Carrie; Onorato, Joelle; Drexler, Dieter M; Josephs, Jonathan L; Poss, Michael; Olah, Timothy

    2014-12-01

    Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

  17. 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.

  18. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Brown, Robert; Stuart, Scott S.; Houel, Stephane; Ahn, Natalie G.; Old, William M.

    2015-07-01

    Collision-induced dissociation (CID) remains the predominant mass spectrometry-based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust nonparametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably because of steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline, which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra, the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss.

  19. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation.

    PubMed

    Brown, Robert; Stuart, Scott A; Stuart, Scott S; Houel, Stephane; Ahn, Natalie G; Old, William M

    2015-07-01

    Collision-induced dissociation (CID) remains the predominant mass spectrometry-based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust nonparametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably because of steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline, which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra, the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss.

  20. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

    PubMed Central

    Brown, Robert; Stuart, Scott A.; Houel, Stephane; Ahn, Natalie G.; Old, William M.

    2015-01-01

    Collision-induced dissociation (CID) remains the predominant mass spectrometry based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust non-parametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably due to steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss. PMID:25851653

  1. Competitive threshold collision-induced dissociation: Gas-phase acidities and bond dissociation energies for a series of alcohols

    SciTech Connect

    DeTuri, V.F.; Ervin, K.M.

    1999-09-02

    Energy-resolved competitive collision-induced dissociation methods are used to measure the gas-phase acidities of a series of alcohols (methanol, ethanol, 2-propanol, and 2-methyl-2-propanol). The competitive dissociation reactions of fluoride-alcohol, [F{sup {minus}}{center{underscore}dot}HOR], alkoxide-water, [RO{sup {minus}}{center{underscore}dot}HOH], and alkoxide-methanol [RO{+-}{center{underscore}dot}HOCH{sub 3}] proton-bound complexes are studied using a guided ion beam tandem mass spectrometer. The reaction cross sections and product branching fractions to the two proton transfer channels are measured as a function of collision energy. The enthalpy difference between the two product channels is found by modeling the reaction cross sections near threshold using RRKM theory to account for the energy-dependent product branching ratio and kinetic shift. From the enthalpy difference, the alcohol gas-phase acidities are determined relative to the well-known values of HF and H{sub 2}O. The measured gas-phase acidities are {Delta}{sub acid}H{sub 298}(CH{sub 3}OH) = 1599 {+-} 3 kJ/mol, {Delta}{sub acid}H{sub 298}(CH{sub 3}CH{sub 2}OH) = 1586 {+-} 5 kJ/mol, {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 2}CHOH) = 1576 {+-} 4 kJ/mol, and {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 3}COH) = 1573 {+-} 3 kJ/mol.

  2. 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

  3. 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

  4. 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

  5. Enhancement of Ion Activation and Collision-Induced Dissociation by Simultaneous Dipolar Excitation of Ions in x- and y-Directions in a Linear Ion Trap.

    PubMed

    Dang, Qiankun; Xu, Fuxing; Xie, Xiaodong; Xu, Chongsheng; Dai, Xinhua; Fang, Xiang; Ding, Li; Ding, Chuan-Fan

    2015-06-01

    Collision-induced dissociation (CID) in linear ion traps is usually performed by applying a dipolar alternating current (AC) signal to one pair of electrodes, which results in ion excitation mainly in one direction. In this paper, we report simulation and experimental studies of the ion excitation in two coordinate directions by applying identical dipolar AC signals to two pairs of electrodes simultaneously. Theoretical analysis and simulation results demonstrate that the ion kinetic energy is higher than that using the conventional CID method. Experimental results show that more activation energy (as determined by the intensity ratio of the a4/b4 fragments from the CID of protonated leucine enkephalin) can be deposited into parent ions in this method. The dissociation rate constant in this method was about 3.8 times higher than that in the conventional method under the same experimental condition, at the Mathieu parameter qu (where u = x, y) value of 0.25. The ion fragmentation efficiency is also significantly improved. Compared with the conventional method, the smaller qu value can be used in this method to obtain the same internal energy deposited into ions. Consequently, the "low mass cut-off" is redeemed and more fragment ions can be detected. This excitation method can be implemented easily without changing any experimental parameters.

  6. Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification.

    PubMed

    Zinnel, Nathanael F; Russell, David H

    2014-05-20

    Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.

  7. Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Schachel, Tilo D.; Metwally, Haidy; Popa, Vlad; Konermann, Lars

    2016-11-01

    Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na( n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase.

  8. Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Schachel, Tilo D.; Metwally, Haidy; Popa, Vlad; Konermann, Lars

    2016-09-01

    Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na(n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase.

  9. Effect of the reducing-terminal substituents on the high energy collision-induced dissociation matrix-assisted laser desorption/ionization mass spectra of oligosaccharides.

    PubMed

    Küster, B; Naven, T J; Harvey, D J

    1996-01-01

    High-energy collision-induced dissociation (CID) matrix-assisted laser desorption/ionization mass spectra of N-linked oligosaccharides bearing different, commonly encountered, reducing terminal modifications (hydroxyl, 2-aminobenzamide, asparagine and a tetrapeptide) were recorded on a magnetic sector instrument equipped with an orthogonal-acceleration time-of-flight (OA-TOF) analyser. All the compounds formed abundant molecular (MNa+) and fragment ions, the latter corresponding to glycosidic and cross-ring cleavages as well as to internal fragment ions, all of which provided much insight into the oligosaccharide structure. The nature of the modification considerably influenced the CID behaviour. The strongest and most complete series of glycosidic cleavage ions (mainly Y and B--Domon and Costello nomenclature) was formed by the underivatized oligosaccharide whereas most cross-ring fragment ions, diagnostic of linkage, were found in the spectra of the glycopeptides. A-type cross-ring cleavage ions were particularly abundant in the spectrum of the asparagine derivative. Reductive amination using 2-aminobenzamide resulted in an opened reducing-terminal sugar ring and suppression of the cross-ring fragment ions carrying information associated with that ring. This information was present in the spectra of the free carbohydrate and the peptide derivatives. PMID:8914337

  10. 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.

  11. Linkage determination of linear oligosaccharides by MS(n) (n > 2) collision-induced dissociation of Z₁ ions in the negative ion mode.

    PubMed

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2014-02-01

    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 (MS(n), n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides (18)O-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. MS(3) 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 MS(n) 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.

  12. 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

    2013-07-02

    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

  13. Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB.

    PubMed

    Miracco, Edward J; Bogdanov, Bogdan; Mueller, Eugene G

    2011-09-30

    As part of the investigation of the pseudouridine synthases, 5-fluorouridine in RNA was employed as a mechanistic probe. The hydrated, rearranged product of 5-fluorouridine was isolated as part of a dinucleotide and found to undergo unusual fragmentation during mass spectrometry, with the facile loss of HNCO from the product pyrimidine ring favored over phosphodiester bond rupture. Although the loss of HNCO from uridine and pseudouridine is well established, the pericyclic process leading to their fragmentation cannot operate with the saturated pyrimidine ring in the product of 5-fluorouridine. Based on the MS(n) results and calculations reported here, a new mechanism relying on the peculiar disposition of the functional groups of the product pyrimidine ring is proposed to account for the unusually facile fragmentation.

  14. Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB.

    PubMed

    Miracco, Edward J; Bogdanov, Bogdan; Mueller, Eugene G

    2011-09-30

    As part of the investigation of the pseudouridine synthases, 5-fluorouridine in RNA was employed as a mechanistic probe. The hydrated, rearranged product of 5-fluorouridine was isolated as part of a dinucleotide and found to undergo unusual fragmentation during mass spectrometry, with the facile loss of HNCO from the product pyrimidine ring favored over phosphodiester bond rupture. Although the loss of HNCO from uridine and pseudouridine is well established, the pericyclic process leading to their fragmentation cannot operate with the saturated pyrimidine ring in the product of 5-fluorouridine. Based on the MS(n) results and calculations reported here, a new mechanism relying on the peculiar disposition of the functional groups of the product pyrimidine ring is proposed to account for the unusually facile fragmentation. PMID:23657957

  15. Fatty acid neutral losses observed in tandem mass spectrometry with collision-induced dissociation allows regiochemical assignment of sulfoquinovosyl-diacylglycerols.

    PubMed

    Zianni, Rosalia; Bianco, Giuliana; Lelario, Filomena; Losito, Ilario; Palmisano, Francesco; Cataldi, Tommaso R I

    2013-02-01

    A full characterization of sulfoquinovosyldiacylglycerols (SQDGs) in the lipid extract of spinach leaves has been achieved using liquid chromatography/electrospray ionization-linear quadrupole ion trap mass spectrometry (MS). Low-energy collision-induced dissociation tandem MS (MS/MS) of the deprotonated species [M - H](-) was exploited for a detailed study of sulfolipid fragmentation. Losses of neutral fatty acids from the acyl side chains (i.e. [M - H - RCOOH](-)) were found to prevail over ketene losses ([M - H - R'CHCO](-)) or carboxylates of long-chain fatty acids ([RCOO](-)), as expected for gas-phase acidity of SQDG ions. A new concerted mechanism for RCOOH elimination, based on a charge-remote fragmentation, is proposed. The preferential loss of a fatty acids molecule from the sn-1 position (i.e. [M - H - R(1)COOH](-)) of the glycerol backbone, most likely due to kinetic control of the gas-phase fragmentation process, was exploited for the regiochemical assignment of the investigated sulfolipids. As a result, 24 SQDGs were detected and identified in the lipid extract of spinach leaves, their number and variety being unprecedented in the field of plant sulfolipids. Moreover, the prevailing presence of a palmitic acyl chain (16:0) on the glycerol sn-2 position of spinach SQDGs suggests a prokaryotic or chloroplastic path as the main route for their biosynthesis.

  16. Tandem mass spectrometric characterization of bile acids and steroid conjugates based on low-energy collision-induced dissociation.

    PubMed

    Maekawa, Masamitsu; Shimada, Miki; Iida, Takashi; Goto, Junichi; Mano, Nariyasu

    2014-02-01

    We examined the characteristics of several bile acids and some steroid conjugates under low-energy-collision-induced dissociation conditions using a triple quadrupole tandem mass spectrometer. According to conjugation types, we observed characteristic product ions and/or neutral losses in the product ion spectra. Amino acid conjugates afforded specific product ions. For example, glycine-conjugated metabolites routinely produced a product ion at m/z 74, and taurine-conjugated metabolites produced product ions at m/z 124, 107, and 80. When a strong peak appeared at m/z 97, the molecule contained a sulfate group. In contrast to amino acid conjugates, carbohydrate conjugates required a combination of product ions and neutral losses for identification. We could discriminate a glucoside from an acyl galactoside according to the presence or absence of a product ion at m/z 161 and a neutral loss of 180 Da. Discrimination among esters, aliphatic ethers, and phenolic ether types of glucuronides was based upon differences in the intensities of a product ion at m/z 175 and a neutral loss of 176 Da. Furthermore, N-acetylglucosamine conjugates showed a characteristic product ion at m/z 202 and a neutral loss of 203 Da, and the appearance of a product ion at m/z 202 revealed the existence of N-acetylglucosamine conjugated to an aliphatic hydroxyl group without a double bond in the immediate vicinity. Together, the data presented here will help to enable the identification of unknown conjugated cholesterol metabolites by using low-energy collision-induced dissociation.

  17. A comparison of the effects of amide and acid groups at the C-terminus on the collision-induced dissociation of deprotonated peptides.

    PubMed

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

    2012-09-01

    The dissociative behavior of peptide amides and free acids was explored using low-energy collision-induced dissociation and high level computational theory. Both positive and negative ion modes were utilized, but the most profound differences were observed for the deprotonated species. Deprotonated peptide amides produce a characteristic c(m-2)(-) product ion (where m is the number of residues in the peptide) that is either absent or in low abundance in the analogous peptide acid spectrum. Peptide acids show an enhanced formation of c(m-3)(-); however, this is not generally as pronounced as c(m-2)(-) production from amides. The most notable occurrence of an amide-specific product ion is for laminin amide (YIGSR-NH(2)) and this case was investigated using several modified peptides. Mechanisms involving 6- and 9-membered ring formation were proposed, and their energetic properties were investigated using G3(MP2) molecular orbital theory calculations. For example, with C-terminal deprotonation of pentaglycine amide, formation of c(m-2)(-) and a 6-membered ring diketopiperazine neutral requires >31.6 kcal/mol, which is 26.1 kcal/mol less than the analogous process involving the peptide acid. The end group specific fragmentation of peptide amides in the negative ion mode may be useful for identifying such groups in proteomic applications.

  18. A Comparison of the Effects of Amide and Acid Groups at the C-Terminus on the Collision-Induced Dissociation of Deprotonated Peptides

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    The dissociative behavior of peptide amides and free acids was explored using low-energy collision-induced dissociation and high level computational theory. Both positive and negative ion modes were utilized, but the most profound differences were observed for the deprotonated species. Deprotonated peptide amides produce a characteristic cm-2 - product ion (where m is the number of residues in the peptide) that is either absent or in low abundance in the analogous peptide acid spectrum. Peptide acids show an enhanced formation of cm-3 -; however, this is not generally as pronounced as cm-2 - production from amides. The most notable occurrence of an amide-specific product ion is for laminin amide (YIGSR-NH2) and this case was investigated using several modified peptides. Mechanisms involving 6- and 9-membered ring formation were proposed, and their energetic properties were investigated using G3(MP2) molecular orbital theory calculations. For example, with C-terminal deprotonation of pentaglycine amide, formation of cm-2 - and a 6-membered ring diketopiperazine neutral requires >31.6 kcal/mol, which is 26.1 kcal/mol less than the analogous process involving the peptide acid. The end group specific fragmentation of peptide amides in the negative ion mode may be useful for identifying such groups in proteomic applications.

  19. 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.

  20. Fragmentation of singly, doubly, and triply charged hydrogen deficient peptide radical cations in infrared multiphoton dissociation and electron induced dissociation.

    PubMed

    Kalli, Anastasia; Hess, Sonja

    2012-02-01

    Gas phase fragmentation of hydrogen deficient peptide radical cations continues to be an active area of research. While collision induced dissociation (CID) of singly charged species is widely examined, dissociation channels of singly and multiply charged radical cations in infrared multiphoton dissociation (IRMPD) and electron induced dissociation (EID) have not been, so far, investigated. Here, we report on the gas phase dissociation of singly, doubly and triply charged hydrogen deficient peptide radicals, [M + nH]((n+1)+·) (n=0, 1, 2), in MS(3) IRMPD and EID and compare the observed fragmentation pathways to those obtained in MS(3) CID. Backbone fragmentation in MS(3) IRMPD and EID was highly dependent on the charge state of the radical precursor ions, whereas amino acid side chain cleavages were largely independent of the charge state selected for fragmentation. Cleavages at aromatic amino acids, either through side chain loss or backbone fragmentation, were significantly enhanced over other dissociation channels. For singly charged species, the MS(3) IRMPD and EID spectra were mainly governed by radical-driven dissociation. Fragmentation of doubly and triply charged radical cations proceeded through both radical- and charge-driven processes, resulting in the formation of a wide range of backbone product ions including, a-, b-, c-, y-, x-, and z-type. While similarities existed between MS(3) CID, IRMPD, and EID of the same species, several backbone product ions and side chain losses were unique for each activation method. Furthermore, dominant dissociation pathways in each spectrum were dependent on ion activation method, amino acid composition, and charge state selected for fragmentation.

  1. Unimolecular and collision-induced dissociation of Ar/sub 2/ /sup +/ produced by electron ionization of Ar/sub 2/

    SciTech Connect

    Stephan, K.; Stamatovic, A.; Mark, T.D.

    1983-11-01

    Unimolecular and collision-induced dissociation of Ar/sub 2/ /sup +/ produced by electron-impact ionization of Ar/sub 2/ were studied quantitatively with a double-focusing mass spectrometer. The occurrence of the metastable dissociation process Ar/sub 2/ /sup +asterisk/..-->..Ar/sup +/+Ar is interpreted qualitatively in terms of potential-energy curves calculated recently using quantum-mechanical methods.

  2. 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

  3. High-energy collision induced dissociation of biomolecules: MALDI-TOF/RTOF mass spectrometry in comparison to tandem sector mass spectrometry.

    PubMed

    Pittenauer, Ernst; Allmaier, Günter

    2009-02-01

    MALDI in combination with high-energy collision-induced dissociation (CID) performed by tandem time-of-flight mass spectrometry (TOF/RTOF) is a relatively new technology for the structural analysis of various classes of biomolecules as e.g., peptides, carbohydrates, glycoconjugate drugs and lipids. Fragmentation mechanisms for these classes of compounds as well as corresponding fragment ion nomenclatures based mainly on data from tandem magnetic sector mass spectrometers are summarized in this article. The major instrumental differences between the present commercially available TOF/RTOFs are compiled (e.g., ion gate, gas-collision cell, type of reflectron, etc.). Whereas peptides have been investigated by MALDI-TOF/RTOF and their CID spectra are well understood, other classes of compounds (e.g., carbohydrates or lipids) are far less well investigated. By comparing data from two different MALDI-TOF/RTOF-instruments, it becomes evident that as they are operated at rather different collision energies for CID (1 versus 20 keV) strong differences in corresponding CID spectra for the same analyte are observed, causing problems with library searches in databases as e.g., abundant peptide side-chain fragmentations mainly occurring in the 8 to 20 keV collision regime are not considered. In contrast, differences in CID spectra of carbohydrates among different TOF/RTOF instruments are less clear-cut, because the required collision energy is spread across a wide range. Especially, carbohydrate cross-ring cleavages require less collision energy in the keV-range than the corresponding peptide side-chain fragmentations. Some of these carbohydrate cross-ring fragmentations are even observed by very low energy CID (< 1 eV fragmentation amplitude). Similar observations can also be made for glycoconjugates (e.g., the drug tylosin A). The lipid class triacylglycerol needs rather high collision energies for dissociating carbon-carbon bonds based upon classical charge

  4. 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.

  5. Nonuniform isotope patterns produced by collision-induced dissociation of homogeneously labeled ubiquitin: implications for spatially resolved hydrogen/deuterium exchange ESI-MS studies.

    PubMed

    Ferguson, Peter L; Konermann, Lars

    2008-06-01

    There is an ongoing debate whether collision-induced dissociation (CID) of electrosprayed proteins after solution-phase hydrogen/deuterium exchange (HDX) is a viable approach for determining spatially resolved deuteration patterns. This work explores the use of two methods, source-CID and hexapole tandem mass spectrometry (MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer, for measuring the fragment deuteration levels of regioselectively labeled ubiquitin. Both methods reveal that b-ions exhibit HDX levels significantly below that of the intact protein, whereas several y'' fragments are labeled to a much greater extent. These results are consistent with earlier source-CID data (Akashi, S.; Naito, Y.; Takio, K. Anal. Chem. 1999, 71, 4974-4980). However, the measured b-ion deuteration levels are in disagreement with the known solution-phase behavior of ubiquitin. Partial agreement is observed for y''-ions. Control experiments on homogeneously labeled ubiquitin (having the same average deuteration level at every exchangeable site) result in highly nonuniform fragment HDX levels. In particular, b-ions exhibit deuteration levels significantly below that of intact ubiquitin, thereby mimicking the behavior seen for the regioselectively labeled protein. This effect is likely caused by isotope fractionation during collisional activation, facilitated by the high mobility of charge carriers (scrambling) in the gas phase. The observation that the b-ion labeling behavior is largely independent of the spatial isotope distribution within solution-phase ubiquitin invalidates these ions as reporters of the protein deuteration pattern. This work questions the common practice of interpreting any nonuniformities in fragment deuteration as being indicative of regioselective solution-phase labeling. Artifactual deuterium enrichment or depletion during collisional activation may have contributed to the current lack of consensus as to whether HDX/CID represents a potentially

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. DART-MS in-source collision induced dissociation and high mass accuracy for new psychoactive substance determinations.

    PubMed

    Musah, Rabi A; Cody, Robert B; Domin, Marek A; Lesiak, Ashton D; Dane, A John; Shepard, Jason R E

    2014-11-01

    The influx of new psychoactive substances is a problem that is challenging the analytical capabilities of enforcement agencies. Cathinone designer drugs are less likely to be included in routine drug screens and typical drug formulations are commonly mixtures with continually shifting components. Ambient ionization mass spectrometry employs relatively mild conditions to desorb and ionize solid samples, imparting much less energy than that associated with conventional mass spectrometry methods. Direct analysis in real time mass spectrometry (DART-MS) is an ambient ionization method that was employed to rapidly screen cathinones, alone and in mixtures, readily enabling differentiation of the active drug(s) from various cutting agents. Accurate mass determinations provided preliminary identification of the various components of drug mixtures. The data generated in forensic mass spectrometry can be used for both elemental composition formulations and isotope abundance calculations for determination of unknown psychoactive substances, and we demonstrate how this data could be applied to the presence of new drugs as the active components shift in response to regulations. Isotope abundance calculations were used to develop a candidate pool of possible molecular formulas associated with cathinones as a specific class of designer drugs. Together, the combination of a time-of-flight (TOF) mass analyzer along with in-source collision-induced dissociation (CID) spectra were used to drastically narrow the pool of candidates to a single molecular formula. The [M+H](+) and product ion peaks provided data for presumptive analysis of various substituted synthetic cathinones in a manner that is complementary to conventional GC-MS analysis of new psychoactive substances.

  13. 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.

  14. 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

  15. 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

  16. 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

    2015-07-20

    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.

  17. Towards understanding the tandem mass spectra of protonated oligopeptides. 2: The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp).

    PubMed

    Bleiholder, Christian; Suhai, Sándor; Harrison, Alex G; Paizs, Béla

    2011-06-01

    The product ion spectra of proline-containing peptides are commonly dominated by y(n) ions generated by cleavage at the N-terminal side of proline residues. This proline effect is investigated in the current work by collision-induced dissociation (CID) of protonated Ala-Ala-Xxx-Pro-Ala (Xxx includes Ala, Ser, Leu, Val, Phe, and Trp) in an electrospray/quadrupole/time-of-flight (QqTOF) mass spectrometer and by quantum chemical calculations on protonated Ala-Ala-Ala-Pro-Ala. The CID spectra of all investigated peptides show a dominant y(2) ion (Pro-Ala sequence). Our computational results show that the proline effect mainly arises from the particularly low threshold energy for the amide bond cleavage N-terminal to the proline residue, and from the high proton affinity of the proline-containing C-terminal fragment produced by this cleavage. These theoretical results are qualitatively supported by the experimentally observed y(2)/b(3) abundance ratios for protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). In the post-cleavage phase of fragmentation the N-terminal oxazolone fragment with the Ala-Ala-Xxx sequence and Pro-Ala compete for the ionizing proton for these peptides. As the proton affinity of the oxazolone fragment increases, the y(2)/b(3) abundance ratio decreases.

  18. 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)

  19. 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

  20. Collision Induced Dissociation of [4Fe-4S] Cubane Cluster Complexes: [Fe4S4C14-x(SC2H5)x]2-/1- (x=0-4)

    SciTech Connect

    Fu, Youjun; Laskin, Julia; Wang, Lai S.

    2006-09-01

    Collision-induced dissociation (CID) experiments on a series of [4Fe-4S] cluster ions, [Fe4S4Cl4-x(SC2H5)x]2-/1- (x = 0 - 4), revealed that their fragmentation channels change with the coordination environment. Among the three Coulomb repulsion related channels for the doubly charged species, the collision induced electron detachment channel was found to become more significant from x = 0 to 4 due to the decreasing electron binding energies and the magnitude of the repulsion Coulomb barrier, while both the ligand detachment of Cl- and the fission of the [Fe4S4]2+ core became more and more significant with the increase of the Cl- coordination, and eventually became the dominant channel at x = 0. From the parents containing the -SC2H5 ligand, neutral losses of HSC2H5 (62) and/or HSCH=CH2 (60) were observed. It was proposed that inter- and intra-ligand proton transfer could happen during the CID process, resulting in hydrogen coordination to the [4Fe-4S] cluster. In the presence of O2, [Fe4S4Cl3(SC2H5)]2- and [Fe4S4Cl4]2- can form the O2-substituted products [Fe4S4Cl2(SC2H5)O2]- and [Fe4S4Cl3O2]-, respectively. It was shown that the O2 complexation occurs by coordination to the empty iron site of the [4Fe-4S] cubane core after dissociation of one Cl- ligand.

  1. 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.

    PubMed

    Vilkov, Andrey N; Bogdanov, Bogdan; Pasa-Tolić, Ljiljana; Prior, Dave C; Anderson, Gordon A; Masselon, Christophe D; Moore, Ronald J; Smith, Richard D

    2004-01-01

    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 (FTICR-MS), 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 the 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.

  2. Threshold collision-induced dissociation of Sr(2+)(H(2)O)(x) complexes (x=1-6): An experimental and theoretical investigation of the complete inner shell hydration energies of Sr(2+).

    PubMed

    Carl, D R; Chatterjee, B K; Armentrout, P B

    2010-01-28

    The sequential bond energies of Sr(2+)(H(2)O)(x) complexes, where x=1-6, are determined by threshold collision-induced dissociation using a guided ion beam tandem mass spectrometer equipped with an electrospray ionization source. The electrospray source produces an initial distribution of Sr(2+)(H(2)O)(x) complexes, where x=6-9. Smaller Sr(2+)(H(2)O)(x) complexes, where x=1-5, are accessed using a recently developed in-source fragmentation technique that takes place in the high pressure region of a rf-only hexapole ion guide. This work constitutes the first experimental study for the complete inner shell of any multiply charged ion. The kinetic energy dependent cross sections are determined over a wide energy range to monitor all possible dissociation products and are modeled to obtain 0 and 298 K binding energies for loss of a single water molecule. These binding energies decrease monotonically for the Sr(2+)(H(2)O) complex to Sr(2+)(H(2)O)(6). Our experimental results agree well with previous literature results obtained by equilibrium and kinetic studies for x=5 and 6. Because there has been limited theory for the hydration of Sr(2+), we also present an in-depth theoretical study on the energetics of the Sr(2+)(H(2)O)(x) systems by employing several levels of theory with multiple effective core potentials for Sr and different basis sets for the water molecules.

  3. 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

  4. High-field asymmetric waveform ion mobility spectrometry for determining the location of in-source collision-induced dissociation in electrospray ionization mass spectrometry.

    PubMed

    Xia, Yuan-Qing; Jemal, Mohammed

    2009-09-15

    The understanding and control of the in-source collision-induced dissociation (CID) of analytes is important for the accurate LC-MS/MS quantitation of drugs and metabolites in biological samples. Accordingly, it was of interest to us to establish whether such in-source CID takes place after and/or before the orifice of an electrospray ionization (ESI) mass spectrometer. A high-field asymmetric waveform ion mobility spectrometry (FAIMS) system that is physically located between the sprayer and the orifice of a mass spectrometer can serve as an ion filter to control ions entering the orifice of the mass spectrometer. In such a configuration, FAIMS could conceivably be used to determine if the in-source CID of an analyte occurs after and/or before the mass spectrometer orifice. We demonstrated this capability of FAIMS using ifetroban acylglucuronide metabolite as a model compound. Under the conditions used, the results showed that the in-source CID conversion of the acylglucuronide metabolite to its parent drug ifetroban occurred almost entirely after the orifice of the mass spectrometer, with the conversion upstream of the orifice accounting for only 5.6% of the conversion. Under the circumstance, the term "post-orifice CID" rather than "in-source CID" may be more appropriate in describing such a dissociation occurring in the front end of a mass spectrometer.

  5. Experimental investigation of the complete inner shell hydration energies of Ca2+: threshold collision-induced dissociation of Ca(2+)(H2O)x Complexes (x = 2-8).

    PubMed

    Carl, Damon R; Armentrout, P B

    2012-04-19

    The sequential bond energies of Ca(2+)(H(2)O)(x) complexes, where x = 1-8, are measured by threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer. From an electrospray ionization source that produces an initial distribution of Ca(2+)(H(2)O)(x) complexes where x = 6-8, complexes down to x = 2 are formed using an in-source fragmentation technique. Ca(2+)(H(2)O) cannot be formed in this source because charge separation into CaOH(+) and H(3)O(+) is a lower energy pathway than simple water loss from Ca(2+)(H(2)O)(2). The kinetic energy dependent cross sections for dissociation of Ca(2+)(H(2)O)(x) complexes, where x = 2-9, are examined over a wide energy range to monitor all dissociation products and are modeled to obtain 0 and 298 K binding energies. Analysis of both primary and secondary water molecule losses from each sized complex provides thermochemistry for the sequential hydration energies of Ca(2+) for x = 1-8 and the first experimental values for x = 1-4. Additionally, the thermodynamic onsets leading to the charge separation products from Ca(2+)(H(2)O)(2) and Ca(2+)(H(2)O)(3) are determined for the first time. Our experimental results for x = 1-6 agree well with previously calculated binding enthalpies as well as quantum chemical calculations performed here. Agreement for x = 1 is improved when the basis set on calcium includes core correlation.

  6. Threshold collision-induced dissociation of hydrated magnesium: experimental and theoretical investigation of the binding energies for Mg(2+)(H2O)x complexes (x=2-10).

    PubMed

    Carl, Damon R; Armentrout, Peter B

    2013-03-18

    The sequential bond energies of Mg(2+)(H2O)x complexes, in which x=2-10, are measured by threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. From an electrospray ionization source that produces an initial distribution of Mg(2+)(H2O)x complexes in which x=7-10, complexes down to x=3 are formed by using an in-source fragmentation technique. Complexes smaller than Mg(2+)(H2O)3 cannot be formed in this source because charge separation into MgOH(+)(H2O) and H3O(+) is a lower-energy pathway than simple water loss from Mg(2+)(H2O)3. The kinetic energy dependent cross sections for dissociation of Mg(2+)(H2O)x complexes, in which x=3-10, are examined over a wide energy range to monitor all dissociation products and are modeled to obtain 0 and 298 K binding energies. Analysis of both primary and secondary water molecule losses from each sized complex provides thermochemistry for the sequential hydration energies of Mg(2+) for x=2-10 and the first experimental values for x=2-4. Additionally, the thermodynamic onsets leading to the charge-separation products from Mg(2+)(H2O)3 and Mg(2+)(H2O)4 are determined for the first time. Our experimental results for x=3-7 agree well with quantum chemical calculations performed here and previously calculated binding enthalpies, as well as previous measurements for x=6. The present values for x=7-10 are slightly lower than previous experimental results and theory, but within experimental uncertainties.

  7. Liquid chromatography coupled with ultraviolet absorbance detection, electrospray ionization, collision-induced dissociation and tandem mass spectrometry on a triple quadrupole for the on-line characterization of polyphenols and methylxanthines in green coffee beans.

    PubMed

    Alonso-Salces, Rosa Maria; Guillou, Claude; Berrueta, Luis A

    2009-02-01

    Liquid chromatography coupled with a photodiode array detector, electrospray ionization, collision-induced dissociation and tandem mass spectrometry (LC-DAD/ESI-CID-MS/MS) on a triple quadrupole (QqQ) has been used to detect and characterize polyphenols and methylxanthines in green coffee beans: three phenolic acids (caffeic acid, ferulic acid and dimethoxycinnamic acid), three isomeric caffeoylquinic acids (M(r) 354), three feruloylquinic acids (M(r) 368), one p-coumaroylquinic acid (M(r) 338), three dicaffeoylquinic acids (M(r) 516), three feruloyl-caffeoylquinic acids (M(r) 530), four p-coumaroyl-caffeoylquinic acids (M(r) 500), three diferuloylquinic acids (M(r) 544), six dimethoxycinnamoyl-caffeoylquinic acids (M(r) 544), three dimethoxycinnamoyl-feruloylquinic acids (M(r) 558), six cinnamoyl-amino acid conjugates, three cinnamoyl glycosides, and three methylxanthines (caffeine, theobromine and theophylline). Dimethoxycinnamic acid, three isomers of dimethoxycinnamoyl-caffeoylquinic acids and another three of dimethoxycinnamoyl-feruloylquinic acids, as well as the three cinnamoyl glycosides, had not previously been reported in coffee beans. Structures have been assigned on the basis of the complementary information obtained from UV-visible spectra, relative hydrophobicity, scan mode MS spectra, and fragmentation patterns in MS(2) spectra (both in the positive and negative ion modes) obtained using a QqQ at different collision energies. A structure diagnosis scheme is provided for the identification of different isomers of polyphenols and methylxanthines.

  8. Sialylation analysis of O-glycosylated sialylated peptides from urine of patients suffering from Schindler's disease by Fourier transform ion cyclotron resonance mass spectrometry and sustained off-resonance irradiation collision-induced dissociation.

    PubMed

    Froesch, Martin; Bindila, Laura; Zamfir, Alina; Peter-Katalinić, Jasna

    2003-01-01

    A strategy based on Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) for screening of complex glycoconjugate mixtures containing O-linked glycopeptides and O-glycosylated amino acids with alpha-N-acetylgalactosaminyl residues is presented. To detect and identify O-glycoforms present in urine of patients suffering from hereditary N-acetylhexosaminidase deficiency (known as Schindler's disease), present at 100 times higher concentrations than in urine of healthy controls, new accurate methods for mapping and sequencing were required. In the mass spectrometric analysis particular attention has to be paid to original sialylation patterns, because of the potential lability of the sialic acid moiety during the desorption/ionization process. Negative ion nanoelectrospray ionization (nanoESI) FTICR-MS at 9.4 T is shown here to represent a method of choice for identification of single components in such complex glycomixtures due to high resolution and mass accuracy. By optimization of sustained off-resonance irradiation collision-induced dissociation tandem mass spectrometry (SORI-CID-MS(2)) in the negative ion mode, the type and sequence of the sialylated glycopeptide components were determined from their fragmentation patterns. Additionally, implementation of SORI-CID-MS(3) provides detailed information for sialylation analysis. The potential diagnostic value of this approach is discussed.

  9. 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

    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 MS(2) and MS(3) 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.

  10. 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

  11. 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.

  12. Biradical thermochemistry from collision-induced dissociation threshold energy measurements. Absolute heats of formation of ortho-, meta-, and para-benzyne

    SciTech Connect

    Wenthold, P.G.; Squires, R.R. )

    1994-07-13

    The absolute heats of formation of 1,2-, 1,3-, and 1,4-dehydrobenzene (ortho, meta-, and para-benzyne) have been determined from measurements of the threshold energies for collision-induced dissociation (CID) of ortho, meta-, and para-chlorophenyl anions in a flowing afterglow-triple quadrupole apparatus. The 298 K heats of formation for ortho-, meta-, and para-benzyne derived in this manner are 106.6 [+-] 3.0, 122.0 [+-] 3.1, and 137.3 [+-] 3.3 kcal/mol, respectively. The values for meta- and para-benzyne are higher than those reported previously but are in excellent agreement with recently reported MCSCF and CI calculations. Several control experiments are described which demonstrate that the earlier results for meta- and para-benzyne suffered from an acid-catalyzed isomerization of the reactant chlorophenyl anions in the flowing afterglow prior to CID threshold analysis. 70 refs., 5 figs., 4 tabs.

  13. 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

  14. Dissociation and memory fragmentation in post-traumatic stress disorder: an evaluation of the dissociative encoding hypothesis.

    PubMed

    Bedard-Gilligan, Michele; Zoellner, Lori A

    2012-01-01

    Several prominent theories of post-traumatic 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 summarise 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 towards 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.

  15. Formation of the bisulfite anion (HSO(3) (-) , m/z 81) upon collision-induced dissociation of anions derived from organic sulfonic acids.

    PubMed

    Jariwala, Freneil B; Wood, Ryan E; Nishshanka, Upul; Attygalle, Athula B

    2012-04-01

    In the negative-ion collision-induced dissociation mass spectra of most organic sulfonates, the base peak is observed at m/z 80 for the sulfur trioxide radical anion (SO(3) (-·) ). In contrast, the product-ion spectra of a few sulfonates, such as cysteic acid, aminomethanesulfonate, and 2-phenylethanesulfonate, show the base peak at m/z 81 for the bisulfite anion (HSO(3) (-) ). An investigation with an extensive variety of sulfonates revealed that the presence of a hydrogen atom at the β-position relative to the sulfur atom is a prerequisite for the formation of the bisulfite anion. The formation of HSO(3) (-) is highly favored when the atom at the β-position is nitrogen, or the leaving neutral species is a highly conjugated molecule such as styrene or acrylic acid. Deuterium-exchange experiments with aminomethanesulfonate demonstrated that the hydrogen for HSO(3) (-) formation is transferred from the β-position. The presence of a peak at m/z 80 in the spectrum of 2-sulfoacetic acid, in contrast to a peak at m/z 81 in that of 3-sulfopropanoic acid, corroborated the proposed hydrogen transfer mechanism. For diacidic compounds, such as 4-sulfobutanoic acid and cysteic acid, the m/z 81 ion can be formed by an alternative mechanism, in which the negative charge of the carboxylate moiety attacks the α-carbon relative to the sulfur atom. Experiments conducted with deuterium-exchanged and deuterium-labeled analogs of sulfocarboxylic acids demonstrated that the formation of the bisulfite anion resulted either from a hydrogen transfer from the β-carbon, or from a direct attack by the carboxylate moiety on the α-carbon.

  16. 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.

  17. Memory fragmentation in dissociative identity disorder.

    PubMed

    van der Hart, Onno; Bolt, Hilde; van der Kolk, Bessel A

    2005-01-01

    This study examined the quality of self-reported memories of traumatic experiences in participants with dissociative identity disorder (DID) and compared them with their memories of non-traumatic, but emotionally significant life experiences. Systematic interview data were gathered from 30 DID patients in The Netherlands. All participants reported a history of severe childhood abuse; 93.3% reported some period of amnesia for the index traumatic event, and 33.3% reported periods of amnesia for significant non-traumatic childhood experiences. All participants who had been amnestic for their trauma reported that their memories were initially retrieved in the form of somatosensory flashbacks. This suggests that, like PTSD patients, DID patients at least initially recall their trauma not as a narrative, but as somatosensory re-experiencing. Surprisingly, however, DID participants also recalled emotionally charged non-traumatic life events with significant somatosensory components, a phenomenon that has not been previously reported. This finding raises important issues regarding basic memory processing abnormalities in DID patients.

  18. Reduction of in-source collision-induced dissociation and thermolysis of sulopenem prodrugs for quantitative liquid chromatography/electrospray ionization mass spectrometric analysis by promoting sodium adduct formation.

    PubMed

    Wujcik, Chad E; Kadar, Eugene P

    2008-10-01

    Six chromatographically resolved sulopenem prodrugs were monitored for their potential to undergo both in-source collision-induced dissociation (CID) and thermolysis. Initial Q1 scans for each prodrug revealed the formation of intense [Prodrug2 + H]+, [Prodrug2 + Na]+, [Prodrug + Na]+, and [Sulopenem + Na]+ ions. Non-adduct-associated sulopenem ([Sulopenem + H]+) along with several additional lower mass ions were also observed. Product ion scans of [Prodrug3 + Na]+ showed the retention of the sodium adduct in the collision cell continuing down to opening of the beta-lactam ring. In-source CID and temperature experiments were conducted under chromatographic conditions while monitoring several of the latter ion transitions (i.e., adducts, dimers and degradants/fragments) for a given prodrug. The resulting ion profiles indicated the regions of greatest stability for temperature and declustering potential (DP) that provided the highest signal intensity for each prodrug and minimized in-source degradation. The heightened stability of adduct ions, relative to their appropriate counterpart (i.e., dimer to dimer adduct and prodrug to prodrug adduct ions), was observed under elevated temperature and DP conditions. The addition of 100 microM sodium to the mobile phase further enhanced the formation of these more stable adduct ions, yielding an optimal [Prodrug + Na]+ ion signal at temperatures from 400 to 600 degrees C. A clinical liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for sulopenem prodrug PF-04064900 in buffered whole blood was successfully validated using sodium-fortified mobile phase and the [PF-04064900 + Na]+ ion for quantitation. A conservative five-fold increase in sensitivity from previously validated preclinical assays using the [PF-04064900 + H]+ precursor ion was achieved.

  19. Dissociative excitation and fragmentation of S8 by electron impact.

    PubMed

    Brotton, S J; McConkey, J W

    2011-05-28

    The vacuum-ultraviolet emission spectrum from 136 nm to 168 nm following the dissociative excitation of a predominantly S(8) target by electron impact at 100 eV incident energy was measured. The relative cross sections for the dominant multiplets at 138.9, 142.9, 147.9, and 166.7 nm are presented. Excitation functions are shown for electron-impact energies from below threshold to 360 eV for the two most prominent emissions at 142.5 nm and 147.4 nm. Five thresholds are clearly apparent in both excitation functions. For the four highest energy channels, the energy separation between the adjacent thresholds is approximately constant and the cross sections reduce regularly as the threshold energies increase. We suggest possible fragmentation pathways of the dissociating S(8) molecule that reproduce the energies of our observed thresholds.

  20. 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.

  1. Mechanisms of peptide fragmentation from time- and energy-resolved surface-induced dissociation studies: Dissociation of angiotensin analogs

    NASA Astrophysics Data System (ADS)

    Laskin, Julia; Bailey, Thomas H.; Futrell, Jean H.

    2006-03-01

    Energetics and mechanism of dissociation of singly protonated angiotensin III (RVYIHPF) and its analogs RVYIFPF, RVYIYPF, RVYIHAF and RVYIHDF was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of peptide fragmentation were deduced by modeling the time- and energy-resolved survival curves for each precursor ion using an RRKM-based approach developed in our laboratory. Fragmentation mechanisms were inferred from comparison of time- and energy-resolved fragmentation efficiency curves (TFECs) of different fragment ions followed by RRKM modeling of dissociation of angiotensin III into six major families of fragment ions. Detailed modeling demonstrated that dissociation of these peptides is dominated by loss of ammonia from the precursor ion and characterized by a high-energy barrier of 1.6 eV. Loss of NH3 and subsequent rearrangement of the MH+-NH3 ion results in proton mobilization and release of ca. 30 kcal/mol into internal excitation of the MH+-NH3 ion. The resulting highly excited ion accesses a variety of non-specific dissociation pathways with very high rate constants. Fast fragmentation of excited MH+-NH3 ion forms a variety of abundant bn-NH3 and an-NH3 fragment ions. Abundant XH and HX internal fragments are also formed, reflecting the stability of histidine-containing diketopiperazine structures.

  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. Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

    PubMed

    Nose, Holliness; Chen, Yu; Rodgers, M T

    2013-05-23

    The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated. PMID:23565706

  5. Collision-induced dissociation of diazirine-labeled peptide ions. Evidence for Brønsted-acid assisted elimination of nitrogen.

    PubMed

    Marek, Aleš; Tureček, František

    2014-05-01

    Gas-phase dissociations were investigated for several peptide ions containing the Gly-Leu* N-terminal motif where Leu* was a modified norleucine residue containing the photolabile diazirine ring. Collisional activation of gas-phase peptide cations resulted in facile N₂ elimination that competed with backbone dissociations. A free lysine ammonium group can act as a Brønsted acid to facilitate N₂ elimination. This dissociation was accompanied by insertion of a lysine proton in the side chain of the photoleucine residue, as established by deuterium labeling and gas-phase sequencing of the products. Electron structure calculations were used to provide structures and energies of reactants, intermediates, and transition states for Gly-Leu*-Gly-Gly-Lys amide ions that were combined with RRKM calculations of unimolecular rate constants. The calculations indicated that Brønsted acid-catalyzed eliminations were kinetically preferred over direct loss of N₂ from the diazirine ring. Mechanisms are proposed to explain the proton-initiated reactions and discuss the reaction products. The non-catalyzed diazirine ring cleavage and N₂ loss is proposed as a thermometer dissociation for peptide ion dissociations. PMID:24549894

  6. Collision-Induced Dissociation of Diazirine-Labeled Peptide Ions. Evidence for Brønsted-Acid Assisted Elimination of Nitrogen

    NASA Astrophysics Data System (ADS)

    Marek, Aleš; Tureček, František

    2014-05-01

    Gas-phase dissociations were investigated for several peptide ions containing the Gly-Leu* N-terminal motif where Leu* was a modified norleucine residue containing the photolabile diazirine ring. Collisional activation of gas-phase peptide cations resulted in facile N2 elimination that competed with backbone dissociations. A free lysine ammonium group can act as a Brønsted acid to facilitate N2 elimination. This dissociation was accompanied by insertion of a lysine proton in the side chain of the photoleucine residue, as established by deuterium labeling and gas-phase sequencing of the products. Electron structure calculations were used to provide structures and energies of reactants, intermediates, and transition states for Gly-Leu*-Gly-Gly-Lys amide ions that were combined with RRKM calculations of unimolecular rate constants. The calculations indicated that Brønsted acid-catalyzed eliminations were kinetically preferred over direct loss of N2 from the diazirine ring. Mechanisms are proposed to explain the proton-initiated reactions and discuss the reaction products. The non-catalyzed diazirine ring cleavage and N2 loss is proposed as a thermometer dissociation for peptide ion dissociations.

  7. Gas phase reaction of substituted isoquinolines to carboxylic acids in ion trap and triple quadrupole mass spectrometers after electrospray ionization and collision-induced dissociation.

    PubMed

    Thevis, Mario; Kohler, Maxie; Schlörer, Nils; Schänzer, Wilhelm

    2008-01-01

    Within the mass spectrometric study of bisubstituted isoquinolines that possess great potential as prolylhydroxylase inhibitor drug candidates (e.g., FG-2216), unusually favored gas-phase formations of carboxylic acids after collisional activation were observed. The protonated molecule of [(1-chloro-4-hydroxy-isoquinoline-3-carbonyl)-amino]-acetic acid was dissociated, yielding the 1-chloro-4-hydroxy-isoquinoline-3-carboxylic acid methyleneamide cation. Subsequent dissociation caused the nominal elimination of 11 u that resulted from the loss of HCN and concomitant addition of oxygen to the product ion, which formed the protonated 1-chloro-4-hydroxy-isoquinoline-3-carboxylic acid. The preference of this structure under mass spectrometric conditions was substantiated by tandem mass spectrometry analyses using the corresponding methyl ester (1-chloro-4-hydroxy-isoquinoline-3-carboxylic acid methyl ester) that eliminated methylene (-14 u) upon collisional activation. Moreover, the major product ion of 1-chloro-4-hydroxy-isoquinoline-3-carboxylic acid, which resulted from the loss of water in MS3 experiments, restored the precursor ion structure by re-addition of H2O. Evidences for these phenomena were obtained by chemical synthesis of proposed gas-phase intermediates, H/D exchange experiments, high-resolution/high accuracy mass spectrometry at MSn level, and "ping-pong" analyses (MS7, in which the precursor ion was dissociated and the respective product ion isolated to regenerate the precursor ion for repeated dissociation. Based on these results, dissociation pathways for [(1-chloro-4-hydroxy-isoquinoline-3-carbonyl)-amino]-acetic acid were suggested that can be further utilized for the characterization of structurally related compounds or metabolic products in clinical, forensic, or doping control analysis.

  8. Dynamic Collision-Induced Dissociation (DCID) in a Quadrupole Ion Trap Using a Two-Frequency Excitation Waveform: II. Effects of Frequency Spacing and Scan Rate

    SciTech Connect

    Laskay, Unige A.; Collin, Olivier L.; Nichol, Brad; Jackson, Glen P.; Pasilis, Sofie P.; Duckworth, Doug C.

    2007-11-01

    Dynamic CID of selected precursor ions is achieved by the application of a two-frequency excitation waveform to the end-cap electrodes during the mass instability scan of a quadrupole ion trap mass spectrometer (QIT-MS). The time period normally allotted for resonance excitation and collisional cooling of the trapped ion are excluded and fragmentation instead takes place simultaneously with the mass acquisition scan. This new method permits a shorter scanning time when compared to conventional on-resonance CID. When the excitation waveform consists of two closely-spaced frequencies, the relative phase-relationship of the two frequencies plays a critical role in the fragmentation dynamics. However, at wider frequency spacings (>8 kHz) these phase effects are diminished, while maintaining the efficacy of closely-spaced excitation frequencies. The fragmentation efficiencies and energetics of n-butylbenzene and tetraalanine are studied under different experimental conditions and the results are compared at various scan rate parameters between 0.1 and 1.0 ms/Th. Although faster scan rates reduce the analysis time, the maximum observed fragmentation efficiencies rarely exceed 30%, compared to values in excess of 50% achieved at slower scan rates. The internal energies calculated from the simulations of n-butylbenzene at fast scan rates are ~4 eV for most experimental conditions, while at slow scan rates internal energies above 5.5 eV are observed for a wide range of conditions. Extensive ITSIM simulations support the observation that slowing the scan rate has a similar effect on fragmentation as widening the frequency spacing between the two excitation frequencies. Both approaches generally enhance CID efficiencies and make fragmentation less dependent upon the relative phase angle between the excitation waveform and the ion motion. This could be useful for optimizing the CID efficiencies for a wide range of precursor ion mass-to-charge ratios.

  9. 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…

  10. 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.

  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. 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.

  13. Can collision-induced negative-ion fragmentations of [M-H](-) anions be used to identify phosphorylation sites in peptides?

    PubMed

    Tran, T T Nha; Wang, Tianfang; Hack, Sandra; Hoffmann, Peter; Bowie, John H

    2011-12-15

    A joint experimental and theoretical investigation of the fragmentation behaviour of energised [M-H](-) anions from selected phosphorylated peptides has confirmed some of the most complex rearrangement processes yet to be reported for peptide negative ions. In particular: pSer and pThr (like pTyr) may transfer phosphate groups to C-terminal carboxyl anions and to the carboxyl anion side chains of Asp and Glu, and characteristic nucleophilic/cleavage reactions accompany or follow these rearrangements. pTyr may transfer phosphate to the side chains of Ser and Thr. The reverse reaction, namely transfer of a phosphate group from pSer or pThr to Tyr, is energetically unfavourable in comparison. pSer can transfer phosphate to a non-phosphorylated Ser. The non-rearranged [M-H](-) species yields more abundant product anions than its rearranged counterpart. If a peptide containing any or all of Ser, Thr and Tyr is not completely phosphorylated, negative-ion cleavages can determine the number of phosphated residues, and normally the positions of Ser, Thr and Tyr, but not which specific residues are phosphorylated. This is in accord with comments made earlier by Lehmann and coworkers.

  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. Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA.

    PubMed

    Taucher, Monika; Rieder, Ulrike; Breuker, Kathrin

    2010-02-01

    In recent years, new classes of nonprotein-coding ribonucleic acids (ncRNAs) with important cellular functions have been discovered. Of particular interest for biomolecular research and pharmaceutical developments are small ncRNAs that are involved in gene regulation, such as small interfering RNAs (21-28 nt), pre-microRNAs (70-80 nt), or riboswitches (34-200 nt). De novo sequencing of RNA by top-down mass spectrometry has so far been limited to RNA consisting of up to approximately 20 nt. We report here complete sequence coverage for 34 nt RNA (10.9 kDa), along with 30 out of 32 possible complementary ion pairs from collisionally activated dissociation (CAD) experiments. The key to minimizing undesired base loss and internal fragmentation is to minimize the internal energy of fragment ions from primary backbone cleavage. This can be achieved by collisional cooling of primary fragment ions and selection of precursor ions of relatively low negative net charge (about -0.2/nt).

  16. Fragmentation pathways of protonated peptides.

    PubMed

    Paizs, Béla; Suhai, Sándor

    2005-01-01

    The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the 'mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the 'pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented. PMID:15389847

  17. Fragmentation energetics for angiotensin II and its analogs from time- and energy-resolved surface-induced dissociation studies

    NASA Astrophysics Data System (ADS)

    Laskin, Julia; Bailey, Thomas H.; Futrell, Jean H.

    2004-05-01

    Surface-induced dissociation (SID) of four model peptides: DRVYIHPF, RVYIHPF, RVYIHAF, and RVYIHDF was studied using a novel Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for SID experiments. The energetics and dynamics of peptide fragmentation were deduced by modeling the time- and energy-resolved survival curves for each precursor ion using an RRKM based approach developed in our laboratory. Accurate dissociation parameters can be obtained from these experiments because collision-energy-resolved SID data are very sensitive to both the energetics and dynamics of dissociation. We found that transition from selective to non-selective fragmentation as ion kinetic energy is increased is associated with a substantial (ca. 0.5 eV) increase in the dissociation energy and a 3-4 orders of magnitude increase in the pre-exponential factor. Dissociation thresholds for angiotensin analogs derived from the experimental data are as follows: 1.62 eV for RVYIHAF and RVYIHPF, 1.14 eV for RVYIHDF and 1.13 eV for DRVYIHPF. Pre-exponential factors of 8.2×1011, 7.2×1012, 3.1×108, and 5.0×107 s-1 were obtained for RVYIHPF, RVYIHAF, RVYIHDF, and DRVYIHPF, respectively. Contribution from shattering to the total decomposition of the precursor ion increases for kinetically hindered fragmentation. The largest contribution is observed for a peptide ion that has the largest negative reaction entropy--DRVYIHPF.

  18. Production of CO /a 3Pi/ and other metastable fragments by electron impact dissociation of CO2.

    NASA Technical Reports Server (NTRS)

    Wells, W. C.; Borst, W. L.; Zipf, E. C.

    1972-01-01

    The dissociative excitation of CO (a 3Pi) and other metastable fragments produced by electron impact on CO2 has been investigated from threshold to 50 eV. The observed threshold for CO (a 3Pi) production at 11.9 (plus or minus 0.5) eV was near the minimum required energy of 11.5 eV.

  19. The Effect of the Secondary Structure on Dissociation of Peptide Radical Cations: Fragmentation of Angiotensin III and Its Analogues

    SciTech Connect

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

    2008-09-28

    Fragmentation of protonated RVYIHPF and RVYIHPF-OMe and the corresponding radical cations was studied using time- and collision energy-resolved surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. Both the energetics and mechanisms of dissociation of even-electron and odd-electron angiotensin III ions are quite different. Protonated molecules are much more stable towards fragmentation than the corresponding radical cations. RRKM modeling of the experimental data suggests that this stability is largely attributed to differences in threshold energies for dissociation while activation entropies are very similar. Detailed analysis of the experimental data obtained for radical cations demonstrated the presence of two distinct structures separated by a high free-energy barrier. The two families of structures were ascribed to the canonical and zwitterionic forms of the radical cations produced in our experiments.

  20. High-Rydberg fragment formation via core dissociation of superexcited Rydberg molecules

    SciTech Connect

    Pinnaduwage, L.A. |; Zhu, Y.

    1998-04-01

    Formation of high-Rydberg iodine atoms via core dissociation of ArF-excimer-laser excited methyl iodide high-Rydberg molecules is observed using a time-resolved, mass-analyzed, pulsed field ionization technique. This observation confirms that the Rydberg electron is essentially a spectator in the core dissociation process. {copyright} {ital 1998 American Institute of Physics.}

  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. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

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

    PubMed Central

    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

  8. 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.

  9. 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

  10. Kinetic energies of fragment ions produced by dissociative photoionization of NO

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Angel, G. C.; Rstgi, O. P.

    1985-01-01

    The kinetic energies of ions produced by dissociative photoionization of NO have been measured at the discrete resonance lines of He (584A) and Ne (736A), and with undispersed synchrotron radiation. O sup + ions were identified with energies from 0 to approximately 0.5 eV and two groups of N sup + ions one with energy of 0.36 eV and another with energies between 0.9 and 1.5 eV, apparently produced by predissociation of the C sup 3 P 1 and B'1 sigma states respectively.

  11. Fragmentation dynamics in dissociative electron attachment to CO probed by velocity slice imaging.

    PubMed

    Nag, Pamir; Nandi, Dhananjay

    2015-03-21

    Complete dissociation dynamics in electron attachment to carbon monoxide (CO) have been studied using the newly developed velocity slice imaging (VSI) technique. Both kinetic energy and angular distributions of O(-) ions formed by dissociative electron attachment (DEA) to CO molecules have been measured for 9, 9.5, 10, 10.5, 11, and 11.5 eV incident electron energies around the resonance. Detailed observations conclusively show that two separate DEA reactions lead to the formation of O(-) ions in the ground (2)P state along with the neutral C atoms in the ground (3)P state and the first excited (1)D state, respectively. Within the axial recoil approximation and involving four partial waves, our angular distribution results clearly indicate that the two reactions leading to O(-) formation proceed through the specific resonant state(s). For the first process, more than one intermediate state is involved. On the other hand, for the second process, only one state is involved. The observed forward-backward asymmetry is explained in terms of the interference between the different partial waves that are involved in the processes.

  12. Efficient and scalable culture of single dissociated human pluripotent stem cells using recombinant E8 fragments of human laminin isoforms.

    PubMed

    Miyazaki, Takamichi; Kawase, Eihachiro

    2015-01-01

    This unit describes a protocol for efficient expansion of human pluripotent stem cells (hPSCs). A key feature of this method is subculture of hPSCs by single-cell dissociation passaging on substrates coated with recombinant E8 fragments of human laminin isoforms (LM-E8s). LM-E8s, provide superior adhesion over intact laminin isoforms and Matrigel. Single hPSCs seeded on LM-E8s show accelerated migration and rapid reconstruction of clusters, resulting in robust survival and proliferation. This protocol yields 200-fold more hPSCs than conventional subculture methods in 1 month of culture. Furthermore, this protocol can be easily adapted to most hPSC lines in combination with the use of various xeno-free, defined culture media, and large-scale expansion of hPSCs is easily achievable to facilitate the practical applications of hPSCs.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Kopyra, Janina; Abdoul-Carime, Hassan

    2015-05-01

    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)- 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 × 10-19 cm2. 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.

  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. Contingent dissociation between recognition and fragment completion: the method of triangulation.

    PubMed

    Hayman, C A; Tulving, E

    1989-03-01

    Two experiments conforming to the logic of the method of triangulation were conducted. Following the study of a list of words, the first of two successive tests (recognition) was identical for two groups of subjects, but the second one, in which the same word-fragment cues were presented to both groups, differed with respect to retrieval instructions. Subjects in one group engaged in cued recall of study-list words, whereas those in the second group completed the fragments with the first word that came to mind. Both experiments yielded the same result: The dependency between the first and second tests, indexed by Yule's Q statistic, was greater for recognition and cued recall than it was for recognition and fragment completion. These results speak to the controversial issue of the usefulness of contingency analyses of data from successive memory tests. The results are interpreted in a theoretical framework consisting of an integration of the idea of a hypothetical quasi-memory system with the transfer-appropriate procedural approach.

  17. Reliable determination of site-specific in vivo protein N-glycosylation based on collision-induced MS/MS and chromatographic retention time.

    PubMed

    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. PMID:24549892

  18. 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.

  19. Spectroscopic Evidence for an Oxazolone Structure in Anionic b-Type Peptide Fragments

    NASA Astrophysics Data System (ADS)

    Grzetic, Josipa; Oomens, Jos

    2012-02-01

    Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b2 fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800-1800 cm-1 spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b2 fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability.

  20. Collision-induced constructive quantum interference

    SciTech Connect

    Yang, Xihua; Xie, Hankun

    2003-06-01

    We theoretically study the collision-induced constructive quantum interference in an open four-level system with the density-matrix approach based on the experimental observation of constructive quantum interference between two transition pathways 3P{sub 1/2}-5S (or 4D) and 3P{sub 3/2}-5S (or 4D) via equal-frequency hybrid excitation in the Na{sub 2}-Na system. The effects of the collision-induced coherent and incoherent decay rates and the ratio of the two transition dipole moments on the interference are analyzed. It is shown that through the incoherent process (collision), the coherence between a widely separated doublet and subsequent constructive quantum interference can be realized. The physical origin of the constructive interference can be seen clearly in the dressed-atom picture. The theoretical results can also be used to qualitatively explain the dependence of quantum interference on the experimental buffer gas pressure and sample temperature.

  1. Electron Transfer Dissociation of Milk Oligosaccharides

    NASA Astrophysics Data System (ADS)

    Han, Liang; Costello, Catherine E.

    2011-06-01

    For structural identification of glycans, the classic collision-induced dissociation (CID) spectra are dominated by product ions that derived from glycosidic cleavages, which provide only sequence information. The peaks from cross-ring fragmentation are often absent or have very low abundances in such spectra. Electron transfer dissociation (ETD) is being applied to structural identification of carbohydrates for the first time, and results in some new and detailed information for glycan structural studies. A series of linear milk sugars was analyzed by a variety of fragmentation techniques such as MS/MS by CID and ETD, and MS3 by sequential CID/CID, CID/ETD, and ETD/CID. In CID spectra, the detected peaks were mainly generated via glycosidic cleavages. By comparison, ETD generated various types of abundant cross-ring cleavage ions. These complementary cross-ring cleavages clarified the different linkage types and branching patterns of the representative milk sugar samples. The utilization of different MS3 techniques made it possible to verify initial assignments and to detect the presence of multiple components in isobaric peaks. Fragment ion structures and pathways could be proposed to facilitate the interpretation of carbohydrate ETD spectra, and the main mechanisms were investigated. ETD should contribute substantially to confident structural analysis of a wide variety of oligosaccharides.

  2. Serum Lipidomics Profiling using LC-MS and High Energy Collisional Dissociation Fragmentation: Focus on Triglyceride Detection and Characterization

    PubMed Central

    Bird, Susan S.; Marur, Vasant R.; Sniatynski, Matthew J.; Greenberg, Heather K.; Kristal, Bruce S.

    2011-01-01

    There is a growing need both clinically and experimentally to improve the characterization of blood lipids. A liquid chromatography-mass spectrometry (LC-MS) method, developed for the qualitative and semi-quantitative detection of lipids in biological samples and previously validated in mitochondrial samples, was now evaluated for the profiling of serum lipids. Data were acquired using high resolution full scan MS and high energy collisional dissociation (HCD) all ion fragmentation. The method was designed for efficient separation and detection in both positive and negative ionization mode and evaluated using standards spanning 7 lipid classes. Platform performance, related to the identification and characterization of serum triglycerides (TGs) was assessed using extracted ion chromatograms with mass tolerance windows of 5 ppm or less from full scan exact mass measurements determined using SIEVE non-differential LC-MS analysis software. The platform showed retention time coefficients of variation (CV) < 0.3%, mass accuracy values < 2 ppm error and peak area CV < 13%, with the majority of that error coming from sample preparation and extraction rather than the LC-MS analysis and linearity was shown to be over four orders of magnitude (r2=0.999) for the standard TG (15:0)3 spiked into serum. Instrument mass accuracy and precision were critical to the identification of unknown TG species, in part because these parameters enabled us to reduce false positives. In addition to detection and relative quantitation of TGs in serum, TG structures were characterized through the use of alternating HCD scans at different energies to produce diagnostic fragmentations on all ions in the analysis. The lipidomics method was applied to serum samples from 192 rats maintained on diets differing in macronutrient composition. The analysis identified 86 TG species with 81 unique masses that varied over 3.5 orders of magnitude and showed diet-dependency - consistent with TGs linking diet

  3. 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

  4. 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.

  5. 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.

  6. A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides.

    PubMed

    Aboufazeli, Forouzan; Kolli, Venkata; Dodds, Eric D

    2015-04-01

    Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.

  7. 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.

  8. Radical-driven peptide backbone dissociation tandem mass spectrometry.

    PubMed

    Oh, Han Bin; Moon, Bongjin

    2015-01-01

    In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach.

  9. DISSOCIATION OF B2H6 AND ADSORPTION OF THE FRAGMENTS OF B2H6 ON THE STEPPED Ge(100) SURFACE

    NASA Astrophysics Data System (ADS)

    Türkmenoğlu, Mustafa; Katircioğlu, Şenay

    2012-06-01

    In this work, the p-type doping of the SA type stepped Ge(100) surface by a diborane (B2H6) gas flow has been simulated by the possible dissociation and adsorption models. The most probable dissociation model of B2H6 and adsorption models of the fragments of B2H6 on the stepped Ge(100) surface have been determined by the local minimum total energy and/or binding energy calculations based on the Density functional (B3LYP/6-3g) and Hartree-Fock (HF/STO-3g) theories, respectively. The present calculations have shown that, the step region (for both up and down terraces) of the stepped Ge(100) surface has the most attractive sites for BH3 molecules determined to be the first dissociation fragments of B2H6 by an external energy of 1.3 eV. It has been found that, at the first step of the adsorption, BH3 can dissociate to BH2 and BH fragments on the stepped Ge(100) surface. While BH3 and BH2 products prefer to be attached to a single surface Ge atom, BH is bridged between two adjacent surface Ge atoms. According to the present optimization calculations, the p-type doping process of the stepped Ge(100) surface has started with the adsorption of BH3 on the electron deficient site (buckled down) of the Ge dimer bond close to the step edge and ended with the substitutional occupation of the Ge site in the layers of the surface by B atom. The beginning of the p-type doping of the stepped Ge(100) surface has been illustrated by the electronic states of B appeared in the optical energy gap of Ge very close to the edge of the HOMO.

  10. Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides.

    PubMed

    Ledvina, Aaron R; Chung, Thomas W; Hui, Renjie; Coon, Joshua J; Tureček, Frantisek

    2012-08-01

    Dissociations of z(4) ions from pentapeptides AAXAR where X=H, Y, F, W, and V produce dominant z(2) ions that account for >50 % of the fragment ion intensity. The dissociation has been studied in detail by experiment and theory and found to involve several isomerization and bond-breaking steps. Isomerizations in z(4) ions proceed by amide trans→cis rotations followed by radical-induced transfer of a β-hydrogen atom from the side chain, forming stable C(β) radical intermediates. These undergo rate-determining cleavage of the C(α)-CO bond at the X residue followed by loss of the neutral AX fragment, forming x(2) intermediates. The latter were detected by energy-resolved resonant excitation collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments. The x(2) intermediates undergo facile loss of HNCO to form z(2) fragment ions, as also confirmed by energy-resolved CID and IRMPD MS(4) experiments. The loss of HNCO from the x(2) ion from AAHWR is kinetically hampered by the Trp residue that traps the OCNH radical group in a cyclic intermediate. PMID:22669762

  11. Partial de novo sequencing and unusual CID fragmentation of a 7 kDa, disulfide-bridged toxin.

    PubMed

    Medzihradszky, Katalin F; Bohlen, Christopher J

    2012-05-01

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

  12. Characterization of the iron-binding properties of pyoverdine using electron-capture dissociation-tandem mass spectrometry.

    PubMed

    Qi, Yulin; Hayen, Heiko; Volmer, Dietrich A

    2016-02-01

    Pyoverdines (PVD) are a group of siderophores produced by fluorescent Pseudomonads. Identification of PVD variants mostly relies on liquid chromatography-tandem mass spectrometry (LC-MS/MS) using collision-induced dissociation (CID). Here, both CID and the novel dissociation technique electron-capture dissociation (ECD) were applied to characterize PVD succinamide and its Fe(III)-chelated complex. The results clearly showed that ECD produced diagnostic side chain fragmentation of the PVD peptide chain and preserved the labile Fe(III) binding to the chromophore in contrast to CID. The ECD technique is therefore expected to support the understanding of strain-specific Fe(III) transport processes of PVDs. PMID:26596281

  13. 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

  14. 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.

  15. Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

    NASA Astrophysics Data System (ADS)

    DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

    2016-09-01

    Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

  16. 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.

  17. Gas phase fragmentation of protonated betaine and its clusters.

    PubMed

    Wyer, Jean Ann; Feketeová, Linda; Brøndsted Nielsen, Steen; O'Hair, Richard A J

    2009-10-21

    Betaine [(CH(3))(3)N(+)CH(2)COO(-)] is a methylated version of glycine and is a zwitterion in its neutral form. In this work, we have subjected protonated betaine, (+)(CH(3))(3)NCH(2)COOH, to a range of fragmentation experiments which involve vibrational excitation, electronic excitation and electron capture. Low-energy (eV) collisions in combination with deuterium labelling reveal that the lowest energy dissociation pathway is the formation of N(CH(3))(3)(+) and CH(2)COOH. The dominant channel after 50 keV collisions with molecular oxygen is the same as that after low-energy collisions; however, more fragmentation is seen which is most likely due to electronic excitation of the ions in the collision processes. Subsequent dissociation of the radical N(CH(3))(3)(+) was observed in agreement with the electron ionisation spectrum of N(CH(3))(3). Electron-induced dissociation by 22 eV electrons produced similar fragments to those formed after high-energy collision-induced dissociation. With caesium atoms as the target gas, protonated betaine captured electrons to give neutrals. These were reionised to cations a microsecond later in collisions with O(2). The dominant dissociation channel of the betaine radical, [(CH(3))(3)NCH(2)COOH] , involves formation of N(CH(3))(3) and CH(2)COOH, as revealed from the presence of N(CH(3))(3)(+) radical cations. This channel is associated with a kinetic energy release of 0.1-0.2 eV. The CH(2)COOH radical is unstable to dissociation into CH(3) and CO(2) but in charge reversal experiments (two Cs collisions), CH(2)[double bond, length as m-dash]C(OH)O(-) anions were formed due to the short time between the collisions (nanoseconds). Density functional theory calculations support the spectral interpretations. Collision-induced dissociation of protonated betaine clusters resulted dominantly in loss of neutral betaines. PMID:20449019

  18. 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.

  19. Energetics and dynamics of the fragmentation reactions of protonated peptides containing methionine sulfoxide or aspartic acid via energy- and time-resolved surface induced dissociation.

    PubMed

    Lioe, Hadi; Laskin, Julia; Reid, Gavin E; O'Hair, Richard A J

    2007-10-25

    The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64 Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility in these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (nonmobile proton conditions) to lysine (partially mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFECs) reveal that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1-2 orders of magnitude lower than nonselective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to nonselective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes

  20. Energetics and Dynamics of the Fragmentation Reactions of Protonated Peptides Containing Methionine Sulfoxide or Aspartic Acid via Energy- and Time-Resolved Surface Induced Dissociation

    SciTech Connect

    Lioe, Hadi; Laskin, Julia; Reid, Gavin E.; O'Hair, Richard Aj

    2007-10-25

    The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility on these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (non-mobile proton conditions) to lysine (partially-mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFEC) reveals that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1–2 orders of magnitude lower than non-selective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to non-selective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these

  1. Metastable atom-activated dissociation mass spectrometry of phosphorylated and sulfonated peptides in negative ion mode.

    PubMed

    Cook, Shannon L; Jackson, Glen P

    2011-06-01

    The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were C(α) - C peptide backbone cleavages and neutral losses of CO(2), H(2)O, and [CO(2) + H(2)O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

  2. Structures and fragmentation of [Cu(uracil-H)(uracil)]+ in the gas phase.

    PubMed

    Ali, Osama Y; Fridgen, Travis D

    2012-02-01

    Complexes of copper (II) ions and uracil were studied using tandem mass spectrometry (Fourier transform ion cyclotron resonance, FTICR, mass spectrometry) including extensive isotopic labeling as well as theoretical calculations. Positive ion electrospray mass spectra of aqueous solutions of CuCl(2) and uracil show that the [Cu(Ura-H)(Ura)](+) ion is the most abundant ion even at low concentrations of uracil. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) experiments show that the lowest energy decomposition pathway for [Cu(Ura-H)(Ura)](+) , surprisingly, is not the loss of uracil, but the loss of HNCO followed by HCN as the most abundant secondary fragmentation product. MS(n) studies identified primary, secondary and tertiary fragmentation products. Extensive isotopic labeling studies, as well as computational studies allowed for a detailed fragmentation scheme for the [Cu(Ura-H)(Ura)](+) ion, beginning with the lowest energy structure. PMID:22183913

  3. Vicinage forces between molecular and atomic fragments dissociated from small hydrogen clusters and their effects on energy distributions

    SciTech Connect

    Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

    2003-12-01

    In this paper we analyze the dynamic evolution of molecular and atomic fragments of small hydrogen clusters interacting with thin solid foils. We compare the vicinage forces, calculated within the dielectric formalism, for H{sup +}, H{sup 0}, and H{sub 2}{sup +} fragments. Using a molecular dynamics numerical code we determine the energy distribution of the fragments after interacting with the target. This distribution is compared to experimental results for protons coming from the fragmentation of v=2.02 a.u. H{sub 2}{sup +} ions impinging on an aluminum foil; a fraction of neutral H{sup 0} is needed to be included in the simulation to get a good agreement with the experimental results. The H{sub 2}{sup +} energy spectra for v=5.42 a.u. H{sub 3}{sup +} interacting with amorphous carbon is also determined. The asymmetry in the Coulomb peaks appearing in the energy spectra both experimentally and in our calculation is opposite for H{sub 2}{sup +} than in H{sup +}; kinematic effects and differences in the electronic stopping are enough to reproduce the difference in the alignment of H{sub 2}{sup +} and H{sup +} fragments.

  4. Formation, isomerization, and dissociation of alpha-carbon-centered and pi-centered glycylglycyltryptophan radical cations

    SciTech Connect

    Ng, Dominic C.; Song, Tao; Siu, Shiu On; Siu, Chi-Kit; Laskin, Julia; Chu, Ivan K.

    2010-02-11

    Gas phase fragmentations of two isomeric radical cationic tripeptides of glycylglycyltryptophan-G•GW+ and [GGW]•+—with well-defined initial radical sites at the α-carbon atom and the 3-methylindole ring, respectively, have been studied using collision-induced dissociation (CID), density functional theory (DFT), and Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Substantially different low-energy CID spectra were obtained for these two isomeric GGW structures, suggesting that they did not interconvert on the time scale of these experiments. DFT and RRKM calculations were used to investigate the influence of the kinetics, stabilities, and locations of the radicals on the competition between the isomerization and dissociation channels. The calculated isomerization barrier between the GGW radical cations (>35.4 kcal/mol) was slightly higher than the barrier for competitive dissociation of these species (<30.5 kcal/mol); the corresponding microcanonical rate constants for isomerization obtained from RRKM calculations were all considerably lower than the dissociation rates at all internal energies. Thus, interconversion between the GGW isomers examined in this study cannot compete with their fragmentations.

  5. On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

    PubMed Central

    Li, Sujun; Arnold, Randy J.; Tang, Haixu; Radivojac, Predrag

    2011-01-01

    We estimated the reproducibility of tandem mass fragmentation spectra for the widely-used collision-induced dissociation (CID) instruments. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). We further investigated the accuracy of current predictors of peptide fragmentation spectra and found that they are more accurate than the ad-hoc models generally used by search engines (e.g. SEQUEST) and, surprisingly, approaching the empirical upper limit set by the average across-experiment spectral reproducibility (especially for charge +1 and charge +2 precursor ions). These results provide evidence that, in terms of accuracy of modeling, predicted peptide fragmentation spectra provide a viable alternative to spectral libraries for peptide identification, with a higher coverage of peptides and lower storage requirements. Furthermore, using five data sets of proteome digests by two different proteases, we find that PeptideART (a data-driven machine learning approach) is generally more accurate than MassAnalyzer (an approach based on a kinetic model for peptide fragmentation) in predicting fragmentation spectra, but that both models are significantly more accurate than the ad-hoc models. Availability: PeptideART is freely available at www.informatics.indiana.edu/predrag. PMID:21175207

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

    DOE PAGES

    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

  7. 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.

  8. 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

  9. Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments.

    PubMed

    Zaccone, A; Terentjev, I; Herling, T W; Knowles, T P J; Aleksandrova, A; Terentjev, E M

    2016-09-14

    While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends koff is larger than fragmentation rate k- and establish the law koff/k- = exp[(ε‖ - ε⊥)/kBT] = exp[0.5ε/kBT], which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments. PMID:27634278

  10. Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments

    NASA Astrophysics Data System (ADS)

    Zaccone, A.; Terentjev, I.; Herling, T. W.; Knowles, T. P. J.; Aleksandrova, A.; Terentjev, E. M.

    2016-09-01

    While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends koff is larger than fragmentation rate k- and establish the law koff/k- = exp[(ɛ‖ - ɛ⊥)/kBT] = exp[0.5ɛ/kBT], which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments.

  11. 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.

  12. 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.

  13. Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals.

    PubMed

    Sun, Qingyu; Nelson, Hosea; Ly, Tony; Stoltz, Brian M; Julian, Ryan R

    2009-02-01

    A crown ether based, photolabile radical precursor which forms noncovalent complexes with peptides has been prepared. The peptide/precursor complexes can be electrosprayed, isolated in an ion trap, and then subjected to laser photolysis and collision induced dissociation to generate hydrogen deficient peptide radicals. It is demonstrated that these peptide radicals behave very differently from the hydrogen rich peptide radicals generated by electron capture methods. In fact, it is shown that side chain chemistry dictates both the occurrence and relative abundance of backbone fragments that are observed. Fragmentation at aromatic residues occurs preferentially over most other amino acids. The origin of this selectivity relates to the mechanism by which backbone dissociation is initiated. The first step is abstraction of a beta-hydrogen from the side chain, followed by beta-elimination to yield primarily a-type fragment ions. Calculations reveal that those side chains which can easily lose a beta-hydrogen correlate well with experimentally favored sites for backbone fragmentation. In addition, radical mediated side chain losses from the parent peptide are frequently observed. Eleven amino acids exhibit unique mass losses from side chains which positively identify that particular amino acid as part of the parent peptide. Therefore, side chain losses allow one to unambiguously narrow the possible sequences for a parent peptide, which when combined with predictable backbone fragmentation should lead to greatly increased confidence in peptide identification.

  14. 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

  15. Alternate dissociation pathways identified in charge-reduced protein complex ions.

    PubMed

    Pagel, Kevin; Hyung, Suk-Joon; Ruotolo, Brandon T; Robinson, Carol V

    2010-06-15

    Tandem mass spectrometry (MS) of large protein complexes has proven to be capable of assessing the stoichiometry, connectivity, and structural details of multiprotein assemblies. While the utility of tandem MS is without question, a deeper understanding of the mechanism of protein complex dissociation will undoubtedly drive the technology into new areas of enhanced utility and information content. We present here the systematic analysis of the charge state dependent decay of the noncovalently associated complex of human transthyretin, generated by collision-induced dissociation (CID). A crown ether based charge reduction approach was applied to generate intact transthyretin tetramers with charge states ranging from 15+ to 7+. These nine charge states were subsequently analyzed by means of tandem MS and ion mobility spectrometry. Three different charge-dependent mechanistic regimes were identified: (1) common asymmetric dissociation involving ejection of unfolded monomers, (2) expulsion of folded monomers from the intact tetramer, and (3) release of C-terminal peptide fragments from the intact complex. Taken together, the results presented highlight the potential of charge state modulation as a method for directing the course of gas-phase dissociation and unfolding of protein complexes.

  16. 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

  17. New aspects in fragmentation of peptide nucleic acids: comparison of positive and negative ions by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Ziehe, Matthias; Grossmann, Tom N; Seitz, Oliver; Linscheid, Michael W

    2009-04-01

    The use of peptide nucleic acids (PNAs) is steadily increasing in biochemistry and diagnostics. So far, PNAs have mostly been investigated using cationic conditions in mass spectrometry. Furthermore, the use of fragmentation techniques developed for peptides and proteins like infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD) has barely been examined. However, especially the fragmentation behavior of PNA oligomers in negative ion mode is of high importance, due to the ability to interact with nucleic acids which are almost exclusively analyzed in the negatively charged state. In the current study PNA fragmentations under cationic and anionic conditions were investigated and different fragmentation techniques like collision-induced dissociation (CID), IRMPD and ECD were applied. Especially when using CID and IRMPD, amide bonds were broken, whereas ECD resulted in the elimination of nucleobases. Differences were also observed between positive and negative ionization, while the sequence coverage for the negative ions was superior to positive ions. The fragmentation behavior using IRMPD led to almost complete sequence coverage. Additionally, in anions the interesting effect of multiple eliminations of HNCO was found. PMID:19280610

  18. Formation and Dissociation of Phosphorylated Peptide Radical Cations

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  19. Study of the dissociation of a charge-reduced phosphopeptide formed by electron transfer from an alkali metal target.

    PubMed

    Hayakawa, Shigeo; Hashimoto, Mami; Nagao, Hirofumi; Awazu, Kunio; Toyoda, Michisato; Ichihara, Toshio; Shigeri, Yasushi

    2008-01-01

    Doubly protonated phosphopeptide (YGGMHRQET(p)VDC) ions obtained by electrospray ionization were collided with Xe and Cs targets to give singly and doubly charged positive ions via collision-induced dissociation (CID). The resulting ions were analyzed and detected by using an electrostatic analyzer (ESA). Whereas doubly charged fragment ions resulting from collisionally activated dissociation (CAD) were dominant in the CID spectrum with the Xe target, singly charged fragment ions resulting from electron transfer dissociation (ETD) were dominant in the CID spectrum with the Cs target. The most intense peak resulting from ETD was estimated to be associated with the charge-reduced ion with H2 lost from the precursor. Five c-type fragment ions with amino acid residues detached consecutively from the C-terminal were clearly observed without a loss of the phosphate group. These ions must be formed by N--Calpha bond cleavage, in a manner similar to the cases of electron capture dissociation (ECD) and ETD from negative ions. Although the accuracy in m/z of the CID spectra was about +/-1 Th because of the mass analysis using the ESA, it is supposed from the m/z values of the c-type ions that these ions were accompanied by the loss of a hydrogen atom. Four z-type (or y--NH3, or y--H2O) ions analogously detached consecutively from the N-terminal were also observed. The fragmentation processes took place within the time scale of 4.5 micros in the high-energy collision. The present results demonstrated that high-energy ETD with the alkali metal target allowed determination of the position of phosphorylation and the amino acid sequence of post-translational peptides.

  20. A review of electron-capture and electron-transfer dissociation tandem mass spectrometry in polymer chemistry.

    PubMed

    Hart-Smith, Gene

    2014-01-15

    Mass spectrometry (MS)-based studies of synthetic polymers often characterise detected polymer components using mass data alone. However when mass-based characterisations are ambiguous, tandem MS (MS/MS) offers a means by which additional analytical information may be collected. This review provides a synopsis of two particularly promising methods of dissociating polymer ions during MS/MS: electron-capture and electron-transfer dissociation (ECD and ETD, respectively). The article opens with a summary of the basic characteristics and operating principles of ECD and ETD, and relates these techniques to other methods of dissociating gas-phase ions, such as collision-induced dissociation (CID). Insights into ECD- and ETD-based MS/MS, gained from studies into proteins and peptides, are then discussed in relation to polymer chemistry. Finally, ECD- and ETD-based studies into various classes of polymer are summarised; for each polymer class, ECD- and ETD-derived data are compared to CID-derived data. These discussions identify ECD and ETD as powerful means by which unique and diagnostically useful polymer ion fragmentation data may be generated, and techniques worthy of increased utilisation by the polymer chemistry community.

  1. 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

  2. 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.

  3. 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.

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

    PubMed

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

    2012-06-01

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

  5. Conformation-Specific Spectroscopy of Peptide Fragment Ions in a Low-Temperature Ion Trap

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  6. 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

  7. Characterization of 4-hydroxy-2-nonenal-modified peptides by liquid chromatography-tandem mass spectrometry using data-dependent acquisition: neutral loss-driven MS3 versus neutral loss-driven electron capture dissociation.

    PubMed

    Rauniyar, Navin; Stevens, Stanley M; Prokai-Tatrai, Katalin; Prokai, Laszlo

    2009-01-15

    Reactive oxygen species generated during oxidative stress can lead to unfavorable cellular consequences, predominantly due to formation of 4-hydroxy-2-nonenal (HNE) during lipid peroxidation. Data-dependent and neutral loss (NL)-driven MS(3) acquisition have been reported for the identification of HNE adducts by mass spectrometry-based proteomics. However, the limitation associated with this method is the ambiguity in correct assignment of the HNE modification site when more than one candidate site is present as MS(3) is triggered on the neutral loss ion. We introduce NL-triggered electron capture dissociation tandem mass spectrometry (NL-ECD-MS/MS) for the characterization of HNE-modification sites in peptides. With this method performed using a hybrid linear ion trap-Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, ECD in the FTICR unit of the instrument is initiated on precursor ions of peptides showing the neutral loss of 156 Da corresponding to an HNE molecule in the prescan acquired via collision-induced dissociation tandem mass spectrometry in the linear ion trap. In addition to manifold advantages associated with the ECD method of backbone fragmentation, including extensive sequence fragments, ECD tends to retain the HNE group during MS/MS of the precursor ion, facilitating the correct localization of the modification site. The results also suggest that predisposition of a peptide molecular ion to lose HNE during collision-induced dissociation-based fragmentation is independent of its charge state (2+ or 3+). In addition, we have demonstrated that coupling of solid-phase enrichment of HNE-modified peptides facilitates the detection of this posttranslational modification by NL-driven strategies for low-abundance proteins that are susceptible to substoichiometric carbonylation during oxidative stress.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  10. 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.

  11. 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.

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

    PubMed Central

    2016-01-01

    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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize 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. However, th...

  1. 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...

  2. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize 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. For phytochem...

  3. Fragmentation studies and electrospray ionization mass spectrometry of lapachol: protonated, deprotonated and cationized species.

    PubMed

    Vessecchi, Ricardo; Emery, Flavio S; Galembeck, Sérgio E; Lopes, Norberto P

    2010-07-30

    Electrospray ionization mass spectrometric analysis of lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone) was accomplished in order to elucidate the gas-phase dissociation reactions of this important biologically active natural product. The occurrence of protonated and cationized species in the positive mode and of deprotonated species in the negative mode was explored by means of collision-induced dissociation (CID) experiments. For the protonated molecule, the H(2)O and C(4)H(8) losses occur by two competitive channels. For the deprotonated molecule, the even-electron rule is not conserved, and the radicalar species are eliminated by formation of distonic anions. The fragmentation mechanism for each ion was suggested on the basis of computational thermochemistry. Atomic charges, relative energies, and frontier orbitals were employed aiming at a better understanding of the gas-phase reactivity of lapachol. Potential energy surfaces for fragmentation reactions were obtained by the B3LYP/6-31+G(d,p) model. PMID:20552691

  4. 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

  5. The role of proton mobility in determining the energy-resolved vibrational activation/dissociation channels of N-glycopeptide ions.

    PubMed

    Kolli, Venkata; Roth, Heidi A; De La Cruz, Gabriela; Fernando, Ganga S; Dodds, Eric D

    2015-10-01

    Site-specific glycoproteomic analysis largely hinges on the use of tandem mass spectrometry (MS/MS) to identify glycopeptides. Experiments of this type are usually aimed at drawing connections between individual oligosaccharide structures and their specific sites of attachment to the polypeptide chain. These determinations inherently require ion dissociation methods capable of interrogating both the monosaccharide and amino acid connectivity of the glycopeptide. Collision-induced dissociation (CID) shows potential to satisfy this requirement, as the vibrational activation/dissociation of protonated N-glycopeptides has been observed to access cleavage of either glycosidic bonds of the glycan or amide bonds of the peptide in an energy-resolved manner. Nevertheless, the relative energy requirement for these fragmentation pathways varies considerably among analytes. This research addresses the influence of proton mobility on the vibrational energy necessary to achieve either glycan or peptide cleavage in a collection of protonated N-glycopeptide ions. While greater proton mobility of the precursor ion was found to correlate with lower energy requirements for precursor ion depletion and appearance of glycosidic fragments, the vibrational energy deposition necessary for appearance of peptide backbone fragments showed no relation to the precursor ion proton mobility. These results are consistent with observations suggesting that peptide fragments arise from an intermediate fragment which is generally of lower proton mobility than the precursor ion. Such findings have potential to facilitate the rational selection of CID conditions which are best suited to provide either glycan or peptide cleavage products in MS/MS based N-glycoproteomic analysis.

  6. 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).

  7. 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

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

    PubMed

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

    2014-06-12

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

  9. Dissociative electron attachment to methyl chloride: A quasi-diatomic potential curve for the fragmentation of the metastable CH3Cl- anion

    NASA Astrophysics Data System (ADS)

    Mach, P.; Urban, J.; Staemmler, V.

    2009-02-01

    Potential energy curves have been calculated for the dissociation of the neutral CH3Cl molecule and its negative ion into CH3 + Cl and CH3 +Cl- , respectively. The neutral molecule and the anion could be treated by means of standard wave function based quantum chemical ab initio methods for C-Cl distances larger than about 2.4 Å, where CH3Cl- is a stable anion. In the present calculation MP3 and CCSD(T) were employed. At shorter C-Cl distances the CH3Cl- anion is only metastable and cannot be treated by such methods. We have applied a stabilization scheme, first proposed by Nestmann and Peyerimhoff, to stabilize the metastable anion by adding extra positive charges to the molecule. By this trick it was possible to generate the resonance energy Eres and width Γ as functions of the C-Cl distance in the resonance regime between 1.5 and 2.5 Å. The calculated values for the threshold energy Ethresh and the exothermicity ΔE0 of the DEA (dissociative electron attachment) process are in very good agreement with experiment; the vertical attachment energy (VAE) is smaller than its experimental counterpart.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Dissociative disorders.

    PubMed

    Kihlstrom, John F

    2005-01-01

    The dissociative disorders, including "psychogenic" or "functional" amnesia, fugue, dissociative identity disorder (DID, also known as multiple personality disorder), and depersonalization disorder, were once classified, along with conversion disorder, as forms of hysteria. The 1970s witnessed an "epidemic" of dissociative disorder, particularly DID, which may have reflected enthusiasm for the diagnosis more than its actual prevalence. Traditionally, the dissociative disorders have been attributed to trauma and other psychological stress, but the existing evidence favoring this hypothesis is plagued by poor methodology. Prospective studies of traumatized individuals reveal no convincing cases of amnesia not attributable to brain insult, injury, or disease. Treatment generally involves recovering and working through ostensibly repressed or dissociated memories of trauma; at present, there are few quantitative or controlled outcome studies. Experimental studies are few in number and have focused largely on state-dependent and implicit memory. Depersonalization disorder may be in line for the next "epidemic" of dissociation.

  16. Diagnosing the Protonation Site of b 2 Peptide Fragment Ions using IRMPD in the X-H (X = O, N, and C) Stretching Region

    NASA Astrophysics Data System (ADS)

    Sinha, Rajeev K.; Erlekam, Undine; Bythell, Benjamin J.; Paizs, Béla; Maître, Philippe

    2011-09-01

    Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b 2 ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800-3800 cm-1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO2 laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm-1, corresponding to the asymmetric N-H stretch of the (nonprotonated) N-terminal NH2 group, is a distinct vibrational signature of the ring-protonated oxazolone structure.

  17. Gas-phase peptide fragmentation: how understanding the fundamentals provides a springboard to developing new chemistry and novel proteomic tools.

    PubMed

    Barlow, Christopher K; O'Hair, Richard A J

    2008-10-01

    This tutorial provides an overview of the evolution of some of the key concepts in the gas-phase fragmentation of different classes of peptide ions under various conditions [e.g. collision-induced dissociation (CID) and electron transfer dissociation (ETD)], and then demonstrates how these concepts can be used to develop new methods. For example, an understanding of the role of the mobile proton and neighboring group interactions in the fragmentation reactions of protonated peptides has led to the design of the 'SELECT' method. For ETD, a model based on the Landau-Zener theory reveals the role of both thermodynamic and geometric effects in the electron transfer from polyatomic reagent anions to multiply protonated peptides, and this predictive model has facilitated the design of a new strategy to form ETD reagent anions from precursors generated via ESI. Finally, two promising, emerging areas of gas-phase ion chemistry of peptides are also described: (1) the design of new gas-phase radical chemistry to probe peptide structure, and (2) selective cleavage of disulfide bonds of peptides in the gas phase via various physicochemical approaches.

  18. Dissociative amnesia.

    PubMed

    Staniloiu, Angelica; Markowitsch, Hans J

    2014-08-01

    Dissociative amnesia is one of the most enigmatic and controversial psychiatric disorders. In the past two decades, interest in the understanding of its pathophysiology has surged. In this report, we review new data about the epidemiology, neurobiology, and neuroimaging of dissociative amnesia and show how advances in memory research and neurobiology of dissociation inform proposed pathogenetic models of the disorder. Dissociative amnesia is characterised by functional impairment. Additionally, preliminary data suggest that affected people have an increased and possibly underestimated suicide risk. The prevalence of dissociative amnesia differs substantially across countries and populations. Symptoms and disease course also vary, indicating a possibly heterogeneous disorder. The accompanying clinical features differ across cultural groups. Most dissociative amnesias are retrograde, with memory impairments mainly involving the episodic-autobiographical memory domain. Anterograde dissociative amnesia occurring without significant retrograde memory impairments is rare. Functional neuroimaging studies of dissociative amnesia with prevailing retrograde memory impairments show changes in the network that subserves autobiographical memory. At present, no evidence-based treatments are available for dissociative amnesia and no broad framework exists for its rehabilitation. Further research is needed into its neurobiology, course, treatment options, and strategies to improve differential diagnoses.

  19. 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.

  20. Unimolecular dissociation of anthracene and acridine cations: The importance of isomerization barriers for the C{sub 2}H{sub 2} loss and HCN loss channels

    SciTech Connect

    Johansson, H. A. B.; Zettergren, H.; Holm, A. I. S.; Haag, N.; Schmidt, H. T.; Cederquist, H.; Nielsen, S. Broendsted; Wyer, J. A.; Kirketerp, M.-B. S.; Stoechkel, K.; Hvelplund, P.

    2011-08-28

    The loss of C{sub 2}H{sub 2} is a low activation energy dissociation channel for anthracene (C{sub 14}H{sub 10}) and acridine (C{sub 13}H{sub 9}N) cations. For the latter ion another prominent fragmentation pathway is the loss of HCN. We have studied these two dissociation channels by collision induced dissociation experiments of 50 keV anthracene cations and protonated acridine, both produced by electrospray ionization, in collisions with a neutral xenon target. In addition, we have carried out density functional theory calculations on possible reaction pathways for the loss of C{sub 2}H{sub 2} and HCN. The mass spectra display features of multi-step processes, and for protonated acridine the dominant first step process is the loss of a hydrogen from the N site, which then leads to C{sub 2}H{sub 2}/HCN loss from the acridine cation. With our calculations we have identified three pathways for the loss of C{sub 2}H{sub 2} from the anthracene cation, with three different cationic products: 2-ethynylnaphthalene, biphenylene, and acenaphthylene. The third product is the one with the overall lowest dissociation energy barrier. For the acridine cation our calculated pathway for the loss of C{sub 2}H{sub 2} leads to the 3-ethynylquinoline cation, and the loss of HCN leads to the biphenylene cation. Isomerization plays an important role in the formation of the non-ethynyl containing products. All calculated fragmentation pathways should be accessible in the present experiment due to substantial energy deposition in the collisions.

  1. Bond breaking in a Morse chain under tension: Fragmentation patterns, higher index saddles, and bond healing

    NASA Astrophysics Data System (ADS)

    Mauguière, F. A. L.; Collins, P.; Ezra, G. S.; Wiggins, S.

    2013-04-01

    We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices), and energy of all equilibria for the general n-particle chain, and have highlighted the importance of saddle points with index >1. We show that for an n = 2-particle chain under tensile stress the index 2 saddle plays a central role in organizing the dynamics. We apply normal form theory to analyze phase space structure and dynamics in a neighborhood of the index 2 saddle. We define a phase dividing surface (DS) that enables us to classify trajectories passing through a neighborhood of the saddle point using the values of the integrals associated with the normal form. We also generalize our definition of the dividing surface and define an extended dividing surface (EDS), which is used to sample and classify all trajectories that pass through a phase space neighborhood of the index 2 saddle at total energies less than that of the saddle. Classical trajectory simulations are used to study fragmentation patterns for the n = 2 chain under tension. That is, we investigate the relative probability for breaking one bond versus concerted fission of several (two, in this case) bonds. Initial conditions for trajectories are obtained by sampling the EDS at constant energy. We sample trajectories at fixed energies both above and below the energy of the saddle. The fate of trajectories (single versus multiple bond breakage) is explored as a function of the location of the initial condition on the EDS, and a connection made to the work of Chesnavich on collision-induced dissociation. A significant finding is that we can readily identify trajectories that exhibit bond healing. Such trajectories pass outside the nominal (index 1) transition state for single bond dissociation, but return to the potential well region, possibly several times, before ultimately dissociating.

  2. 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.

  3. 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.

  4. 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

  5. Qualitative Characterization of the Rat Liver Mitochondrial Lipidome using LC-MS Profiling and High Energy Collisional Dissociation (HCD) All Ion Fragmentation

    PubMed Central

    Bird, Susan S.; Marur, Vasant R.; Stavrovskaya, Irina G.; Kristal, Bruce S.

    2013-01-01

    Lipids play multiple roles essential for proper mitochondrial function, from their involvement in membrane structure and fluidity, cellular energy storage, and signaling. Lipids are also major targets for reactive species, and their peroxidation byproducts themselves mediate further damage. Thousands of lipid species, from multiple classes and categories, are involved in these processes, suggesting lipid quantitative and structural analysis can help provide a better understanding of mitochondrial physiological status. Due to the diversity of lipids that contribute to and reflect mitochondrial function, analytical methods should ideally cover a wide range of lipid classes, and yield both quantitative and structural information. We developed a high resolution LC-MS method that is able to monitor the major lipid classes found in biospecimens (ie. biofluids, cells and tissues) with relative quantitation in an efficient, sensitive, and robust manner while also characterizing individual lipid side-chains, by all ion HCD fragmentation and chromatographic alignment. This method was used to profile the liver mitochondrial lipids from 192 rats undergoing a dietary macronutrient study in which changes in mitochondria function are related to changes in the major fat and glycemic index component of each diet. A total of 381 unique lipids, spanning 5 of the major LIPID MAPS defined categories, including fatty acyls, glycerophospholipids, glycerolipids, sphingolipids and prenols, were identified in mitochondria using the non-targeted LC-MS analysis in both positive and negative mode. The intention of this report is to show the breadth of this non-targeted LC-MS profiling method with regards to its ability to profile, identify and characterize the mitochondrial lipidome and the details of this will be discussed. PMID:23646040

  6. Application of ESI/MS, CID/MS and tandem MS/MS to the fragmentation study of eriodictyol 7-O-glucosyl-(1-->2)-glucoside and luteolin 7-O-glucosyl-(1-->2)-glucoside

    NASA Astrophysics Data System (ADS)

    Es-Safi, Nour-Eddine; Kerhoas, Lucien; Einhorn, Jacques; Ducrot, Paul-Henri

    2005-12-01

    A mass spectrometric method based on the combined use of positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry has been applied to the structural characterization of the eriodictyol 7-O-glucosyl-(1-->2)-glucoside and luteolin 7-O-glucosyl-(1-->2)-glucoside. The low-energy product ion mass spectrum of [M + H]+ and [M - H]- ions showed extensive fragmentation of the diglucose moiety, loss of the glycan residue, and fragmentation of the aglycon units that permit characterization of the interglycosidic linkage and the substituents in the A- and B-rings. Both glycosides were shown to yield the 0,2X00,2X1 ion which can be considered as characteristic of the 1-->2 interglycosidic linkage in the glucoglucoside adducts, since it can not be formed in the case of other interglycosidic types. In the case of the eriodictyol diglucoside the 1, 3 fragmentation of the C-ring was observed before those involving the carbohydrates thus allowing the position determination of the diglucoside moiety on the A-ring. In the negative ion mode only the luteolin diglucoside was shown to undergo collision-induced homolytic and heterolytic cleavages of the O-glycosidic bond producing the aglycone radical-anion [Y0-H]-- and Y0- product ions, while this was not observed in the case of eriodictyol glycoside. CID MS/MS analysis of the sodiated molecules gave complementary informations for the structural characterization of the studied compounds. The B2+ fragment which is useful for establishing that the terminal carbohydrate unit is linked to another carbohydrate and not directly to the aglycone was obtained as base peak. This result is of analytical value for the differentiation of O-diglycosyl and di-O-glycosyl flavonoids.

  7. Gas phase fragmentation of eta2 coordinated aldehydes in [VO2(eta2-OCHR)]-: aldehyde structure dictates the nature of the products.

    PubMed

    Waters, Tom; Khairallah, George N; O'Hair, Richard A J

    2009-09-28

    The gas phase fragmentation reactions of eta2 coordinated aldehydes in [VO2(eta2-OCHR)]-, which have previously been shown to play a role in the catalytic oxidation of alcohols to aldehydes, were examined using a combination of isotope labelling experiments and collision induced dissociation in a quadrupole ion trap mass spectrometer. The experimental data were interpreted with the aid of density functional theory calculations (DFT). The types of fragmentation reactions observed depend on the nature of the R group. When R = H, the dominant fragmentation channel involves formation of [VO2H2]-via loss of CO. Minor losses of H2 and CH2O are also observed. When R = Me, loss of H2 is observed to give rise to an ion at m/z 125 corresponding to the formula [V, O3, C2, H2]-. DFT calculations on the [VO2(eta2-OCHR)]- and their CID reaction products have identified minimum energy structures for all reactants and products involved. DFT calculations also provided insights into key intermediates on the potential energy surface associated with these fragmentation reactions, including: [(H2)VO2(CO)]- in the case of R = H; and [HVO2(eta1-OCHCH2)]- in the case of R = Me. The results presented provide insights into potential side reactions occurring during catalysis of alcohols over vanadium oxides, for instance, the over-oxidation of methanol to carbon monoxide. PMID:19727457

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

    PubMed

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

    2013-09-24

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

  9. Fragmentation Chemistry of [Met-Gly]•+, [Gly-Met]•+, and [Met-Met]•+ Radical Cations

    NASA Astrophysics Data System (ADS)

    Lau, Justin Kai-Chi; Lo, Seydina; Zhao, Junfang; Siu, K. W. Michael; Hopkinson, Alan C.

    2013-04-01

    Radical cations [Met-Gly]•+, [Gly-Met]•+, and [Met-Met]•+ have been generated through collision-induced dissociation (CID) of [CuII(CH3CN)2(peptide)]•2+ complexes. Their fragmentation patterns and dissociation mechanisms have been studied both experimentally and theoretically using density functional theory at the UB3LYP/6-311++G(d,p) level. The captodative structure, in which the radical is located at the α-carbon of the N-terminal residue and the proton is on the amide oxygen, is the lowest energy structure on each potential energy surface. The canonical structure, with the charge and spin both located on the sulfur, and the distonic ion with the proton on the terminal amino group, and the radical on the α-carbon of the C-terminal residue have similar energies. Interconversion between the canonical structures and the captodative isomers is facile and occurs prior to fragmentation. However, isomerization to produce the distonic structure is energetically less favorable and cannot compete with dissociation except in the case of [Gly-Met]•+. Charge-driven dissociations result in formation of [ b n - H]•+ and a 1 ions. Radical-driven dissociation leads to the loss of the side chain of methionine as CH3-S-CH = CH2 producing α-glycyl radicals from both [Gly-Met]•+ and [Met-Met]•+. For [Met-Met]•+, loss of the side chain occurs at the C-terminal as shown by both labeling experiments and computations. The product, the distonic ion of [Met-Gly]•+, NH3 +CH(CH2CH2SCH3)CONHCH•COOH dissociates by loss of CH3S•. The isomeric distonic ion NH3 +CH2CONHC•(CH2CH2SCH3)COOH is accessible directly from the canonical [Gly-Met]•+ ion. A fragmentation pathway that characterizes this ion (and the distonic ion of [Met-Met]•+) is homolytic fission of the Cβ-Cγ bond to lose CH3SCH2 •.

  10. Collision-induced absorption in the O2 B-band region near 670 nm.

    PubMed

    Spiering, Frans R; Kiseleva, Maria B; Filippov, Nikolay N; van Kesteren, Line; van der Zande, Wim J

    2011-05-28

    We have determined the collision-induced absorption (CIA) spectrum in the O(2) B-band in pure oxygen. We present absolute extinction coefficients of the minimums in between rotational lines using cavity ring-down spectroscopy. The measured extinction is corrected for the B-band magnetic dipole absorption using a model which includes line-mixing. The remaining extinction consists of collision-induced absorption and Rayleigh scattering. We retrieve the magnitude of the Rayleigh scattering and the CIA spectrum based on their individual different behavior with density. The CIA spectrum of the B-band resembles that of the oxygen A-band in shape but not in magnitude. The contribution of CIA to the total B-band absorption is 40% higher in comparison to that of the A-band.

  11. 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.

  12. ATOMIC AND MOLECULAR PHYSICS: Collision-Induced Coherence Effect on Coherent Population Transfer

    NASA Astrophysics Data System (ADS)

    Yang, Xi-Hua; Zhang, Jun; Zhang, Hui-Fang; Yan, Xiao-Na

    2009-07-01

    We investigate the effect of collision-induced coherence on coherent population transfer with the stimulated Raman adiabatic passage technique in a double A-type four-level system with a widely separated excited doublet. It is shown that when the two pulsed lasers with Rabi frequencies nearly comparable to the energy separation of the doublet are tuned to the particular frequency where the condition for quantum interference is satisfied, the very low transfer efficiency due to the nonadiabatic coupling between the two degenerate adiabatic states could be enhanced significantly with the increase of the collisional decay rates in a moderate range. The enhanced transfer efficiency results from the weakening of the nonadiabatic coupling between the two degenerate adiabatic states realized through collision-induced destructive quantum interference.

  13. 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.

  14. 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.

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

    PubMed

    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 (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. PMID:25978892

  16. Exploring rearrangements along the fragmentation pathways of diuron anion: A combined experimental and computational investigation

    NASA Astrophysics Data System (ADS)

    Kanawati, Basem; Harir, Mourad; Schmitt-Kopplin, Philippe

    2009-12-01

    Diuron (3-(3,4-dichlorophenyl)-1,1-dimethylurea), a common herbicide from phenyl urea class, was investigated by studying the formation of several negative ions [M-H]- in the gas phase and the fragmentation behaviour of the thermodynamically most probably formed isomeric anions upon linear ion acceleration/collision experiments. The collision induced dissociation experiments (CID) were carried out in a hexapole-quadrupole-hexapole hybrid system coupled to 12 T magnet with infinity ICR cell for high resolution measurements. Two distinctive main pathways were observed in the MS/MS spectrum. Sustained off-resonance irradiation (SORI) experiments inside the ICR cell reinforce the fragmentation channels obtained from linear ion acceleration experiments. The fragmentation pathways were also completely investigated by the use of B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d) level of theory. Elimination of dimethylamine takes place in a two-step process, by which two successive 1,3 proton shifts occur. The second 1,3 proton shift is concerted with the departure of dimethylamine. The driving force for the (CH3)2NH elimination is the formation of isocyanate group. The formed primary product ion can further decompose to release HCl through a new transition state. A stable new aromatic product ion is formed with 10[pi] electrons. Loss of C3H5NO neutral from another anionic isomer of the precursor ion was also observed and is characteristic for the amide terminal of the diamide functional group. A concerted mechanism is proposed, by which N-C bond breakage and cyclization of the eliminated neutral fragment C3H5NO takes place simultaneously to form 1-methyl-aziridin-2-one.

  17. Supramolecular modification of ion chemistry: modulation of peptide charge state and dissociation behavior through complexation with cucurbit[n]uril (n = 5, 6) or alpha-cyclodextrin.

    PubMed

    Zhang, Haizhen; Grabenauer, Megan; Bowers, Michael T; Dearden, David V

    2009-02-26

    Electrospray Fourier transform ion cyclotron resonance mass spectrometry, ion mobility spectrometry, and computational methods were utilized to characterize the complexes between lysine or pentalysine with three prototypical host molecules: alpha-cyclodextrin (alpha-CD), cucurbit[5]uril (CB[5]), and cucurbit[6]uril (CB[6]). Ion mobility measurements show lysine forms externally bound, singly charged complexes with either alpha-CD or CB[5], but a doubly charged complex with the lysine side chain threaded through the host cavity of CB[6]. These structural differences result in distinct dissociation behaviors in collision-induced dissociation (CID) experiments: the alpha-CD complex dissociates via the simple loss of intact lysine, whereas the CB[5] complex dissociates to yield [CB[5] + H(3)O](+), and the CB[6] complex loses neutral NH(3) and CO, the product ion remaining a doubly charged complex. These results are consistent with B3LYP/6-31G* binding energies (kJ mol(-1)) of D(Lys + H(+)-alpha-CD) = 281, D(Lys + H(+)-CB[5]) = 327, and D(Lys + 2H(2+)-CB[6]) = 600. B3LYP/6-31G* geometry optimizations show complexation with alpha-CD stabilizes the salt bridge form of protonated lysine, whereas complexation with CB[6] stabilizes doubly protonated lysine. Complexation of the larger polypeptide pentalysine with alpha-CD forms a nonspecific adduct: no modification of the pentalysine charge state distribution is observed, and dissociation occurs via the simple loss of alpha-CD. Complexation of pentalysine with the cucurbiturils is more specific: the observed charge state distribution shifts higher on complexation, and fragmentation patterns are significantly altered relative to uncomplexed pentalysine: C-terminal fragment ions appear that are consistent with charge stabilization by the cucurbiturils, and the cucurbiturils are retained on the fragment ions. Molecular mechanics calculations suggest CB[5] binds to two protonated sites on pentalysine without threading onto the

  18. Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry.

    PubMed

    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 (C(15)H(31)CO(+), m/z 239) or 18:1 (9Z) (C(17)H(33)CO(+), 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 (+H(2)C-HC = CH-CH = CH(2)). 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 (13)C 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.

  19. Selective and nonselective cleavages in positive and negative CID of the fragments generated from in-source decay of intact proteins in MALDI-MS.

    PubMed

    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.

  20. 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.

  1. Simultaneous ESI-APCI+ ionization and fragmentation pathways for nine benzodiazepines and zolpidem using single quadrupole LC-MS.

    PubMed

    Galaon, Toma; Vacaresteanu, Catalina; Anghel, Dan-Florin; David, Victor

    2014-05-01

    Nine important 1,4-benzodiazepines and zolpidem were characterized by liquid chromatography-mass spectrometry using a multimode ionization source able to generate ions using both electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), and a single quadrupole mass analyzer. An optimum chromatographic separation was applied for all target compounds in less than 8 minutes using a Zorbax Eclipse Plus column (100 × 4.6 mm, 3.5 µm) kept at 35°C and a 0.3% HCOOH/ACN/IPA (61:34:5) mobile phase pumped at 1 ml/min. Optimization of LC-MS method generated low limit of quantitation (LOQ) values situated in the range 0.3-20.5 ng/ml. Comparison between differences in method sensitivity, under specified chromatographic conditions, when using ESI-only, APCI-only, and simultaneous ESI-APCI ionization with such a multimode source was discussed. Mixed ESI-APCI(+) mode proved to be the most sensitive ionization generating an average 35% detector response increase compared to ESI-only ionization and 350% detector response increase with respect to APCI-only ionization. Characterization of the nine benzodiazepines and zolpidem concerning their MS fragmentation pathway following 'in-source' collision-induced dissociation is discussed in detail and some general trends regarding these fragmentations are set.

  2. 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.

  3. Computation of Collision-Induced Absorption by Simple Molecular Complexes, for Astrophysical Applications

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

    The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of various types of planets and cool stars, such as late stars, low-mass stars, brown dwarfs, cool white dwarf stars, the ambers of the smaller, burnt out main sequence stars, exoplanets, etc., and therefore of special astronomical interest 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. First results for H_2-He complexes have already been applied to astrophysical models have shown great improvements in these models. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin, Int. J. of Spect., 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, 115, 6805-6812, 2011} 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 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Infrared absorption by collisional H_2-He complexes

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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://prime.psc.riken.jp/ .

  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. Collision-induced energy transfer in intermediate excited states of cesium

    NASA Astrophysics Data System (ADS)

    Lukaszewski, M.; Jackowska, I.

    1993-09-01

    We report an application of laser spectroscopy techniques to a study of collision-induced interactions in atomic excited states. Due to pulsed dye laser excitation a considerable selective population of highly excited states of ccsium is obtained. Collision-induced transfer of excitation energy between the excited states results in modifications in time and spectral characteristics of observed atomic fluorescence. Quantitative information on the efficiency of collisional processes can be obtained from the measurements of time constants of the time-resolved fluorescence signals and/or from those of the integrated intensities of the fluorescence lines. Both possibilities are used in the present work. Perturbation of nD (n=8-14) and nS (n=1O-15) states of cesium in collisions with noble-gas atoms is investigated. The cross sections for the transfer of excitation between fine-structure substates of the nD states (J mixing) and for the nS-(n-4)F intermultiplet transfer are obtained.

  12. Theoretical development of a simplified wheelset model to evaluate collision-induced derailments of rolling stock

    NASA Astrophysics Data System (ADS)

    Koo, Jeong Seo; Choi, Se Young

    2012-06-01

    A theoretical method is proposed to predict and evaluate collision-induced derailments of rolling stock by using a simplified wheelset model and is verified with dynamic simulations. Because the impact forces occurring during collision are transmitted from the car body to the bogies and axles through suspensions, rolling stock leads to derailment as a result of the combination of horizontal and vertical impact forces applied to the axle and a simplified wheelset model enforced at the axle can be used to theoretically formulate derailment behaviors. The derailment type depends on the combination of the horizontal and vertical forces, the flange angle and the friction coefficient. According to collision conditions, wheel-climb, wheel-lift or roll-over derailment can occur between the wheel and the rail. In this theoretical derailment model of a simplified wheelset, the derailment types are classified as Slip-up, Slip/roll-over, Climb-up, Climb/roll-over and pure Roll-over according to the derailment mechanisms between the wheel and the rail and the theoretical conditions needed to generate each derailment mechanism are proposed. The theoretical wheelset model is verified by dynamic simulation and its applicability is demonstrated by comparing the simulation results of the theoretical wheelset model with those of an actual wheelset model. The theoretical derailment wheelset model is in good agreement with the virtual testing model simulation for a collision-induced derailment of rolling stock.

  13. Interactions of protons with furan molecules studied by collision-induced emission spectroscopy at the incident energy range of 50-1000 eV

    NASA Astrophysics Data System (ADS)

    Wasowicz, Tomasz J.; Pranszke, Boguslaw

    2016-08-01

    Investigations of the ion-molecule reactions provide insight into many fields ranging from the stellar wind interaction with interstellar media, up to medicine and industrial applications. Besides the applications, the understanding of these processes is itself a problem of fundamental importance. Thus, interactions of protons with the gas-phase furan molecules have been investigated for the first time in the energy range of 50-1000 eV exploiting collision-induced emission spectroscopy. Recorded spectra reveal emission of the atomic H β to H θ lines of the hydrogen Balmer series and the molecular bands of vibrationally and rotationally excited diatomic CH fragments created in the A2 Δ and B2Σ- electronic states. The measurements of the emission yields of the excited fragments by recording their intensities at different projectile energies have been performed. The highest yields have been observed for production of hydrogen atoms which intensities rapidly decreased with increasing principal quantum number n . From the H ( n = 4-7) intensity ratios depopulation factors of hydrogen excited states have been determined at each impact energy and possible collisional mechanisms leading to enhanced production of the hydrogen atoms have been suggested. We compare and discuss our results with improved data set of proton collisions with tetrahydrofuran (THF) molecules, the hydrogenated derivatives of furan.

  14. Interactions of protons with furan molecules studied by collision-induced emission spectroscopy at the incident energy range of 50-1000 eV

    NASA Astrophysics Data System (ADS)

    Wasowicz, Tomasz J.; Pranszke, Boguslaw

    2016-08-01

    Investigations of the ion-molecule reactions provide insight into many fields ranging from the stellar wind interaction with interstellar media, up to medicine and industrial applications. Besides the applications, the understanding of these processes is itself a problem of fundamental importance. Thus, interactions of protons with the gas-phase furan molecules have been investigated for the first time in the energy range of 50-1000 eV exploiting collision-induced emission spectroscopy. Recorded spectra reveal emission of the atomic Hβ to Hθ lines of the hydrogen Balmer series and the molecular bands of vibrationally and rotationally excited diatomic CH fragments created in the A2Δ and B2Σ- electronic states. The measurements of the emission yields of the excited fragments by recording their intensities at different projectile energies have been performed. The highest yields have been observed for production of hydrogen atoms which intensities rapidly decreased with increasing principal quantum number n. From the H (n = 4-7) intensity ratios depopulation factors of hydrogen excited states have been determined at each impact energy and possible collisional mechanisms leading to enhanced production of the hydrogen atoms have been suggested. We compare and discuss our results with improved data set of proton collisions with tetrahydrofuran (THF) molecules, the hydrogenated derivatives of furan. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic, B. Sivaraman.

  15. 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.

  16. 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

  17. 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.

  18. Structures and fragmentations of cobalt(II)-cysteine complexes in the gas phase.

    PubMed

    Buchmann, William; Spezia, Riccardo; Tournois, Guewen; Cartailler, Thierry; Tortajada, Jeanine

    2007-04-01

    The electronebulization of a cobalt(II)/cysteine(Cys) mixture in water/methanol (50/50) produced mainly cobalt-cationized species. Three main groups of the Co-cationized species can be distinguished in the ESI-MS spectrum: (1) the cobalt complexes including the cysteine amino acid only (they can be singly charged, for example, [Co(Cys)n- H]+ with n = 1-3 or doubly charged such as [Co + (Cys)2]2+); (2) the cobalt complexes with methanol: [Co(CH3OH)n- H]+ with n = 1-3, [Co(CH3OH)4]2+; and (3) the complexes with the two different types of ligands: [Co(Cys)(CH3OH) - H]+. Only the singly charged complexes were observed. Collision-induced dissociation (CID) products of the [Co(Cys)2]2+, [Co(Cys)2 - H]+ and [Co(Cys) - H]+ complexes were studied as a function of the collision energy, and mechanisms for the dissociation reactions are proposed. These were supported by the results of deuterium labelling experiments and by density functional theory calculations. Since [Co(Cys) - H]+ was one of the main product ions obtained upon the CID of [Co(Cys)2]2+ and of [Co(Cys)2 - H]+ under low-energy conditions, the fragmentation pathways of [Co(Cys) - H]+ and the resulting product ion structures were studied in detail. The resulting product ion structures confirmed the high affinity of cobalt(II) for the sulfur atom of cysteine. PMID:17323419

  19. 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.

  20. 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.

  1. 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.

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

    DOE PAGES

    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

  3. 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.

  4. Effect of laser frequency on a collision-induced radiative process

    NASA Technical Reports Server (NTRS)

    Devries, P. L.; George, T. F.

    1981-01-01

    A review is presented of the principles of collision induced radiative processes, followed by an examination of the effects of laser frequencies on these processes. A one-dimensional problem involving two electron states is considered, and it is found that the Hamiltonian of the radiation field is dominated by electric-dipole interaction which couples states of different parity. Transitions are noted to be dependent on collisions, and the complexities of three-dimensional systems are expressed as considerations of the angular momentum of the photon, the necessity of treating different states simultaneously, and the fact that a radiation field destroys rotational invariance. Changing the radiation frequency alters the crossing point and offers opportunities to study the interplay of potential surfaces with molecular dynamics. Experiments on Na+A systems are outlined for several collision energies and various laser frequencies. Multiple crossings were obtained, although the total cross-section, at all energies, decreased at 18,350/cm.

  5. 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.

  6. Collision-induced photon echo at the transition 0{r_reversible}1 in ytterbium vapor: Direct proof of depolarizing collision anisotropy

    SciTech Connect

    Rubtsova, N. N.; Gol'dort, V. G.; Ishchenko, V. N.; Khvorostov, E. B.; Kochubei, S. A.; Reshetov, V. A.; Yevseyev, I. V.

    2011-09-15

    A collision-induced photon echo arising at the transition 0{r_reversible}1 of ytterbium in the presence of heavy atomic buffer is investigated. Collision-induced echo signal appears in the case of mutually orthogonal linear polarizations of exciting pulses and it is absent without buffer. Collision-induced echo power grows with buffer pressure up to the maximum value and decays exponentially at further buffer pressure growth. Collision-induced echo power is essentially less than that of the ordinary echo generated by pulses with parallel polarizations in the same mixture, and its polarization is linear with the polarization vector directed along that of the first exciting pulse. All the properties of collision-induced photon echo are explained on the basis of collision relaxation dependence on the direction of active atom velocity.

  7. Origin of abnormally sharp features in collision-induced spectra of cryosolutions

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    A weak, paradoxically narrow resonance feature (shortly, the r-line) near the O2 fundamental frequency in the collision-induced absorption spectrum of oxygen dissolved in liquid argon and liquid nitrogen (T = 89 K) is resolved for the first time. An accurate band shape fitting routine to separate the r-line from the by-far more intense diffuse background and to study its behavior versus the oxygen mole fraction x which ranged from 0.03 up to 0.23 has been elaborated. At small x (≲0.07), the r-line intensity was found to scale as x2 leaving no doubt that it is due to the solute-solute (O2-O2) interactions. In line with our results on the pH2-LNe cryosystem [Herrebout, Phys. Rev. Lett. 101, 093001 (2008)], the Lorentzian r-line shape and its extraordinary sharpness (half width at half height ≈ 1 cm-1) are indicative of the motional narrowing of the relative solute-solute translational spectrum. As x is further raised, ternary solute-solute interactions impede the r-line growth in the O2-LAr spectrum because of the cancellation effect [J. Van Kranendonk, Physica 23, 825 (1957)]. Theoretical arguments are given that multiple interactions between the solutes should finally destroy the solute-solute induced r-line when the mixed solution approaches the limit of the pure liquid (x = 1). Interestingly, the nonbinary effects are too weak to appreciably affect the quadratic r-line scaling in the O2-LN2 cryosystem which persists up to x = 0.23. It is emphasized that studies of the resonant features in the collision-induced spectra of binary cryosolutions open up unique opportunities to spectroscopically trace the microscopic-scale diffusion.

  8. Vibrational nonequilibrium effects on diatomic dissociation rates

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1993-01-01

    The collision-induced dissociation rate of diatomic molecules from a ladder of rotational and anharmonic vibrational states is developed, and the correction for vibrational nonequilibrium is considered. The result is similar to an analytic correction derived by Hammerling et al. (1959) for harmonic oscillators. An empirical correction algorithm suggested by Park (1987, 1990) gives similar results when vibrational temperature is comparable to kinetic temperature but underestimates the dissociation rate when vibrational temperature is small compared with the kinetic temperature. This algorithm uses an effective temperature in the experimentally determined Arrhenius expression for the rate coefficient, which is a weighted average of the vibrational and kinetic temperature, whereas theory indicates that kinetic temperature should appear only in the exponential term of the Arrhenius expression. Nevertheless, an effective temperature can always be found that will numerically duplicate the proper rate coefficient at any given condition, but a constant weighting factor cannot be expected to provide this. However, the algorithm can he adjusted to give reasonable results over a range of conditions if the geometric weighting factor is taken to be a simple linear function of the ratio of vibrational to kinetic temperature in the gas.

  9. Unimolecular dissociation of anions derived from maleic acid (MaH2) in the gas phase: MaH- and MaMgCl--- relationship to Grignard chemistry and reductive CO2 fixation.

    PubMed

    Miller, Glenn B S; Fäseke, Vincent; Uggerud, Einar

    2015-01-01

    We have conducted collision induced dissociation experiments on the hydrogen maleate anion (MaH(-), m/z = 115) and the anionic maleate MgCl complex (MaMgC(-), m/z = 173). In addition, we have computationally investigated the observed fragmentation reactions. We find that both anions readily undergo two consecutive decarboxylations resulting in product ions at m/z = 71 and 27 for MaH(-), and at m/z = 129 and 85 for MaMgCl(-). The first decarboxylation is more facile for MaMgCl(-) than for MaH(-), while loss of CO(2) from Ma(-CO(2))H(-) is more facile than for Ma(-CO(2))MgCl(-). We also find that MaH(-) loses water, and we propose a mechanism for this loss. No first-generation fragmentation product other than Ma(-CO(2))MgCl(-) is seen for MaMgCl(-). Based on the observed unimolecular chemistry, we discuss some of its implications on reductive CO(2)-fixation and Grignard chemistry. PMID:26307734

  10. Dissociative Photoionization of Diethyl Ether.

    PubMed

    Voronova, Krisztina; Mozaffari Easter, Chrissa M; Covert, Kyle J; Bodi, Andras; Hemberger, Patrick; Sztáray, Bálint

    2015-10-29

    The dissociative photoionization of internal energy selected diethyl ether ions was investigated by imaging photoelectron photoion coincidence spectroscopy. In a large, 5 eV energy range Et2O(+) cations decay by two parallel and three sequential dissociative photoionization channels, which can be modeled well using statistical theory. The 0 K appearance energies of the CH3CHOCH2CH3(+) (H-loss, m/z = 73) and CH3CH2O═CH2(+) (methyl-loss, m/z = 59) fragment ions were determined to be 10.419 ± 0.015 and 10.484 ± 0.008 eV, respectively. The reemergence of the hydrogen-loss ion above 11 eV is attributed to transition-state (TS) switching, in which the second, outer TS is rate-determining at high internal energies. At 11.81 ± 0.05 eV, a secondary fragment of the CH3CHOCH2CH3(+) (m/z = 73) ion, protonated acetaldehyde, CH3CH═OH(+) (m/z = 45) appears. On the basis of the known thermochemical onset of this fragment, a reverse barrier of 325 meV was found. Two more sequential dissociation reactions were examined, namely, ethylene and formaldehyde losses from the methyl-loss daughter ion. The 0 K appearance energies of 11.85 ± 0.07 and 12.20 ± 0.08 eV, respectively, indicate no reverse barrier in these processes. The statistical model of the dissociative photoionization can also be used to predict the fractional ion abundances in threshold photoionization at large temperatures, which could be of use in, for example, combustion diagnostics. PMID:26444101

  11. Dissociative phenomenology of dissociative identity disorder.

    PubMed

    Dell, Paul F

    2002-01-01

    The goal of this study was to investigate the dissociative phenomenology of dissociative identity disorder (DID). The Multidimensional Inventory of Dissociation (MID) was administered to 34 patients with DID, 23 patients with dissociative disorder not otherwise specified (DDNOS), 52 patients with mixed psychiatric disorders, and 58 normal individuals. DID patients obtained significantly higher scores than the other three groups on 27 dissociation-related variables. DDNOS patients had significantly higher scores than normals and mixed psychiatric patients on 17 and 15 dissociation-related variables, respectively. The findings of the present study are virtually identical to a large body of replicated findings about the dissociative phenomenology of DID. This broad range of dissociation-related phenomena, which routinely occurs in individuals with DID, is largely absent from the DSM-IV-TR account of DID. Factor analysis of the 11 dimensions of dissociation that are measured by the MID extracted only one factor that accounted for 85% of the variance. It was concluded that dissociation is a unifactorial taxon or natural type that has different aspects or epiphenomena (i.e., amnesia, depersonalization, voices, trance, etc.).

  12. 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.

  13. Comparing the gas-phase fragmentation reactions of protonated and radical cations of the tripeptides GXR

    NASA Astrophysics Data System (ADS)

    Wee, Sheena; O'Hair, Richard A. J.; McFadyen, W. David

    2004-05-01

    Electrospray ionization (ESI) mass spectrometry of methanolic solutions of mixtures of the copper salt (2,2':6',2''-terpyridine)copper(II) nitrate monohydrate ([Cu(II)(tpy)(NO3)2].H2O) and a tripeptide GXR (where X = 1 of the 20 naturally occurring amino acids) yielded [Cu(II)(tpy)(GXR)][radical sign]2+ ions, which were then subjected to collision induced dissociation (CID). In all but one case (GRR), these [Cu(II)(tpy)(GXR)][radical sign]2+ ions fragment to form odd electron GXR[radical sign]+ radical cations with sufficient abundance to examine their gas-phase fragmentation reactions. The GXR[radical sign]+ radical cations undergo a diverse range of fragmentation reactions which depend on the nature of the side chain of X. Many of these reactions can be rationalized as arising from the intermediacy of isomeric distonic ions in which the charge (i.e. proton) is sequestered by the highly basic arginine side chain and the radical site is located at various positions on the tripeptide including the peptide back bone and side chains. The radical sites in these distonic ions often direct the fragmentation reactions via the expulsion of small radicals (to yield even electron ions) or small neutrals (to form radical cations). Both classes of reaction can yield useful structural information, allowing for example, distinction between leucine and isoleucine residues. The gas-phase fragmentation reactions of the GXR[radical sign]+ radical cations are also compared to their even electron [GXR+H]+ and [GXR+2H]2+ counterparts. The [GXR+H]+ ions give fewer sequence ions and more small molecule losses while the [GXR+2H]2+ ions yield more sequence information, consistent with the [`]mobile proton model' described in previous studies. In general, all three classes of ions give complementary structural information, but the GXR[radical sign]+ radical cations exhibit a more diverse loss of small species (radicals and neutrals). Finally, links between these gas-phase results and key

  14. 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.

  15. Collision-induced light scattering in a thin xenon layer between graphite slabs - MD study.

    PubMed

    Dawid, A; Górny, K; Wojcieszyk, D; Dendzik, Z; Gburski, Z

    2014-08-14

    The collision-induced light scattering many-body correlation functions and their spectra in thin xenon layer located between two parallel graphite slabs have been investigated by molecular dynamics computer simulations. The results have been obtained at three different distances (densities) between graphite slabs. Our simulations show the increased intensity of the interaction-induced light scattering spectra at low frequencies for xenon atoms in confined space, in comparison to the bulk xenon sample. Moreover, we show substantial dependence of the interaction-induced light scattering correlation functions of xenon on the distances between graphite slabs. The dynamics of xenon atoms in a confined space was also investigated by calculating the mean square displacement functions and related diffusion coefficients. The structural property of confined xenon layer was studied by calculating the density profile, perpendicular to the graphite slabs. Building of a fluid phase of xenon in the innermost part of the slot was observed. The nonlinear dependence of xenon diffusion coefficient on the separation distance between graphite slabs has been found.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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 ...

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Rannulu, Nalaka S.; Cole, Richard B.

    2012-09-01

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

  10. Analysis and interpretation of satellite fragmentation data

    NASA Technical Reports Server (NTRS)

    Tan, Arjun

    1987-01-01

    The velocity perturbations of the fragments of a satellite can shed valuable information regarding the nature and intensity of the fragmentation. A feasibility study on calculating the velocity perturbations from existing equations was carried out by analyzing 23 major documented fragmentation events. It was found that whereas the calculated values of the radial components of the velocity change were often unusually high, those in the two other orthogonal directions were mostly reasonable. Since the uncertainties in the radial component necessarily translate into uncertainties in the total velocity change, it is suggested that alternative expressions for the radial component of velocity be sought for the purpose of determining the cause of the fragmentation from the total velocity change. The calculated variances in the velocity perturbations in the two directions orthogonal to the radial vector indicate that they have the smallest values for collision induced breakups and the largest values for low-intensity explosion induced breakups. The corresponding variances for high-intensity explosion induced breakups generally have values intermediate between those of the two extreme categories. A three-dimensional plot of the variances in the two orthogonal velocity perturbations and the plane change angle shows a clear separation between the three major types of breakups. This information is used to reclassify a number of satellite fragmentation events of unknown category.

  11. 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.

  12. The Internal-collision-induced Magnetic Reconnection and Turbulence (ICMART) Model of Gamma-ray Bursts

    NASA Astrophysics Data System (ADS)

    Zhang, Bing; Yan, Huirong

    2011-01-01

    The recent Fermi observation of GRB 080916C shows that the bright photosphere emission associated with a putative fireball is missing, which suggests that the central engine likely launches a Poynting-flux-dominated (PFD) outflow. We propose a model of gamma-ray burst (GRB) prompt emission in the PFD regime, namely, the Internal-Collision-induced MAgnetic Reconnection and Turbulence (ICMART) model. It is envisaged that the GRB central engine launches an intermittent, magnetically dominated wind, and that in the GRB emission region, the ejecta is still moderately magnetized (e.g., 1 <~ σ <~ 100). Similar to the internal shock (IS) model, the mini-shells interact internally at the radius R IS ~ Γ2 cΔt. Most of these early collisions, however, have little energy dissipation, but serve to distort the ordered magnetic field lines entrained in the ejecta. At a certain point, the distortion of magnetic field configuration reaches the critical condition to allow fast reconnection seeds to occur, which induce relativistic MHD turbulence in the interaction regions. The turbulence further distorts field lines easing additional magnetic reconnections, resulting in a runway release of the stored magnetic field energy (an ICMART event). Particles are accelerated either directly in the reconnection zone, or stochastically in the turbulent regions, which radiate synchrotron photons that power the observed gamma rays. Each ICMART event corresponds to a broad pulse in the GRB light curve, and a GRB is composed of multiple ICMART events. This model retains the merits of IS and other models, but may overcome several difficulties/issues faced by the IS model (e.g., low efficiency, fast cooling, electron number excess, Amati/Yonetoku relation inconsistency, and missing bright photosphere). Within this model, the observed GRB variability timescales could have two components, one slow component associated with the central engine time history, and another fast component associated with

  13. Collision-Induced Spectra: AN Avenue to Investigate Microscopic-Scale Diffusion in Fluids

    NASA Astrophysics Data System (ADS)

    Herrebout, Wouter A.; van der Veken, Benjamin J.; Kouzov, Alexander

    2014-06-01

    New data on the IR spectra induced by intermolecular interactions in liquid cryogenic mixtures at T=89 K (O2 in LAr and LN2 and binary O2-Ar solutions in LN2) are reported. The induced fundamental bands appear as diffuse pedestals (with FWHH≈100 cm-1) on which weak, paradoxically sharp lines (FWHH≈2 cm-1) develop at the 2326 and 1552 cm-1 frequencies of the free-molecule vibrational transitions in N2 and O2, respectively. In LAr and LN2 these lines were carefully separated and studied at varied O2 concentrations up to c=0.23 mole fractions (mf). While the 1552 cm-1 line scales as c[O2]2 and thus is induced by the O2-O2 interactions in a bulk of cryosolvent (Ar, N2), the 2326 cm-1 feature varies linearly with c[O2] and hence is caused by interaction of a guest (O2) with a vibrating host (N_2). The impurity induction mechanism was further supported by our data on the binary O2-Ar solutions in LN2 %for which the spectra were recorded at the fixed c[O2] (0.03 and 0.06 mf) and the varied c% [Ar]≤0.2 mf. Both series revealed the same (linear) enhancement of the sharp N2 line by argon, in an accord with our previous studies of the Ar-LN2 system. The results suggest that the resonance 2326 cm-1 feature is primarily due to the local distortion of the first coordination sphere around a vibrating N_2 by a guest molecule. We also notice that the resonance lines should be due to the dispersion- and overlap-induced dipole moments independent on the rotational degrees of freedom. As our previous studies of the H2-LNe system showed, the unusual line sharpness is a conspicuous manifestation of the relative solvent-solute and solute-solute translations dramatically retarded in a liquid by a fast velocity relaxation, an effect directly related to the microscopic-scale diffusion. The collision-induced spectra thus open up new vistas for studies of microscopic liquid dynamics. W.A. Herrebout, A.A. Stolov, E.J. Sluyts, and B.J. van der Veken, Chem. Phys. Lett. 295, 223 (1998) J

  14. Primary fragmentation pathways of gas phase [M(uracil-H)(uracil)]+ complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): loss of uracil versus HNCO.

    PubMed

    Ali, Osama Y; Randell, Nicholas M; Fridgen, Travis D

    2012-04-23

    Complexes formed between metal dications, the conjugate base of uracil, and uracil are investigated by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Positive-ion electrospray spectra show that [M(Ura-H)(Ura)](+) (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd, Mg, Ca, Sr, Ba, or Pb) is the most abundant ion even at low concentrations of uracil. SORI-CID experiments show that the main primary decomposition pathway for all [M(Ura-H)(Ura)](+) , except where M=Ca, Sr, Ba, or Pb, is the loss of HNCO. Under the same SORI-CID conditions, when M is Ca, Sr, Ba, or Pb, [M(Ura-H)(Ura)](+) are shown to lose a molecule of uracil. Similar results were observed under infrared multiple-photon dissociation excitation conditions, except that [Ca(Ura-H)(Ura)](+) was found to lose HNCO as the primary fragmentation product. The binding energies between neutral uracil and [M(Ura-H)](+) (M=Zn, Cu, Ni, Fe, Cd, Pd ,Mg, Ca, Sr Ba, or Pb) are calculated by means of electronic-structure calculations. The differences in the uracil binding energies between complexes which lose uracil and those which lose HNCO are consistent with the experimentally observed differences in fragmentation pathways. A size dependence in the binding energies suggests that the interaction between uracil and [M(Ura-H)](+) is ion-dipole complexation and the experimental evidence presented supports this. PMID:22447672

  15. 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.

  16. 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.

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

    DOE PAGES

    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

  18. 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.

  19. 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.

  20. LOVTRAP: an optogenetic system for photoinduced protein dissociation.

    PubMed

    Wang, Hui; Vilela, Marco; Winkler, Andreas; Tarnawski, Miroslaw; Schlichting, Ilme; Yumerefendi, Hayretin; Kuhlman, Brian; Liu, Rihe; Danuser, Gaudenz; Hahn, Klaus M

    2016-09-01

    LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins. PMID:27427858

  1. Influence of Heteroanion and Ammonium Cation Size on the Composition and Gas-Phase Fragmentation of Polyoxovanadates

    SciTech Connect

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

    2013-11-15

    This paper describes the results of a systematic experimental investigation of the influence of different size cationic ammonium ligands and heteroanions on the composition, ionic charge state and gas-phase fragmentation pathways of anionic polyoxovanadates synthesized in solution. Four separate solutions of olyoxometalates (POMs) were prepared using all possible combinations of the tetraethylammonium [(C2H5)4N+] ligand, chloride (Cl-) heteroanion, tetrabutylammonium [(C4H9)4N+] ligand and acetate (CH3CO2-) heteroanion. Employing electrospray ionization combined with high-resolution mass spectrometry (ESI-MS) we demonstrate that POM solutions synthesized using the small [(C2H5)4N+] ligand and Cl-heteroanion are composed predominately of large doubly and triply charged chlorine containing clusters with a size distribution centered at fourteen vanadium atoms. POM solutions prepared using the Cl- anion and [(C4H9)4N+] ligand are shown to contain slightly larger clusters with fifteen and sixteen vanadium atoms, thereby indicating that the size of the cationic ammonium ligand exerts only a weak influence on the polymerization of polyoxovanadates. POM solutions prepared using (C2H5)4NCl and (C4H9)4NCl also produced peaks consistent with the attachment of one and two ammonium cations to the larger clusters. Solutions prepared using the large CH3CO2 - heteroanion, in contrast, are demonstrated to contain much smaller singly and doubly *Manuscript Click here to view linked References 2 charged clusters with a size distribution centered at six vanadium atoms. In addition, while incorporation of one and two ammonium ligands into the smaller clusters was observed, no POMs containing the CH3CO2 - heteroanion were identified. The gas-phase fragmentation pathways of representative POMs containing one and two ammonium ligands were examined using collision induced dissociation (CID) and mass spectrometry. Similar primary fragmentation pathways involving partial loss of a ligand

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. Dissociation energy and dynamics of water clusters

    NASA Astrophysics Data System (ADS)

    Ch'ng, Lee Chiat

    The state-to-state vibrational predissociation (VP) dynamics of water clusters were studied following excitation of a vibrational mode of each cluster. Velocity-map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated center-of-mass translational energy distributions. Product energy distributions and dissociation energies were determined. Following vibrational excitation of the HCl stretch fundamental of the HCl-H2O dimer, HCl fragments were detected by 2 + 1 REMPI via the f 3□2(nu' = 0) ← X 1Sigma+(nu'' = 0) and V1Sigma + (nu' = 11 and 12) ← X1Sigma+ (nu'' = 0) transitions. REMPI spectra clearly show HCl from dissociation produced in the ground vibrational state with J'' up to 11. The fragments' center-of-mass translational energy distributions were determined from images of selected rotational states of HCl and were converted to rotational state distributions of the water cofragment. All the distributions could be fit well when using a dimer dissociation energy of bond dissociation energy D0 = 1334 +/- 10 cm--1. The rotational distributions in the water cofragment pair-correlated with specific rotational states of HCl appear nonstatistical when compared to predictions of the statistical phase space theory. A detailed analysis of pair-correlated state distributions was complicated by the large number of water rotational states available, but the data show that the water rotational populations increase with decreasing translational energy. H2O fragments of this dimer were detected by 2 + 1 REMPI via the C˜1B1(000) ← X˜1A1(000) transition. REMPI clearly shows that H2O from dissociation is produced in the ground vibrational state. The fragment's center-of-mass translational energy distributions were determined from images of selected rotational states of H2O and were converted to rotational state distributions of the HCl cofragment. The distributions gave D0 = 1334 +/- 10 cm --1 and show a clear

  8. The production of CO(+) (B2Sigma +) from dissociative photoionization excitation of CO2

    NASA Astrophysics Data System (ADS)

    Wu, C. Y. R.; Judge, D. L.

    1986-04-01

    The dissociative photoionization excitation process in CO2 is studied. In contrast to previous studies, attention is focused on the vibrational and rotational levels produced in fragment ions, partial cross-section measurements for producing such fragment ions in a specific quantum state, and the mechanisms that govern the dissociative ionization excitation processes. The partial fluorescence cross section for the production of CO(+) (B2Sigma +) from CO2 over a wide wavelength range was measured. It is concluded that the production of the CO(+) (B2Sigma +) fragment near the threshold is through a direct dissociative photoionization process.

  9. The production of CO(+) (B2Sigma +) from dissociative photoionization excitation of CO2

    NASA Technical Reports Server (NTRS)

    Wu, C. Y. R.; Judge, D. L.

    1986-01-01

    The dissociative photoionization excitation process in CO2 is studied. In contrast to previous studies, attention is focused on the vibrational and rotational levels produced in fragment ions, partial cross-section measurements for producing such fragment ions in a specific quantum state, and the mechanisms that govern the dissociative ionization excitation processes. The partial fluorescence cross section for the production of CO(+) (B2Sigma +) from CO2 over a wide wavelength range was measured. It is concluded that the production of the CO(+) (B2Sigma +) fragment near the threshold is through a direct dissociative photoionization process.

  10. 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

  11. 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.

  12. 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.

  13. Unified first principles description from warm dense matter to ideal ionized gas plasma: electron-ion collisions induced friction.

    PubMed

    Dai, Jiayu; Hou, Yong; Yuan, Jianmin

    2010-06-18

    Electron-ion interactions are central to numerous phenomena in the warm dense matter (WDM) regime and at higher temperature. The electron-ion collisions induced friction at high temperature is introduced in the procedure of ab initio molecular dynamics using the Langevin equation based on density functional theory. In this framework, as a test for Fe and H up to 1000 eV, the equation of state and the transition of electronic structures of the materials with very wide density and temperature can be described, which covers a full range of WDM up to high energy density physics. A unified first principles description from condensed matter to ideal ionized gas plasma is constructed.

  14. 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.

  15. 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.

  16. 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.

  17. Generalised dissociative amnesia.

    PubMed

    Sengupta, S N; Jena, S; Saxena, S

    1993-12-01

    A case of generalised dissociative amnesia is presented, which illustrates several characteristic features of this uncommon condition. The case showed poor response to thiopentone interviews and in vivo cueing. Amnesia had persisted at six months follow up.

  18. 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.

  19. Dependence of Decamethylcyclopentasiloxane (DMCPS) Dissociation on Ionized Energy by Using Quadrupole Mass Spectrum

    NASA Astrophysics Data System (ADS)

    Zhang, Haiyan; Ye, Chao; Ning, Zhaoyuan

    2010-12-01

    Dependence of decamethylcyclopentasiloxane (DMCPS) organosilicon dissociation on ionized energy in the energy range of 25 eV to 70 eV is investigated by using a quadrupole mass spectrometry At the ionized energy below 55 eV, the dissociation of DMCPS is dominant. As the ionized energy is above 55 eV, the DMCPS dissociation achieves the maximum cross section, while the fragments from the DMCPS dissociation can further dissociate, which leads to a different ingredient of fragments. At the lower ionized energy of 25 eV, the main fragments are SiOC2H5+, SiCH+, Si+, O2+ and CH3+ ions, which shows an important effect on the SiCOH low-k film deposition.

  20. Multipole storage assisted dissociation, a novel in-source dissociation technique for electrospray ionization generated ions.

    PubMed

    Sannes-Lowery, K; Griffey, R H; Kruppa, G H; Speir, J P; Hofstadler, S A

    1998-01-01

    In this work we present a novel in-source dissociation scheme referred to as multipole storage assisted dissociation (MSAD) for electrospray ionization (ESI) generated ions in which dissociation is effected by employing extended ion accumulation intervals in a high pressure rf-only hexapole assembly prior to mass analysis. Following an extended ion accumulation interval in which ions are confined in the rf-only hexapole, ions are gated out of the hexapole, trapped, and mass analyzed in the trapped ion cell of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The accumulation region is comprised of an rf-only hexapole ion guide which separates two electrodes, a biased skimmer cone, and an auxiliary 'gate' electrode at the low pressure end of the hexapole. This technique should be applicable to other mass spectrometry platforms compatible with pulsed ionization sources including quadrupole ion traps, and time-of-flight mass analyzers. This concept is demonstrated with the dissociation of a small protein in which selective fragmentation is observed at labile amino acid linkages producing primarily y-type fragment ions.

  1. 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.

  2. Electron-Impact Dissociation of Hydrocarbon Molecular Ions

    SciTech Connect

    Bannister, Mark E; Schultz, David Robert

    2014-01-01

    Absolute cross sections for electron-impact dissociation of CH_x^+ (x=1,2,3) producing CH_y^+ (y=0,1,2) fragment ions were measured in the 3-100 eV range using a crossed electron-ion beams technique with total uncertainties of about 11% near the cross section peaks. For CH^+ dissociation, although the measured energy dependence agrees well with two sets of storage ring measurements, the magnitude of the present results lies about 15% to 25% below the other results at the cross section peak near 40 eV. For dissociation of CH_2^+, the cross sections are nearly identical for energies above 15 eV, but they are dramatically different at lower energies. The CH^+ channel exhibits a strong peak rising from an observed threshold of about 6 eV; the C^+ channel is relatively flat down to the lowest measured energy. For dissociation of CH_3^+ and CD_3^+, good agreement is found with other results reported for the CH^+ fragment, but some differences are found for the CD_2^+ and C^+ fragments. A pilot study has also been undertaken to assess the feasibility of applying a molecular dynamics approach to treat the full range of electron-hydrocarbon dissociation processes, especially for energies above a few eV, in order to provide an overarching theoretical model that can be readily applied. Comparison with the experimental data for CH^+ shows favorable agreement.

  3. The importance of momentum transfer in collision-induced breakups in low Earth orbit

    NASA Technical Reports Server (NTRS)

    Reynolds, Robert C.; Lillie, Brian J.

    1991-01-01

    Although there is adequate information on larger objects in low Earth orbit, specifically those objects larger than about 10 cm in diameter, there is little direct information on objects from this size down to 1 mm. Yet, this is the sized regime where objects acting as projectiles represent the ability to seriously damage or destroy a functioning spacecraft if they collide with it. The observed consequences of known collisional breakups in orbit indicates no significant momentum transfer in the resulting debris cloud. The position taken in this paper is that this is an observational selection effect: what is seen in these events is an explosion-like breakup of the target structure arising from shock waves introduced into the structure by the collision, but one that occurs significantly after the collision processes are completed; the collision cloud, in which there is momentum transfer, consists of small, unobserved fragments. Preliminary computations of the contribution of one known collisional breakup, Solwind at 500 km in 1985, and Cosmos 1275 in 1981, assume no momentum transfer on breakup and indicate that these two events are the dominant contributors to the current millimeter and centimeter population. A different story would emerge if momentum transfer was taken into account. The topics covered include: (1) observation of on-orbit collisional breakups; (2) a model for momentum transfer; and (3) velocity space representation of breakup clouds.

  4. Dissociation as complex adaptation.

    PubMed

    Sel, R

    1997-03-01

    In this article the general theory of complex adaptive systems, substantiated by non-linear dynamics, will be used to put the dissociative disorders into a theoretical framework and clarify their genesis and presentation. When a system is far out of equilibrium, dissipative structures may be formed ('order out of chaos', as Prigogine (1) has put it). These structures provide the starting point for further evolution and co-evolution of competing groups of functional schemata divided on a bifurcation surface. Complex adaptation is almost inevitable in a complicated system (such as the brain) driven by non-linear dynamics. Dissociation is thus regarded as a consequence of adaptation to a chaotic environment rich in contrasts. In a sufficiently complex environment a person with dissociative identity disorder is more adapted and thus more likely to occur than a 'normal' monopersonality individual.

  5. 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.

  6. 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…

  7. Dissociation: the clinical realities.

    PubMed

    Frankel, F H

    1996-07-01

    An attempt was made by the authors of DSM-III to restrict its focus to the experimental, the observable, and the measurable. The intention was to free the nosology from the influence of unproven theories, and the philosophy was driven largely by the importance of research being able to identify diagnostic categories to facilitate the study of homogeneous groups. So it is of interest that the authors accepted dissociation-an ambiguous event linked to an explicit theoretical concept that had been introduced by Janet-as the basis for classification of clinical presentations that were formerly included under the rubric of hysteria, a similarly unclear category. Since DSM-III, there have been an increasing number of reports of dissociative experiences and dissociative identity disorder (formerly known as multiple personality disorder), but neither of these clinical presentations seems able to withstand the concern that it is dramatically influenced by environmental cues, e.g., the expectations of the therapist. Thus, a restricted phenomenological perspective does not fully appreciate the distorting potential of suggestibility and imagination on the nature of the emerging clinical picture. These factors might well have contributed to and laid the conceptual groundwork for the growth in the number of reports of dissociation.

  8. Identification and fragmentation pathways of caffeine metabolites in urine samples via liquid chromatography with positive electrospray ionization coupled to a hybrid quadrupole linear ion trap (LTQ) and Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry.

    PubMed

    Bianco, Giuliana; Abate, Salvatore; Labella, Cristiana; Cataldi, Tommaso R I

    2009-04-01

    Liquid chromatography (LC) with positive ion electrospray ionization (ESI+) coupled to a hybrid quadrupole linear ion trap (LTQ) and Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) was employed for the simultaneous determination of caffeine and its metabolites in human urine within a single chromatographic run. LC/ESI-FTICRMS led to the unambiguous determination of the molecular masses of the studied compounds without interference from other biomolecules. A systematic and comprehensive study of the mass spectral behaviour of caffeine and its fourteen metabolites by tandem mass spectrometry (MS/MS) was performed, through in-source ion trap collision-induced dissociation (CID) of the protonated molecules, [M+H](+). A retro-Diels-Alder (RDA) process along with ring-contraction reactions were the major fragmentation pathways observed during CID. The base peak of xanthine precursors originates from the loss of methyl isocyanate (CH(3)NCO, 57 Da) or isocyanic acid (HNCO, 43 Da), which in turn lose a CO unit. Also uric acid derivatives shared a RDA rearrangement as a common fragmentation process and a successive loss of CO(2) or CO. The uracil derivatives showed a loss of a ketene unit (CH(2)CO, 42 Da) from the protonated molecule along with the loss of H(2)O or CO. To assess the potential of the present method three established metabolite ratios to measure P450 CYP1A2, N-acetyltransferase and xanthine oxidase activities were evaluated by a number of identified metabolites from healthy human urine samples after caffeine intake. PMID:19260028

  9. 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.

  10. 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…

  11. 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.

  12. 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.

  13. 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.

  14. Dissociation dynamics in the dissociative electron attachment to carbon dioxide

    NASA Astrophysics Data System (ADS)

    Nag, Pamir; Nandi, Dhananjay

    2015-05-01

    Dissociative electron attachment (DEA) to gas phase CO2 has been probed using a velocity slice imaging technique. DEA to CO2 produces only an O- ionic fragment and shows two major resonances located at 4.4 and 8.2 eV, respectively. The kinetic energy and angular distribution of the O- ions are measured around the second resonance with higher efficiency and sensitivity that provide details of the DEA dynamics. The kinetic energy distributions are in good agreement with the previous reports. However, the distinct angular distributions show substantial difference from the two recent studies within the limited electron energies. Our angular distribution results show two negative ion resonant states are involved in the underlying DEA process at the entire electron energies over the second resonance. We discussed the recent conflicting findings in the angular distribution results. The forward-backward asymmetry observed in the angular distributions is explained due to the interference effect of different partial waves associated with the attaching electron.

  15. 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.

  16. Rovibrational resonance effects in collision-induced electronic energy transfer: I2(E,v=0-2)+CF4

    NASA Astrophysics Data System (ADS)

    Hutchison, J. Matthew; Carlisle, Benjamin R.; Stephenson, Thomas A.

    2006-11-01

    Collisions of I2 in the E(0g +) electronic state with CF4 molecules induce electronic energy transfer to the nearby D, β, and D' ion-pair states. Simulations of dispersed fluorescence spectra reveal collision-induced electronic energy transfer rate constants and final vibrational state distributions within each final electronic state. In comparison with earlier reports on I2(υE=0-2) collisions with He or Ar atoms, we find markedly different dynamics when I2, excited to the same rovibronic states, collides with CF4. Final vibrational state distributions agree with the associated Franck-Condon factors with the initially prepared state to a greater degree than those found with He or Ar collision partners and suggest that internal degrees of freedom in the CF4 molecule represent a substantial means for accepting the accompanying loss of I2 vibronic energy. Comparison of the E →D transfer of I2 excited to the J =23 and J =55 levels of the υE=0 state reveals the onset of specific, nonstatistical dynamics as the available energy is increased above the threshold for excitation of the low frequency ν2 bending mode of CF4.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ–labeled phosphopeptides

    PubMed Central

    Yang, Feng; Wu, Si; Stenoien, David L.; Zhao, Rui; Monroe, Matthew E.; Gristenko, Marina A.; Purvine, Samuel O.; Polpitiya, Ashoka D.; Tolić, Nikola; Zhang, Qibin; Norbeck, Angela D.; Orton, Daniel J.; Moore, Ronald J.; Tang, Keqi; Anderson, Gordon A.; Paša-Tolić, Ljiljana; Camp, David G.; Smith, Richard D.

    2009-01-01

    Here, we report a new approach that integrates pulsed Q dissociation (PQD) and electron transfer dissociation (ETD) techniques for confident and quantitative identification of iTRAQ-labeled phosphopeptides. The use of isobaric tags for relative and absolute quantification enables a high-throughput quantification of peptides via reporter ion signals in the low m/z range of tandem mass spectra. PQD, a form of ion trap collision activated dissociation allows for detection of low mass-to-charge fragment ions and electron transfer dissociation is especially useful for sequencing peptides that contain post-translational modifications. Analysis of the phosphoproteome of human fibroblast cells using a sensitive linear ion trap mass spectrometer demonstrated that this hybrid approach improves both identification and quantification of phosphopeptides. ETD improved phosphopeptide identification, while PQD provides improved quantification of iTRAQ-labeled phosphopeptides. PMID:19371082

  3. Infrared multiphoton dissociation of small-interfering RNA anions and cations.

    PubMed

    Gardner, Myles W; Li, Na; Ellington, Andrew D; Brodbelt, Jennifer S

    2010-04-01

    Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5' P-O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for approximately 25% to 40% of the product ion current, these ions were eliminated through secondary dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5' P-O bonds began to populate the product ion mass spectra as well as higher abundances of [a - Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a - Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H](+), [A + H](+), and [C + H](+), which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID.

  4. 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

  5. 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.

  6. 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.

  7. Dissociative ionization of biomolecules

    NASA Astrophysics Data System (ADS)

    Huo, Winifred

    2004-09-01

    Dissociative ionization (DI) by electron impact plays a role in many different applications, including low-temperature plasma processing, the study of space and astrophysical plasmas, and the study of biological damages by high-energy radiation. In the present study, our goal is to understand the health hazard to humans from exposure to radiation during an extended space flight. DI by secondary electrons can damage the DNA, either directly by causing a DNA lesion, or indirectly by producing radicals and cations that attack the DNA. The theoretical model employed makes use of the fact that electronic motion is much faster than nuclear motion, allowing DI to be treated as a two-step process. The first step is electron-impact ionization resulting in a dissociative state of the molecular ion with the same geometry as the neutral molecule. In the second step the ion relaxes from the initial geometry and undergoes unimolecular dissociation. Thus the DI cross section is given by the product of the ionization cross section and the dissociation probability. For the ionization process we use the improved binary-encounter dipole (iBED) model. For unimolecular dissociation, we use the multiconfigurational self-consistent field (MCSCF) method to determine the minimum energy pathways to possible product channels. This model has been applied to study the DI of H_2O, NH_3, and CH_4, and the results are in good agreement with experiment. The DI from the low-lying channels of benzene has also been studied and the dissociation products are compared with photoionization measurements. The DI of the DNA bases guanine and cytosine are then discussed. Of the four DNA bases, guanine has the largest ionization cross section and cytosine has the smallest. The guanine radical cation is considered to be one of the precursors to the primary, direct-type lesions formed in DNA when it is irradiated. Comparison of DI products of guanine and cytosine will be made to understand the differences in

  8. Electron photodetachment dissociation for structural characterization of synthetic and bio-polymer anions.

    PubMed

    Antoine, Rodolphe; Lemoine, Jérôme; Dugourd, Philippe

    2014-01-01

    Tandem mass spectrometry (MS-MS) is a generic term evoking techniques dedicated to structural analysis, detection or quantification of molecules based on dissociation of a precursor ion into fragments. Searching for the most informative fragmentation patterns has led to the development of a vast array of activation modes that offer complementary ion reactivity and dissociation pathways. Collisional activation of ions using atoms, molecules or surface resulting in unimolecular dissociation of activated ions still plays a key role in tandem mass spectrometry. The discovery of electron capture dissociation (ECD) and then the development of other electron-ion or ion/ion reaction methods, constituted a significant breakthrough, especially for structural analysis of large biomolecules. Similarly, photon activation opened promising new frontiers in ion fragmentation owing to the ability of tightly controlled internal energy deposition and easy implementation on commercial instruments. Ion activation by photons includes slow heating methods such as infrared multiple photon dissociation (IRMPD) and black-body infrared radiative dissociation (BIRD) and higher energy methods like ultra-violet photodissociation (UVPD) and electron photo detachment dissociation (EPD). EPD occurs after UV irradiation of multiply negatively charged ions resulting in the formation of oxidized radical anions. The present paper reviews the hypothesis regarding the mechanisms of electron photo-detachment, radical formation and direct or activated dissociation pathways that support the observation of odd and even electron product ions. Finally, the value of EPD as a complementary structural analysis tool is illustrated through selected examples of synthetic polymers, oligonucleotides, polypeptides, lipids, and polysaccharides.

  9. [A dissociative patient].

    PubMed

    de Jongh, A; Abkhezr, S; Broers, D L M

    2009-08-01

    A 45-year-old woman attended a centre for special dental care. Initially, it seemed that the patient suffered from an extreme form of dental anxiety. However, the fact that she displayed 'dissociations' suggested that she had a severe psychiatric disorder, in this case Dissociative Identity Disorder. The key feature of this condition is a dysfunction of the normal integrative functions of identity, memory and consciousness. In such instances it is recommended to contact a psychologist or psychiatrist and the referring care provider to consider the consequences of the psychiatric condition regarding informed consent, treatment plan and actual treatment. Because it was not likely that the patient would respond to an intervention specifically aimed to reduce anxiety in the dental setting, dental treatment under general anesthesia was the best suited option.

  10. 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.

  11. Mechanistic studies of multipole storage assisted dissociation.

    PubMed

    Håkansson, K; Axelsson, J; Palmblad, M; Håkansson, P

    2000-03-01

    The degree and onset of fragmentation in multipole storage assisted dissociation (MSAD) have been investigated as functions of several hexapole parameters. Strict studies of hexapole charge density (number of ions injected) and hexapole storage time were made possible by placing a pulsed shutter in front of the entrance to the mass spectrometer. The results obtained show that the charge density is the most critical parameter, but also dependencies on storage time, radio-frequency (rf) -amplitude, and pressure are seen. From these data, and from simulations of the ion trajectories inside the hexapole, a mechanism for MSAD, similar to the ones for sustained off-resonance irradiation (SORI), and for low energy collisionally induced dissociation in the collision multipole of a triple quadrupole mass spectrometer, is proposed. It is believed that, at higher charge densities, ions are pushed to larger hexapole radii where the electric potential created by the rf field is higher, forcing the ions to oscillate radially to higher amplitudes and thereby reach higher (but still relatively low) kinetic energies. Multiple collisions with residual gas molecules at these elevated energies then heat up the molecules to their dissociation threshold. Further support for this mechanism is obtained from a comparison of MSAD and SORI spectra which are almost identical in appearance.

  12. Ab initio non-Born-Oppenheimer simulations of rescattering dissociation of H2 in strong infrared laser fields

    NASA Astrophysics Data System (ADS)

    Li, Zhi-Chao; He, Feng

    2014-11-01

    We simulate the time-dependent Schrödinger equation and observe the rescattering dissociation of H2 in strong infrared laser fields. Two dissociation pathways are identified, i.e., the dissociation of H2+ in the 2 p σu state and the dissociation of H2 in doubly excited states. The former accounts for larger proportions as the rescattering energy is larger. The kinetic energy release of dissociative fragments reflects the temporal internuclear distance at the moment the rescattering happens.

  13. Hydrogen Dissociation in a H_2-N2 Pulsed DC Glow Discharge

    NASA Astrophysics Data System (ADS)

    Williamson, J. M.; Ganguly, B. N.

    1999-10-01

    The relative concentration of hydrogen atoms was measured in the afterglow of a parallel-plate, pulsed DC discharge by two-photon allowed, laser induced fluorescence (TALIF). The TALIF signal was measured, relative to pure H_2, in H2 - N2 gas mixtures at constant pressure (2.5 Torr) and current (250 mA) for different fractions of N2 (0 to 1). For short pulse durations, <= 10 μsec, the TALIF signal drops off almost linearly with H2 concentration suggesting H2 is dissociated primarily by direct electron impact. For longer discharge pulses, >= 500 μsec, there is an enhancement in the fractional dissociation that increases with N2 concentration in the gas mixture. By varying the discharge pulse duration from 10 μsec to 1.0 msec at constant current and gas pressure, the change in the hydrogen atom production by direct electron impact compared to heavy particle collision induced dissociation has been measured.

  14. Coordination Sphere Tuning of the Electron Transfer Dissociation Behavior of Cu(II)-Peptide Complexes

    PubMed Central

    Dong, Jia; Vachet, Richard W.

    2011-01-01

    In contrast to previous electron capture dissociation (ECD) studies, we find that electron transfer dissociation (ETD) of Cu(II)-peptide complexes can generate c- and z- type product ions when the peptide has a sufficient number of strongly coordinating residues. Double-resonance experiments, ion-molecule reactions, and collision-induced dissociation (CID) prove that the c and z product ions are formed via typical radical pathways without the associated reduction of Cu(II), despite the high second ionization energy of Cu. A positive correlation between the number of Cu(II) binding groups in the peptide sequence and the extent of c and z ion formation was also observed. This trend is rationalized by considering that the recombination energy of Cu(II) can be lowered by strong binding ligands to an extent that enables electron transfer to non-Cu sites (e.g. protonation sites) to compete with Cu(II) reduction, thereby generating c/z ions in a manner similar to that observed for protonated (i.e. non-metalated) peptides. PMID:22161629

  15. Coordination Sphere Tuning of the Electron Transfer Dissociation Behavior of Cu(II)-Peptide Complexes

    NASA Astrophysics Data System (ADS)

    Dong, Jia; Vachet, Richard W.

    2012-02-01

    In contrast to previous electron capture dissociation (ECD) studies, we find that electron transfer dissociation (ETD) of Cu(II)-peptide complexes can generate c- and z-type product ions when the peptide has a sufficient number of strongly coordinating residues. Double-resonance experiments, ion-molecule reactions, and collision-induced dissociation (CID) prove that the c and z product ions are formed via typical radical pathways without the associated reduction of Cu(II), despite the high second ionization energy of Cu. A positive correlation between the number of Cu(II) binding groups in the peptide sequence and the extent of c and z ion formation was also observed. This trend is rationalized by considering that the recombination energy of Cu(II) can be lowered by strong binding ligands to an extent that enables electron transfer to non-Cu sites (e.g., protonation sites) to compete with Cu(II) reduction, thereby generating c/z ions in a manner similar to that observed for protonated (i.e., nonmetalated) peptides.

  16. 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

  17. Collision-induced dipoles and polarizabilities of pairs of hydrogen molecules: Ab initio calculations and results from spherical tensor analysis

    NASA Astrophysics Data System (ADS)

    Li, Xiaoping; Harrison, James F.; Gustafsson, Magnus; Wang, Fei; Abel, Martin; Frommhold, Lothar; Hunt, Katharine L. C.

    2012-12-01

    New ab initio results are reported for the interaction-induced changes in the dipole moments and polarizabilities of pairs of hydrogen molecules, computed using finite-field coupled-cluster methods in MOLPRO 2000 and GAMESS, with an aug-cc-pV5Z (spdf) basis set. Earlier work by X. Li, C. Ahuja, J. F. Harrison, and K. L. C. Hunt, J. Chem. Phys. 126, 214302 (2007), on collision-induced polarizabilities Δα has been extended with 170 additional geometrical configurations of the H2 pairs. In calculations of Δα, we have used a "random field" technique, with up to 120 different field strengths, having components that range from 0.001 to 0.01 a.u. Numerical tests show that the pair dipoles Δμ can be obtained accurately from calculations limited to 6 values of the field in each direction, so this approach has been used to compute Δμ by X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Int. J. Spectroscopy 2010, 371201 (2010). We have evaluated the collision-induced dipoles of H2 pairs for 28 combinations of bond lengths (ranging from 0.942 a.u. to 2.801 a.u.), 7 intermolecular separations R, and 17 different relative orientations. In our work on Δα, the bond lengths are fixed at 1.449 a.u. Our results agree well with the previous ab initio work of W. Meyer, A. Borysow, and L. Frommhold, Phys. Rev. A 40, 6931 (1989), and of Y. Fu, C. G. Zheng and A. Borysow, J. Quant. Spectroscopy and Rad. Transfer, 67, 303 (2000)-where those data exist-for Δμ of H2 pairs. For Δα, our results agree well with the CCSD(T) results obtained by G. Maroulis, J. Phys. Chem. A 104, 4772 (2000) for two pair orientations and fixed R. The pair polarizability anisotropies also agree well with the small-basis self-consistent field results of D. G. Bounds, Mol. Phys. 38, 2099 (1979), although the trace of the polarizability differs by factors of 2 or more from Bounds' results. We have determined the expansion coefficients for Δμ and Δα, expressed as series in the spherical

  18. [Sacral fracture with spino-pelvic dissociation: a literature review].

    PubMed

    Cearra, I; Alonso, R; Martínez-Ogalla, D; Hoyos, J; Lauzirika, A; Mongil, R; Alvarez-Irusteta, E

    2013-01-01

    The term, sacral fracture with traumatic spino-pelvic dissociation, is applied to those fractures of the sacrum in which there are both transverse and sagittal fracture lines in the sacrum, leading to a mechanical dissociation of the spine and the proximal fragment of the sacrum from the remaining sacrum and the pelvis. It is a quite rare pathological condition, and probably underdiagnosed. As it usually results from a high energy multiple trauma, an early diagnosis and treatment are mandatory for a better functional prognosis. We present a literature review of this relatively unknown injury.

  19. 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

  20. 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.

  1. Recurrent Dissociative Fugue

    PubMed Central

    Mamarde, Abhishek; Navkhare, Praveen; Singam, Amrita; Kanoje, Akash

    2013-01-01

    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

  2. Dissociative state and competence.

    PubMed

    Lin, Yu-Ju; Hsieh, Ming-Hsien; Liu, Shi-Kai

    2007-10-01

    This report presents the results of forensic evaluation of the civil competence of a case of alleged dissociative identity disorder (DID) and discusses whether such dissociative states substantially jeopardize civil competence. A 40-year-old woman claimed that she had had many personalities since her college days. From the age of 37 to 40, she shopped excessively, which left her with millions of dollars of debt. She ascribed her shopping to a certain identity state, over which she had no control. (In this article, we use the term identity state to replace personality as an objective description of a mental state.) She thus raised the petition of civil incompetence. During the forensic evaluation, it was found that the identity states were relatively stable and mutually aware of each other. The switch into another identity state was sometimes under voluntary control. The subject showed consistency and continuity in behavioral patterns across the different identity states, and no matter which identity state she was in, there was no evidence of impairment in her factual knowledge of social situations and her capacity for managing personal affairs. We hence concluded that she was civilly competent despite the claimed DID. Considering that the existence and diagnosis of DID are still under dispute and a diagnosis of DID alone is not sufficient to interdict a persons civil right, important clinical and forensic issues remain to be answered.

  3. 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.

  4. DIFFRACTION DISSOCIATION - 50 YEARS LATER.

    SciTech Connect

    WHITE, S.N.

    2005-04-27

    The field of Diffraction Dissociation, which is the subject of this workshop, began 50 years ago with the analysis of deuteron stripping in low energy collisions with nuclei. We return to the subject in a modern context- deuteron dissociation in {radical}s{sub NN} = 200 GeV d-Au collisions recorded during the 2003 RHIC run in the PHENIX experiment. At RHIC energy, d {yields} n+p proceeds predominantly (90%) through Electromagnetic Dissociation and the remaining fraction via the hadronic shadowing described by Glauber. Since the dissociation cross section has a small theoretical error we adopt this process to normalize other cross sections measured in RHIC.

  5. 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

  6. 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.

  7. The Dynamics of Dissociative Electron Attachment to Small Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    Rescigno, Thomas

    2013-09-01

    Dissociative electron attachment (DEA) is a resonant process in which an electron attaches to a molecule to form an unstable anion which subsequently fragments into stable products. DEA to small polyatomic molecules is often governed by complex electronic and nuclear dynamics that is intrinsically multi-dimensional. One-dimensional treatments of the dissociation dynamics based on resonance scattering theory, while often successful in modeling the energy dependence of total cross sections, can mask the complexity of post-attachment dynamics which is revealed by the observed angular dependence of the reaction products. The dissociation evolves on transient anion potential energy surfaces and often involves conical intersections which can result in a complete breakdown of the axial recoil approximation. I will use the examples of DEA to water, carbon dioxide and methanol to illustrate the discussion. Work performed under auspices of USDOE by LBNL under contract DE-AC02-05CH11231 and supported by OBES, Division of Chemical Sciences.

  8. Reaction paths of phosphine dissociation on silicon (001).

    PubMed

    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. PMID:26747816

  9. Effects of Peptide Backbone Amide-to-Ester Bond Substitution on the Cleavage Frequency in Electron Capture Dissociation and Collision-Activated Dissociation

    NASA Astrophysics Data System (ADS)

    Kjeldsen, Frank; Zubarev, Roman A.

    2011-08-01

    Probing the mechanism of electron capture dissociation on variously modified model peptide polycations has resulted in discovering many ways to prevent or reduce {{N}} - {{{C}}_α } bond fragmentation. Here we report on a rare finding of how to increase the backbone bond dissociation rate. In a number of model peptides, amide-to-ester backbone bond substitution increased the frequency of {{O}} - {{{C}}_α } bond cleavage (an analogue of {{N}} - {{{C}}_α } bonds in normal peptides) by several times, at the expense of reduced frequency of cleavages of the neighboring {{N}} - {{{C}}_α } bonds. In contrast, the ester linkage was only marginally broken in collisional dissociation. These results further highlight the complementarity of the reaction mechanisms in electron capture dissociation (ECD) and collision-activated dissociation (CAD). It is proposed that the effects of amide-to-ester bond substitution on fragmentation are mainly due to the differences in product ion stability (ECD, CAD) as well as proton affinity (CAD). This proposal is substantiated by calculations using density functional theory. The implications of these results in relation to the current understanding of the mechanisms of electron capture dissociation and electron transfer dissociation are discussed.

  10. 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

  11. 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.

  12. 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.

  13. Heats of formation of Co(CO)(2)NOPR(3), R = CH(3) and C(2)H(5), and its ionic fragments.

    PubMed

    Gengeliczki, Zsolt; Sztáray, Bálint; Baer, Tomas; Iceman, Christopher; Armentrout, Peter B

    2005-07-01

    A joint threshold photoelectron photoion coincidence spectrometry (TPEPICO) and collision-induced dissociation (CID) study on the thermochemistry of Co(CO)(2)NOPR(3), R = CH(3) (Me) and C(2)H(5) (Et), complexes is presented. Adiabatic ionization energies of 7.36 +/- 0.04 and 7.24 +/- 0.04 eV, respectively, were extracted from scans of the total ion and threshold electron signals. In the TPEPICO study, the following 0 K onsets were determined for the various fragment ions: CoCONOPMe(3)(+), 8.30 +/- 0.05 eV; CoNOPMe(3)(+), 9.11 +/- 0.05 eV; CoPMe(3)(+) 10.80 +/- 0.05 eV; CoCONOPEt(3)(+), 8.14 +/- 0.05 eV; CoNOPEt(3)(+), 8.92 +/- 0.05 eV; and CoPEt(3)(+), 10.66 +/- 0.05 eV. These onsets were combined with the Co(+)-PR(3) (R = CH(3) and C(2)H(5)) bond dissociation energies of 2.88 +/- 0.11 and 3.51 +/- 0.17 eV, obtained from the TCID experiments, to derive the heats of formation of the neutral and ionic species. Thus, the Co(CO)(2)NOPR(3) (R = CH(3) and C(2)H(5)) 0 K heats of formation were found to be -350 +/- 13 and -376 +/- 18 kJ x mol(-)(1), respectively. These heats of formation were combined with the published heat of formation of Co(CO)(3)NO to determine the substitution enthalpies of the carbonyl to phosphine substitution reactions. Room-temperature values of the heats of formation are also given using the calculated harmonic vibrational frequencies. Analysis of the TCID experimental results provides indirectly the adiabatic ionization energies of the free phosphine ligands, P(CH(3))(3) and P(C(2)H(5))(3), of 7.83 +/- 0.03 and 7.50 +/- 0.03 eV, respectively.

  14. Selective dissociation of HCl in Kr from vibrational overtones

    NASA Astrophysics Data System (ADS)

    Berghof, V.; Schwentner, N.

    2002-11-01

    Vibrational levels v=1, 2, and 3 of HCl in Kr matrices are populated with tunable IR radiation and the excited molecules are dissociated by UV excitation to the repulsive A 1x state. Cl fragments are recorded by laser induced fluorescence of Kr2Cl and dissociation rates are determined from the increase in LIF with UV dose. The enlarged UV Franck-Condon range for overtones allows the study of cage exit of H fragments with small kinetic energy Ekin. A threshold at Ekin=1.4 eV and a steep rise indicate a predominant sudden exit. Monomers, different initial rotational states and transients in the relaxation cascade are preselected with overtone excitation and the feasibility of a discrimination between isotopes, aggregates, and local structures is illustrated.

  15. 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.

  16. 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.

  17. Dissociative recombination of ammonia clusters studied by storage ring experiments

    SciTech Connect

    Oejekull, J.; Andersson, P. U.; Naagaard, M. B.; Pettersson, J. B. C.; Neau, A.; Rosen, S.; Thomas, R. D.; Larsson, M.; Semaniak, J.; Oesterdahl, F.; Danared, H.; Kaellberg, A.; Ugglas, M. af.

    2006-11-21

    Dissociative recombination of ammonia cluster ions with free electrons has been studied at the heavy-ion storage ring CRYRING (Manne Siegbahn Laboratory, Stockholm University). The absolute cross sections for dissociative recombination of H{sup +}(NH{sub 3}){sub 2}, H{sup +}(NH{sub 3}){sub 3}, D{sup +}(ND{sub 3}){sub 2}, and D{sup +}(ND{sub 3}){sub 3} in the collision energy range of 0.001-27 eV are reported, and thermal rate coefficients for the temperature interval from 10 to 1000 K are calculated from the experimental data and compared with earlier results. The fragmentation patterns for the two ions H{sup +}(NH{sub 3}){sub 2} and D{sup +}(ND{sub 3}){sub 2} show no clear isotope effect. Dissociative recombination of X{sup +}(NX{sub 3}){sub 2} (X=H or D) is dominated by the product channels 2NX{sub 3}+X [0.95{+-}0.02 for H{sup +}(NH{sub 3}){sub 2} and 1.00{+-}0.02 for D{sup +}(ND{sub 3}){sub 2}]. Dissociative recombination of D{sup +}(ND{sub 3}){sub 3} is dominated by the channels yielding three N-containing fragments (0.95{+-}0.05)

  18. 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

  19. 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

  20. 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…

  1. Dissociation Patterns in Evolving Populations

    NASA Astrophysics Data System (ADS)

    Moreno, F. J.; Hernández, J. A.; Sánchez, F.

    2011-09-01

    The recent explosion and availability of mobility based technologies such as geographic information systems, cell phones equipped with built-in GPS, among others, are a valuable source of spatio-temporal data. However, only recently there have been works focused on identifying movement patterns in groups of moving entities. We focus on a particular movement pattern: dissociation. A dissociation pattern occurs when an entity that was once associated to a population, eventually separated from it and subsequently reintegrated it again. The backwarding and forwarding patterns are a type of dissociation where an entity stays behind or ahead of another entity, respectively. Dissociation really is a diversity generator, so instead avoiding it, taking advantage could be better to prevent premature convergence in evolutionary algorithms. In this work, we present formal mathematical definitions for these patterns. A discussion of how to use dissociation patterns as a mean to preserve diversity in evolutionary algorithms is also shown.

  2. 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.

  3. Ion mobility-mass spectrometry reveals the influence of subunit packing and charge on the dissociation of multiprotein complexes.

    PubMed

    Boeri Erba, Elisabetta; Ruotolo, Brandon T; Barsky, Daniel; Robinson, Carol V

    2010-12-01

    The composition, stoichiometry, and organization of protein complexes can be determined by collision-induced dissociation (CID) coupled to tandem mass spectrometry (MS/MS). The increased use of this approach in structural biology prompts a better understanding of the dissociation mechanism(s). Here we report a detailed investigation of the CID of two dodecameric, heat-stable and toroidally shaped complexes: heat shock protein 16.9 (HSP16.9) and stable protein 1 (SP-1). While HSP16.9 dissociates by sequential loss of unfolded monomers, SP-1 ejects not only monomers, but also its building blocks (dimers), and multiples thereof (tetramers and hexamers). Unexpectedly, the dissociation of SP-1 is strongly charge-dependent: loss of the building blocks increases with higher charge states of this complex. By combining MS/MS with ion mobility (IM-MS/MS), we have monitored the unfolding and dissociation events for these complexes in the gas phase. For HSP16.9 unfolding occurs at lower energies than the ejection of subunits, whereas for SP-1 unfolding and dissociation take place simultaneously. We consider these results in the light of the structural organization of HSP16.9 and SP-1 and hypothesize that SP-1 is unable to unfold extensively due to its particular quaternary structure and unusually high charge density. This investigation increases our understanding of the factors governing the CID of protein complexes and moves us closer to the goal of obtaining structural information on subunit interactions and packing from gas-phase experiments. PMID:21053918

  4. 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.

  5. Communication: Imaging wavefunctions in dissociative photoionization

    NASA Astrophysics Data System (ADS)

    Scott Hopkins, W.; Mackenzie, Stuart R.

    2011-08-01

    The dissociative ionization dynamics of excited electronic states of the xenon dimer, Xe2, have been studied using velocity map ion imaging (VMI). A one-colour, (2+1) resonant excitation scheme was employed to first excite and then ionize selected vibrational levels of the Xe2 6p 2[1/2]0 0_g^ + Rydberg state. Cationic fragments were then detected by the VMI. The data provide an outstanding example of the reflection principle in photodissociation with the full nodal structure of the Rydberg state wavefunctions clearly observed in the final Xe+ kinetic energy distributions without the need for scanning the excitation energy. Fitting of the observed distributions provides detailed and precise information on the form of the Xe2+ I(1/2g) potential energy curve involved which is in excellent agreement with the results of photoelectron imaging studies [Shubert and Pratt, J. Chem. Phys. 134, 044315 (2011), 10.1063/1.3533361]. Furthermore, the anisotropy of the product angular distributions yields information on the evolution of the electronic character of the ionic state with internuclear separation, R. The combination of the nature of dissociative ionization and the extent of the bound state wavefunctions provide information over an unusually wide range of internuclear separation R (ΔR > 0.75 Å). This would normally require scanning over a considerable energy region but is obtained in these studies at a fixed excitation energy.

  6. 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.

  7. Fractals and fragmentation

    NASA Technical Reports Server (NTRS)

    Turcotte, D. L.

    1986-01-01

    The use of renormalization group techniques on fragmentation problems is examined. The equations which represent fractals and the size-frequency distributions of fragments are presented. Method for calculating the size distributions of asteriods and meteorites are described; the frequency-mass distribution for these interplanetary objects are due to fragmentation. The application of two renormalization group models to fragmentation is analyzed. It is observed that the models yield a fractal behavior for fragmentation; however, different values for the fractal dimension are produced . It is concluded that fragmentation is a scale invariant process and that the fractal dimension is a measure of the fragility of the fragmented material.

  8. The dissociative disorders. Rarely considered and underdiagnosed.

    PubMed

    Coons, P M

    1998-09-01

    A wide variety of dissociative disorders, including dissociative amnesia, dissociative fugue, depersonalization disorder, dissociative identity disorder, and various forms of dissociative disorder not otherwise specified. In many instances, these disorders are either underdiagnosed or misdiagnosed secondary to the clinician's mistaken belief that dissociative disorders are rare. Recent research shows that dissociative disorders may comprise 5% to 10% of psychiatric populations. This article reviews the epidemiology and clinical symptomatology of these disorders. In addition, various screening and diagnostic instruments, such as the DES, Structured Clinical Interview for Dissociative Disorders, and MMPI, are discussed.

  9. 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

  10. 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.

  11. Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration

    NASA Astrophysics Data System (ADS)

    Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.

    2013-10-01

    The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p (GM1)) and corresponding glycosphingolipid (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)n+ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)n+/- ions, as well as for deprotonated (S4 + 4Btl)n- ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)n+ ions was observed as a minor pathway. The (S4 + 4Btl)n+ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)15+ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein

  12. 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.

  13. Are major dissociative disorders characterized by a qualitatively different kind of dissociation?

    PubMed

    Rodewald, Frauke; Dell, Paul F; Wilhelm-Gossling, Claudia; Gast, Ursula

    2011-01-01

    A total of 66 patients with a major dissociative disorder, 54 patients with nondissociative disorders, and 30 nonclinical controls were administered the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised, the Dissociative Experiences Scale, the Multidimensional Inventory of Dissociation, and the Symptom Checklist 90-Revised. Dissociative patients reported significantly more dissociative and nondissociative symptoms than did nondissociative patients and nonclinical controls. When general psychopathology was controlled, the dissociation scores of dissociative patients were still significantly higher than those of both other groups, whereas the dissociation scores of nondissociative patients and nonclinical controls no longer differed. These findings appear to be congruent with a typological model of dissociation that distinguishes between 2 qualitatively different kinds of dissociation. Specifically, the results of this study suggest that the dissociation that occurs in major dissociative disorders (i.e., dissociative identity disorder [DID] and dissociative disorder not otherwise specified, Type 1 [DDNOS-1]) is qualitatively different from the dissociation that occurs in persons who do not have a dissociative disorder. In contrast to previous research, the dissociation of persons who do not have a dissociative disorder is not limited to absorption; it covers a much wider range of phenomena. The authors hypothesize that different mechanisms produce the dissociation of persons with DID and DDNOS-1 as opposed to the dissociation of persons who do not have a dissociative disorder.

  14. 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

  15. 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.

  16. 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".

  17. Electron impact-induced ionization and dissociation of the freon-12 molecule

    NASA Astrophysics Data System (ADS)

    Zavilopulo, A. N.; Agafonova, A. S.; Snegurskii, A. V.

    2010-12-01

    An experimental technique is described, and the relative cross sections of the single and dissociative electron-impact ionizations of the freon-12 molecule (CCl2F2) in the near-threshold energy range are obtained. The experiment is performed on a device that provides the mass separation and recording of ions with a monopole mass spectrometer. The mass spectrum of the freon-12 molecule is measured at various ionizing-electron energies, and the relative cross sections of dissociative ionization are measured for the most intense ion fragments, including isotope-containing fragments. The threshold dependences of these cross sections are used to determine the appearance potentials of the ion fragments. The isotope shift in the thresh-old appearance energies of ion fragments [C35ClF2]+ and [C37ClF2]+ is measured for the first time.

  18. 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.

  19. 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.

  20. Infrared collision-induced absorption by N(2) near 4.3 μm for atmospheric applications: measurements and empirical modeling.

    PubMed

    Lafferty, W J; Solodov, A M; Weber, A; Olson, W B; Hartmann, J M

    1996-10-20

    Accurate measurements of collision-induced absorption by pure nitrogen in the fundamental band near 4.3 μm have been made in the 0-10 atm and 230-300 K pressure and temperature ranges, respectively. A Fourier-transform spectrometer was used with a resolution of 0.5 cm(-1). The current measurements, which agree well with previous ones but are more precise, reveal that weak features are superimposed on the broad N(2) continuum. These features have negligible temperature dependence, and their origin is not clear at the present time. Available experimental data in the 190-300 K temperature range have been used to build a simple empirical model that is suitable for use to compute atmospheric N(2) absorption. Tests indicate that this model is accurate unlike the estimates produced by widely used atmospheric transmission codes.

  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. 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.

  3. Fragmentation mechanisms of cytosine, adenine and guanine ionized bases.

    PubMed

    Sadr-Arani, Leila; Mignon, Pierre; Chermette, Henry; Abdoul-Carime, Hassan; Farizon, Bernadette; Farizon, Michel

    2015-05-01

    The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3-C4/N1-C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1-C2/C5-C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH3 or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1. PMID:25869111

  4. 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

  5. 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.

  6. Gas-phase Dissociation of homo-DNA Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Stucki, Silvan R.; Désiron, Camille; Nyakas, Adrien; Marti, Simon; Leumann, Christian J.; Schürch, Stefan

    2013-12-01

    Synthetic modified oligonucleotides are of interest for diagnostic and therapeutic applications, as their biological stability, pairing selectivity, and binding strength can be considerably increased by the incorporation of unnatural structural elements. Homo-DNA is an oligonucleotide homologue based on dideoxy-hexopyranosyl sugar moieties, which follows the Watson-Crick A-T and G-C base pairing system, but does not hybridize with complementary natural DNA and RNA. Homo-DNA has found application as a bioorthogonal element in templated chemistry applications. The gas-phase dissociation of homo-DNA has been investigated by ESI-MS/MS and MALDI-MS/MS, and mechanistic aspects of its gas-phase dissociation are discussed. Experiments revealed a charge state dependent preference for the loss of nucleobases, which are released either as neutrals or as anions. In contrast to DNA, nucleobase loss from homo-DNA was found to be decoupled from backbone cleavage, thus resulting in stable products. This renders an additional stage of ion activation necessary in order to generate sequence-defining fragment ions. Upon MS3 of the primary base-loss ion, homo-DNA was found to exhibit unspecific backbone dissociation resulting in a balanced distribution of all fragment ion series.

  7. Dissociation as a mediator of child abuse across generations.

    PubMed

    Egeland, B; Susman-Stillman, A

    1996-11-01

    To test the hypothesis that dissociative process is the mechanism that accounts for the transmission of maltreatment across generations, a group of mothers who were abused and maltreated their children were compared to a group of mothers who broke the cycle of abuse. Mothers who were abused and are abusing their children were rated higher on idealization, inconsistency, and escapism in their description of their childhood and they scored higher on the Dissociative Experience Scale compared to mothers who broke the cycle. Mothers who were abused and abused their children recalled the care they received as children in a fragmented and disconnected fashion whereas those who broke the cycle integrated their abusive experience into a more coherent view of self. Even after partialing out the effects of IQ, large differences were found indicating that dissociative process plays a part in the transmission of maltreatment across generations. Possible reasons why some maltreated individuals coped with the trauma by dissociating and others integrate the experience were discussed.

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

    PubMed

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

    2012-05-01

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

  9. 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

  10. Infrared Ion Spectroscopy at Felix: Applications in Peptide Dissociation and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Oomens, Jos

    2016-06-01

    Infrared free electron lasers such as those in Paris, Berlin and Nijmegen have been at the forefront of the development of infrared ion spectroscopy. In this contribution, I will give an overview of new developments in IR spectroscopy of stored ions at the FELIX Laboratory. In particular, I will focus on recent developments made possible by the coupling of a new commercial ion trap mass spectrometer to the FELIX beamline. The possibility to record IR spectra of mass-selected molecular ions and their reaction products has in recent years shed new light on our understanding of collision induced dissociation (CID) reactions of protonated peptides in mass spectrometry (MS). We now show that it is possible to record IR spectra for the products of electron transfer dissociation (ETD) reactions [M + nH]n+ + A- → [M + nH](n-1)+ + A → {dissociation of analyte} These reactions are now widely used in novel MS-based protein sequencing strategies, but involve complex radical chemistry. The spectroscopic results allow stringent verification of computationally predicted product structures and hence reaction mechanisms and H-atom migration. The sensitivity and high dynamic range of a commercial mass spectrometer also allows us to apply infrared ion spectroscopy to analytes in complex "real-life" mixtures. The ability to record IR spectra with the sensitivity of mass-spectrometric detection is unrivalled in analytical sciences and is particularly useful in the identification of small (biological) molecules, such as in metabolomics. We report preliminary results of a pilot study on the spectroscopic identification of small metabolites in urine and plasma samples.

  11. 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.

  12. Subunit dissociation in fish hemoglobins.

    PubMed

    Edelstein, S J; McEwen, B; Gibson, Q H

    1976-12-10

    The tetramer-dimer dissociation equilibria (K 4,2) of several fish hemoglobins have been examined by sedimentation velocity measurements with a scanner-computer system for the ultracentrifuge and by flash photolysis measurements using rapid kinetic methods. Samples studied in detail included hemoglobins from a marine teleost, Brevoortia tyrannus (common name, menhaden); a fresh water teleost, Cyprinus carpio, (common name, carp); and an elasmobranch Prionace glauca (common name, blue shark). For all three species in the CO form at pH 7, in 0.1 M phosphate buffer, sedimentation coefficients of 4.3 S (typical of tetrameric hemoglobin) are observed in the micromolar concentration range. In contrast, mammalian hemoglobins dissociate appreciably to dimers under these conditions. The inability to detect dissociation in three fish hemoglobins at the lowest concentrations examined indicates that K 4,2 must have a value of 10(-8) M or less. In flash photolysis experiments on very dilute solutions in long path length cells, two kinetic components were detected with their proportions varying as expected for an equilibrium between tetramers (the slower component) and dimers (the faster component); values of K 4,2 for the three fish hemoglobins in the range 10(-9) to 10(-8) M were calculated from these data. Thus, the values of K 4,2 for liganded forms of the fish hemoglobins appear to be midway between the value for liganded human hemoglobin (K 4,2 approximately 10(-6) M) and unliganded human hemoglobin (K 4,2 approximately 10(-12) M). This conclusion is supported by measurements on solutions containing guanidine hydrochloride to enhance the degree of dissociation. All three fish hemoglobins are appreciably dissociated at guanidine concentrations of about 0.8 M, which is roughly midway between the guanidine concentrations needed to cause comparable dissociation of liganded human hemoglobin (about 0.4 M) and unliganded human hemoglobin (about 1.6 M). Kinetic measurements on

  13. Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides

    SciTech Connect

    Yang, Feng; Wu, Si; Stenoien, David L.; Zhao, Rui; Monroe, Matthew E.; Gritsenko, Marina A.; Purvine, Samuel O.; Polpitiya, Ashoka D.; Tolic, Nikola; Zhang, Qibin; Norbeck, Angela D.; Orton, Daniel J.; Moore, Ronald J.; Tang, Keqi; Anderson, Gordon A.; Pasa-Tolic, Ljiljana; Camp, David G.; Smith, Richard D.

    2009-05-15

    Multiplex isobaric tags for relative and absolute quantification (iTRAQ) enable high-throughput quantification of peptides via reporter ion signals in the low mass range of tandem mass spectra. A challenging but highly promising application is to analyze iTRAQ-labeled peptides using a sensitive linear ion trap mass spectrometer (LTQ-MS) and pulsed Q dissociation (PQD), a form of ion trap collision activated dissociation (CAD) designed to allow detection of low mass-to-charge fragment ions. Electron dissociation transfer (ETD), on the other hand, is complementary to PQD and is especially useful for sequencing peptides containing post-translational modifications (PTMs). Here, we developed an integrated workflow for robust and accurate quantitative identification of iTRAQ labeled phosphopeptides that integrates the PQD and ETD fragmentation methods together with PQD optimization, data management and bioinformatics tools. Analysis of the phosphoproteome of human fibroblast cells demonstrated that this hybrid mode is superior to either PQD or ETD alone for phosphopeptide identification and quantitation. The combined PQD/ETD approach can qualitatively identify additional phosphopeptides than ETD alone and PQD information can provide better quantitation of ETD identified iTRAQ-labeled phosphopeptides.

  14. 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.

  15. 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.

  16. Are the Radical Centers in Peptide Radical Cations Mobile? The Generation, Tautomerism, and Dissociation of Isomeric α-Carbon-Centered Triglycine Radical Cations in the Gas Phase

    SciTech Connect

    Chu, Ivan K.; Zhao, Junfang; Xu, Minjie; Siu, Shiu On; Hopkinson, Alan C.; Siu , K W Michael

    2008-05-31

    The mobility of the radical center in three isomeric triglycine radical cationss[G•GG]+, [GG•G]+, and [GGG•]+shas been investigated theoretically via density functional theory (DFT) and experimentally via tandem mass spectrometry. These radical cations were generated by collision-induced dissociations (CIDs) of Cu(II)-containing ternary complexes that contain the tripeptides YGG, GYG, and GGY, respectively (G and Y are the glycine and tyrosine residues, respectively). Dissociative electron transfer within the complexes led to observation of [Y•GG]+, [GY•G]+, and [GGY•]+; CID resulted in cleavage of the tyrosine side chain as p-quinomethide, yielding [G•GG]+, [GG•G]+, and [GGG•]+, respectively. Interconversions between these isomeric triglycine radical cations have relatively high barriers (g44.7 kcal/mol), in support of the thesis that isomerically pure [G•GG]+, [GG•G]+, and [GGG•]+ can be experimentally produced. This is to be contrasted with barriers < 17 kcal/mol that were encountered in the tautomerism of protonated triglycine [Rodriquez C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012]. The CID spectra of [G•GG]+, [GG•G]+, and [GGG•]+ were substantially different, providing experimental proof that initially these ions have distinct structures. DFT calculations showed that direct dissociations are competitive with interconversions followed by dissociation.

  17. 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.

  18. Multiphoton dissociative ionization of CS+

    NASA Astrophysics Data System (ADS)

    Rajput, Jyoti; Jochim, Bethany; Zohrabi, M.; Betsch, K. J.; Ablikim, U.; Berry, Ben; Severt, T.; Summers, A. M.; Armstrong, G. S. J.; Esry, B. D.; Carnes, K. D.; Ben-Itzhak, I.

    2015-05-01

    We have studied the dissociative photoionization of a CS+ molecular ion beam in the strong-field regime using <50 fs IR laser pulses (λ ~ 790 nm) from a 10 kHz, ~2 mJ (per pulse) Ti:Sapphire laser system. A coincidence three-dimensional momentum imaging method was used to measure all ions and neutrals formed during this multiphoton process. Two prominent channels were observed: charge-symmetric dissociation, yielding C+ + S+, and charge-asymmetric dissociation, yielding C + S2+. The differences between these two channels with reference to their relative production probability, energetics, and angular distributions is the focus of this work. This work was supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy. BJ is also supported by DOE-SCGF (DE-AC05-06OR23100).

  19. [Dissociative identity disorder or schizophrenia?].

    PubMed

    Tschöke, S; Steinert, T

    2010-01-01

    We present a case of dissociative identity disorder in which Schneiderian first rank symptoms were present besides of various states of consciousness. Thus the diagnosis of schizophrenia had to be considered. Formally, the symptoms met ICD-10 criteria for schizophrenia. However, taking into account the lack of formal thought disorder and of negative symptoms as well as a typical history of severe and prolonged traumatisation, we did not diagnose a co-morbid schizophrenic disorder. There is good evidence for the existence of psychotic symptoms among patients with dissociative disorders. However, in clinical practice this differential diagnosis is rarely considered.

  20. 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.

  1. 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…

  2. Cascade Dissociations of Peptide Cation-Radicals. Part2. Infrared Multiphoton Dissociation and Mechanistic Studies of z-Ions from Pentapeptides

    PubMed Central

    Ledvina, Aaron R.; Chung, Thomas W.; Hui, Renjie; Coon, Joshua J.

    2013-01-01

    Dissociations of z4 ions from pentapeptides AAXAR, where X = H, Y, F, W, and V, produce dominant z2 ions that account for >50% of the fragment ion intensity. The dissociation has been studied in detail by experiment and theory and found to involve several isomerization and bond-breaking steps. Isomerizations in z4 ions proceed by amide transcis rotations followed by radical-induced transfer of a β-hydrogen atom from the side chain, forming stable Cβ radical intermediates. These undergo rate-determining cleavage of the Cα—CO bond at the X residue followed by loss of the neutral AX fragment, forming x2 intermediates. The latter were detected by energy-resolved resonant excitation collision-activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) experiments. The x2 intermediates undergo facile loss of HNCO to form z2 fragment ions, as also confirmed by energy-resolved CAD and IRMPD MS4 experiments. The loss of HNCO from the x2 ion from AAHWR is kinetically hampered by the Trp residue that traps the OCNH radical group in a cyclic intermediate. PMID:22669762

  3. 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.

  4. Formation and fragmentation of unsaturated fatty acid [M - 2H + Na]- ions: stabilized carbanions for charge-directed fragmentation.

    PubMed

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

    2014-02-01

    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  +  Fe(II)Cl](-). 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. PMID:24338213

  5. 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.

  6. Universality of fragment shapes

    PubMed Central

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  7. Universality of fragment shapes.

    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

  8. 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.

  9. Momentum Imaging of the Dynamics of Dissociative Electron Attachment to Uracil

    NASA Astrophysics Data System (ADS)

    Slaughter, Dan; Kawarai, Yu; Weber, Thorsten; Azuma, Yoshiro; Winstead, Carl; McKoy, Vince; Belkacem, Ali

    2013-05-01

    Observation of the dynamics of dissociative electron attachment (DEA) in biomolecules has recently become possible by momentum imaging of the fragments resulting from the dissociating transient anion resonance. A momentum spectrometer featuring a 4 π solid angle of detection is combined with a pulsed electron beam and effusive molecular beam in a crossed geometry to measure the full 3D momentum distribution of dissociating negative ions. Guided by electronic structure calculations that indicate the most likely orientation of the molecule at the time of attachment, we present key aspects of the dynamics of ring-breaking dissociation of the transient anion formed upon DEA to the nucleobase uracil. Performed under the auspices of the US DOE by LBNL under Contract DE-AC02-05CH11231.

  10. [Traditional and modern views of dissociation].

    PubMed

    Merza, Katalin; Kuritárné Szabó, Ildikó

    2012-01-01

    Dissociation is a failure to integrate aspects of identity, memory, perception, and consciousness. Dissociation is conceptualized as a dimensional process existing along a continuum from normal and relatively common dissociative experiences to severe and clinically relevant forms. There is a growing body of clinical and empirical evidence that dissociation may occur especially as a defense during trauma. In case of traumatic events dissociation considered as an attempt to maintain mental control just as physical control is lost. Dissociation can be either a symptom of some complex mental disorder or a distinct clinical entity categorized among dissociative and somatoform disorders in DSM-IV. The article describes the conceptual issues of dissociation and presents a new classification by Nijenhuis where the so-called somatoform dissociative symptoms are included as well in the list of dissociative symptoms. Finally, this paper summarizes the measures of dissociative phenomena and the cognitive-behavioral approaches of dissociation, and highlights the main features of the new structural dissociation model.

  11. 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.

  12. 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.

  13. 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.

  14. Dissociative electron attachment to HBr: A temperature effect

    SciTech Connect

    Fedor, J.; Cingel, M.; Skalny, J. D.; Scheier, P.; Maerk, T. D.; Cizek, M.; Kolorenc, P.; Horacek, J.

    2007-02-15

    The effects of rovibrational temperature on dissociative electron attachment to hydrogen bromide has been investigated from the experimental and theoretical point of view. Theoretical calculations based on the nonlocal resonance model predict a strong temperature effect on the Br{sup -} fragment ion yield due to population of higher vibrational and rotational states. A crossed beam experimental setup consisting of a temperature controlled effusive molecular beam and a trochoidal electron monochromator has been used to confirm this prediction. The high degree of agreement between experiment and theory indicates the validity of the theoretical model and its underlying physical picture.

  15. 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

  16. Dissociation of alkaliated alanine in the gas phase: the role of the metal cation.

    PubMed

    Abirami, Seduraman; Wong, Catherine Chiu Lan; Tsang, Chun Wai; Ma, Ngai Ling

    2005-09-01

    The dissociation of prototypical metal-cationized amino acid complexes, namely, alkaliated alanine ([Ala+M]+, M+ = Li+, Na+, K+), was studied by energy-resolved tandem mass spectrometry with an ion-trap mass analyzer and by density functional theory. Dissociation leads to formation of fragment ions arising from the loss of small neutrals, such as H2O, CO, NH3, (CO+NH3), and the formation of Na+/K+. The order of appearance threshold voltages for different dissociation pathways determined experimentally is consistent with the order of critical energies (energy barriers) obtained theoretically, and this provides the necessary confidence in both experimental and theoretical results. Although not explicitly involved in the reaction, the alkali metal cation plays novel and important roles in the dissociation of alkaliated alanine. The metal cation not only catalyzes the dissociation (via the formation of loosely bound ion-molecule complexes and by stabilizing the more polar intermediates and transition structures), but also affects the dissociation mechanisms, as the cation can alter the shape of the potential energy surfaces. This compression/expansion of the potential energy surface as a function of the alkali metal cation is discussed in detail, and how this affects the competitive loss of H2O versus CO/(CO+NH3) from [Ala+M]+ is illustrated. The present study provides new insights into the origin of the competition between various dissociation channels of alkaliated amino acid complexes.

  17. Pseudospectral calculation of near-dissociative local mode states for the bifluoride anion HF - 2

    NASA Astrophysics Data System (ADS)

    Bramley, M. J.; Corey, G. C.; Hamilton, I. P.

    1995-12-01

    Using a recently reported global potential energy surface, we calculate all vibrational levels of the HF-2 anion up to the dissociation threshold. The equilibrium geometry of the bifluoride anion is linear with the H atom between the F atoms. The vibrational wave functions are symmetric or antisymmetric with respect to reflection in a plane bisecting the F-F axis. We focus on nearly degenerate pairs of symmetric and antisymmetric levels lying close to the dissociation energy. Sums and differences of these levels are local mode states for which the H atom is localized on one of the F atoms. These near-dissociative local mode states, which can exist above the threshold for dissociation into F- and HF or FH and F- fragments, have been proposed as candidates for spectroscopic experiments which probe the dynamics and structure of the transition state in the unimolecular dissociation of polyatomic molecules. Energies of the low-lying vibrational levels, as well as those around the dissociation energy, are presented. Wave functions of highly vibrationally excited states, lying slightly below and slightly above the dissociation threshold, are analyzed graphically.

  18. 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.

  19. 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.

  20. 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.

  1. Progress in the measurement of temperature-dependent N2–N2 collision-induced absorption and H2-broadening of cold and hot CH4

    NASA Astrophysics Data System (ADS)

    Sung, Keeyoon; Wishnow, Ed; Venkataraman, Malathy; Brown, Linda R.; Ozier, Irving; Benner, D. Chris; Crawford, Tomithy J.; Mantz, Arlan; Smith, Mary-Ann H.

    2016-10-01

    We report preliminary measurements from two separate laboratory studies: (A) collision-induced absorption (CIA) of nitrogen in the far-infrared at temperatures between 78 and 130 K; and (B) temperature dependence of H2-broadening of CH4 in the near infrared at temperatures between 100 and 370 K.(A) Nitrogen collision-induced absorption provides the primary opacity of Titan at long wavelengths, thereby playing a critical role in determining the heat balance as well as the atmospheric composition and dynamics. Our new measurements of the nitrogen absorption spectrum at temperatures from 78 to 130 K are consistently ~20% higher than predictions made using theoretical models of Borysow and Frommhold (1986) [ApJ, 311, 1043] and of Karman et al. (2015)[J Chem Phys, 142, 084306]. However, the new data are consistent with the previous measurements at 78 K by the UBC group (Wishnow et al. 1996)[J Chem Phys, 104, 3511]. We present preliminary results for the N2-N2 CIA coefficients and their temperature dependence between 78 and 130 K, and comparisons with the above theoretical calculations.(B) In support of the Jovian and exoplanet atmospheric remote sensing in the near infrared, we have measured the temperature dependence of H2-broadened half width and pressure shift coefficients of CH4, both of which are known to be rotational quantum number dependent. We studied both cold and hot CH4 in the K band (~2.2 μm) with the focus on a) weaker lines in the v2+v3 band at low temperatures for cold giant planets and b) stronger lines in the v3+v4 band at elevated temperatures for extra-solar planets (e.g., hot-Jupiters). Three custom-built gas absorption cells (two cold and one hot) were used to obtain the spectra of CH4 and H2 mixtures at temperatures between 100 and 370 K. We will discuss our on-going spectrum analysis for a few select J manifolds and provide comparisons with published values, which are available only at room temperature.

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

    SciTech Connect

    Teule, J. M.; Hilgeman, M. H.; Janssen, M. H. 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.

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

    SciTech Connect

    Teule, J.M.; Hilgeman, M.H.; Janssen, M.H.; 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.}

  4. 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.

  5. 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.

  6. 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.

  7. Dissociative Functions in the Normal Mourning Process.

    ERIC Educational Resources Information Center

    Kauffman, Jeffrey

    1994-01-01

    Sees dissociative functions in mourning process as occurring in conjunction with integrative trends. Considers initial shock reaction in mourning as model of normal dissociation in mourning process. Dissociation is understood to be related to traumatic significance of death in human consciousness. Discerns four psychological categories of…

  8. Single photon induced symmetry breaking of H2 dissociation

    SciTech Connect

    Martin, F.; Fernandez, J.; Havermeier, T.; Foucar, L.; Weber, Th; Kreidi, K.; Schoffler, M.; Schmidt, L.; Jahnke, T.; Landers, A.L.; Jagutzki, O.; Czasch, A.; Benis, E.; Osipov, T.; Belkacem, A.; Prior,M.H.; Schmidt-Bocking, H.; Cocke, C.L.; Dorner, R.

    2006-12-06

    H{sub 2}, the smallest and most abundant molecule in the universe, has a perfectly symmetric ground state. What does it take to break this symmetry? Here we show that the inversion symmetry can be broken by absorption of a linearly polarized photon, which itself has inversion symmetry. In particular, the emission of a photoelectron with subsequent dissociation of the remaining H{sub 2}{sup +} fragment shows no symmetry with respect to the ionic H+ and neutral H atomic fragments. This result is the consequence of the entanglement between symmetric and antisymmetric H{sub 2}{sup +} states resulting from autoionization. The mechanisms behind this symmetry breaking are general for all molecules.

  9. Dissociation of diglycolamide complexes of Ln3+ (Ln = La-Lu) and An3+ (An = Pu, Am, Cm): redox chemistry of 4f and 5f elements in the gas phase parallels solution behavior.

    PubMed

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

    2014-11-17

    Tripositive lanthanide and actinide ions, Ln(3+) (Ln = La-Lu) and An(3+) (An = Pu, Am, Cm), were transferred from solution to gas by electrospray ionization as Ln(L)3(3+) and An(L)3(3+) complexes, where L = tetramethyl-3-oxa-glutaramide (TMOGA). The fragmentation chemistry of the complexes was examined by collision-induced and electron transfer dissociation (CID and ETD). Protonated TMOGA, HL(+), and Ln(L)(L-H)(2+) are the major products upon CID of La(L)3(3+), Ce(L)3(3+), and Pr(L)3(3+), while Ln(L)2(3+) is increasingly pronounced beyond Pr. A C-Oether bond cleavage product appears upon CID of all Ln(L)3(3+); only for Eu(L)3(3+) is the divalent complex, Eu(L)2(2+), dominant. The CID patterns of Pu(L)3(3+), Am(L)3(3+), and Cm(L)3(3+) are similar to those of the Ln(L)3(3+) for the late Ln. A striking exception is the appearance of Pu(IV) products upon CID of Pu(L)3(3+), in accord with the relatively low Pu(IV)/Pu(III) reduction potential in solution. Minor divalent Ln(L)2(2+) and An(L)2(2+) were produced for all Ln and An; with the exception of Eu(L)2(2+) these complexes form adducts with O2, presumably producing superoxides in which the trivalent oxidation state is recovered. ETD of Ln(L)3(3+) and An(L)3(3+) reveals behavior which parallels that of the Ln(3+) and An(3+) ions in solution. A C-Oether bond cleavage product, in which the trivalent oxidation state is preserved, appeared for all complexes; charge reduction products, Ln(L)2(2+) and Ln(L)3(2+), appear only for Sm, Eu, and Yb, which have stable divalent oxidation states. Both CID and ETD reveal chemistry that reflects the condensed-phase redox behavior of the 4f and 5f elements.

  10. 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.

  11. 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.

  12. 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

  13. Unimolecular thermal fragmentation of ortho-benzyne

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Maccarone, Alan T.; Nimlos, Mark R.; Kato, Shuji; Bierbaum, Veronica M.; Ellison, G. Barney; Ruscic, Branko; Simmonett, Andrew C.; Allen, Wesley D.; Schaefer, Henry F.

    2007-01-01

    The ortho-benzyne diradical, o-C6H4 has been produced with a supersonic nozzle and its subsequent thermal decomposition has been studied. As the temperature of the nozzle is increased, the benzyne molecule fragments: o-C6H4+Δ → products. The thermal dissociation products were identified by three experimental methods: (i) time-of-flight photoionization mass spectrometry, (ii) matrix-isolation Fourier transform infrared absorption spectroscopy, and (iii) chemical ionization mass spectrometry. At the threshold dissociation temperature, o-benzyne cleanly decomposes into acetylene and diacetylene via an apparent retro-Diels-Alder process: o-C6H4+Δ →HCCH+HCC-CCH. The experimental ΔrxnH298(o-C6H4→HCCH+HCC-CCH) is found to be 57±3kcalmol-1. Further experiments with the substituted benzyne, 3,6-(CH3)2-o-C6H2, are consistent with a retro-Diels-Alder fragmentation. But at higher nozzle temperatures, the cracking pattern becomes more complicated. To interpret these experiments, the retro-Diels-Alder fragmentation of o-benzyne has been investigated by rigorous ab initio electronic structure computations. These calculations used basis sets as large as [C(7s6p5d4f3g2h1i)/H(6s5p4d3f2g1h)] (cc-pV6Z) and electron correlation treatments as extensive as full coupled cluster through triple excitations (CCSDT), in cases with a perturbative term for connected quadruples [CCSDT(Q)]. Focal point extrapolations of the computational data yield a 0K barrier for the concerted, C2v-symmetric decomposition of o-benzyne, Eb(o-C6H4→HCCH+HCC-CCH)=88.0±0.5kcalmol-1. A barrier of this magnitude is consistent with the experimental results. A careful assessment of the thermochemistry for the high temperature fragmentation of benzene is presented: C6H6→H+[C6H5]→H+[o-C6H4]→HCCH+HCC-CCH. Benzyne may be an important intermediate in the thermal decomposition of many alkylbenzenes (arenes). High engine temperatures above 1500K may crack these

  14. Unimolecular thermal fragmentation of ortho-benzyne.

    PubMed

    Zhang, Xu; Maccarone, Alan T; Nimlos, Mark R; Kato, Shuji; Bierbaum, Veronica M; Ellison, G Barney; Ruscic, Branko; Simmonett, Andrew C; Allen, Wesley D; Schaefer, Henry F

    2007-01-28

    The ortho-benzyne diradical, o-C(6)H(4) has been produced with a supersonic nozzle and its subsequent thermal decomposition has been studied. As the temperature of the nozzle is increased, the benzyne molecule fragments: o-C(6)H(4)+Delta--> products. The thermal dissociation products were identified by three experimental methods: (i) time-of-flight photoionization mass spectrometry, (ii) matrix-isolation Fourier transform infrared absorption spectroscopy, and (iii) chemical ionization mass spectrometry. At the threshold dissociation temperature, o-benzyne cleanly decomposes into acetylene and diacetylene via an apparent retro-Diels-Alder process: o-C(6)H(4)+Delta-->HC triple bond CH+HC triple bond C-C triple bond CH. The experimental Delta(rxn)H(298)(o-C(6)H(4)-->HC triple bond CH+HC triple bond C-C triple bond CH) is found to be 57+/-3 kcal mol(-1). Further experiments with the substituted benzyne, 3,6-(CH(3))(2)-o-C(6)H(2), are consistent with a retro-Diels-Alder fragmentation. But at higher nozzle temperatures, the cracking pattern becomes more complicated. To interpret these experiments, the retro-Diels-Alder fragmentation of o-benzyne has been investigated by rigorous ab initio electronic structure computations. These calculations used basis sets as large as [C(7s6p5d4f3g2h1i)H(6s5p4d3f2g1h)] (cc-pV6Z) and electron correlation treatments as extensive as full coupled cluster through triple excitations (CCSDT), in cases with a perturbative term for connected quadruples [CCSDT(Q)]. Focal point extrapolations of the computational data yield a 0 K barrier for the concerted, C(2v)-symmetric decomposition of o-benzyne, E(b)(o-C(6)H(4)-->HC triple bond CH+HC triple bond C-C triple bond CH)=88.0+/-0.5 kcal mol(-1). A barrier of this magnitude is consistent with the experimental results. A careful assessment of the thermochemistry for the high temperature fragmentation of benzene is presented: C(6)H(6)-->H+[C(6)H(5)]-->H+[o-C(6)H(4)]-->HC triple bond CH+HC triple bond C

  15. 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

  16. 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...

  17. 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

  18. 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}.

  19. The collision-induced non-adiabatic transitions from the f0 g+ state of the iodine ion-pair second tier

    NASA Astrophysics Data System (ADS)

    Akopyan, M. E.; Chinkova, I. Yu.; Fedorova, T. V.; Poretsky, S. A.; Pravilov, A. M.

    2004-07-01

    Non-adiabatic transitions from the f0 g+ state of the iodine ion-pair (IP) second tier induced by collision with iodine ground state molecules have been studied for the first time. The only I 2( f0g+,v f,J f limit→I2( X) F0u+,v F,J F) transition has been observed. No transitions between the states of the first and second tiers have been found. The dependences of the I 2( f0g+,v f,J f limit→I2( X) F0u+,v F,J F) transition rate constants on the vibrational vf=8-19, vF, rotational Jf≈55,85,105, JF quantum numbers, energy gaps, as well as their correlations with Franck-Condon factors (FCFs) of the initial and final levels have been studied. The principal features of the collision-induced non-adiabatic transitions in the first and second tiers are very similar.

  20. 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.

  1. 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.

  2. [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.

  3. 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.

  4. Paraphilia from a dissociative perspective.

    PubMed

    Ross, Colin A

    2008-12-01

    A dissociative structural model of the psyche can account for a wide range of symptoms across many DSM-IV categories, including sexual compulsions and addictions. The model leads to a distinct overall plan of treatment and a set of operationalized interventions aimed at integration of the self, rather than suppression of impulses. The model could be tested first in epidemiological studies and later in treatment outcome studies.

  5. Dissociative symptoms and REM sleep.

    PubMed

    van Heugten-van der Kloet, Dalena; Merckelbach, Harald; Lynn, Steven Jay

    2013-12-01

    Llewellyn has written a fascinating article about rapid eye movement (REM) dreams and how they promote the elaborative encoding of recent memories. The main message of her article is that hyperassociative and fluid cognitive processes during REM dreaming facilitate consolidation. We consider one potential implication of this analysis: the possibility that excessive or out-of-phase REM sleep fuels dissociative symptomatology. Further research is warranted to explore the psychopathological ramifications of Llewellyn's theory. PMID:24304772

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  9. 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.

  10. 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.

  11. [Differential diagnosis between dissociative disorders and schizophrenia].

    PubMed

    Shibayama, Masatoshi

    2011-01-01

    The differential diagnosis of dissociative disorders includes many psychiatric disorders, such as schizophrenia, bipolar disorders (especially bipolar II disorder), depressive disorder (especially atypical depression), epilepsy, Asperger syndrome, and borderline personality disorder. The theme of this paper is the differential diagnosis between dissociative disorders and schizophrenia. Schneiderian first-rank symptoms in schizophrenia are common in dissociative disorders, especially in dissociative identity disorder (DID). Many DID patients have been misdiagnosed as schizophrenics and treated with neuroleptics. We compared and examined Schneiderian symptoms of schizophrenia and those of dissociative disorders from a structural viewpoint. In dissociative disorders, delusional perception and somatic passivity are not seen. "Lateness" and "Precedence of the Other" originated from the concept of "Pattern Reversal" (H. Yasunaga)" is characteristic of schizophrenia. It is important to check these basic structure of schizophrenia in subjective experiences in differential diagnosis between dissociative disorders and schizophrenia.

  12. 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.

  13. 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.

  14. Auroral fragmentation into patches

    NASA Astrophysics Data System (ADS)

    Shiokawa, Kazuo; Hashimoto, Ayumi; Hori, Tomoaki; Sakaguchi, Kaori; Ogawa, Yasunobu; Donovan, Eric; Spanswick, Emma; Connors, Martin; Otsuka, Yuichi; Oyama, Shin-Ichiro; Nozawa, Satonori; McWilliams, Kathryn

    2014-10-01

    Auroral patches in diffuse auroras are very common features in the postmidnight local time. However, the processes that produce auroral patches are not yet well understood. In this paper we present two examples of auroral fragmentation which is the process by which uniform aurora is broken into several fragments to form auroral patches. These examples were observed at Athabasca, Canada (geomagnetic latitude: 61.7°N), and Tromsø, Norway (67.1°N). Captured in sequences of images, the auroral fragmentation occurs as finger-like structures developing latitudinally with horizontal-scale sizes of 40-100 km at ionospheric altitudes. The structures tend to develop in a north-south direction with speeds of 150-420 m/s without any shearing motion, suggesting that pressure-driven instability in the balance between the earthward magnetic-tension force and the tailward pressure gradient force in the magnetosphere is the main driving force of the auroral fragmentation. Therefore, these observations indicate that auroral fragmentation associated with pressure-driven instability is a process that creates auroral patches. The observed slow eastward drift of aurora during the auroral fragmentation suggests that fragmentation occurs in low-energy ambient plasma.

  15. 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

    2016-07-21

    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.

  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. Dissociative Electron Attachment to Hydrocarbons. A Laboratory Study

    NASA Astrophysics Data System (ADS)

    Szymanska, E.; Mason, N. J.

    2011-05-01

    Laboratory studies of PAHs continue to be essential if we are to interpret the wealth and variety of processes contributing to star formation. In the realm of gas-phase kinetics reactions involving negative ions are being studied to help modellers understand the role of these species in interstellar chemistry. Observations have shown that PAHs molecules are abundant and ubiquitous in the interstellar medium of galaxies, play an important role in its physical and chemical characteristics and form a key link between small hydrocarbon species and large carbonaceous grains. There is therefore considerable interest in the mechanisms by which these molecules and their anions may form. One method is electron induced chemistry within the icy mantles on the surface of dust grains. In particular it has been recently shown that functional group dependence exists in electron attachment processes giving rise to site selective fragmentation of molecules at the C-H, O-H and N-H bonds at energies well beyond the threshold for the breaking of any of these bonds allowing novel forms of chemistry that have little or no activation barriers, such as are necessary in the ISM. In this poster we present the results of recent studies on dissociative electron attachment (DEA) to PAHs using an improved version of a Velocity Map Imaging (VMI) spectrometer comprised of a magnetically collimated and low energy pulsed electron gun, a Faraday cup, an effusive molecular beam, a pulsed field ion extraction, a time of flight analyzer and a two-dimensional position sensitive detector consisting of microchannel plate and a phosphor screen. The VMI spectrometer measures the kinetic energy and angular distribution of the fragment anions produced in the dissociative electron attachment process. Kinetic energy measurements provide information on the internal energies of the fragment anions and determine the dissociation limits of the parent negative ion resonant states responsible for the dissociative

  18. [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

  19. [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