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Sample records for collision-induced dissociation product

  1. Collision induced dissociation of alpha hydroxy acids

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

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

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

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

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

    SciTech Connect

    Roberge, W.; Dalgarno, A.

    1982-04-01

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

  6. 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

  7. 4-HNE Adduct Stability Characterized by Collision-Induced Dissociation and Electron Transfer Dissociation Mass Spectrometry

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

    Futrell, Jean H.

    2001-04-19

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

  9. 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).

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

    PubMed

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

    2011-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Ingólfsson, Oddur; Takeo, Harutoshi; Nonose, Shinji

    1999-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  13. 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. 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.

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

    SciTech Connect

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

    2002-05-15

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

  16. 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.

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

    PubMed

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

    2016-10-01

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

  18. 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

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    SciTech Connect

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

    1998-04-10

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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  5. 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.

  6. 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.

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

    PubMed

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

    2014-04-17

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    SciTech Connect

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

    1998-04-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  11. 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

  12. 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.

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

    PubMed

    Sekimoto, Kanako; Takayama, Mitsuo

    2013-05-01

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

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

    PubMed

    Chu, Ivan K; Lam, Corey N W

    2005-11-01

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

  15. 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

  16. 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.

  17. 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

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

    PubMed

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

    2016-04-01

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

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

    SciTech Connect

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

    1995-12-31

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

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2016-06-16

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

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

    PubMed

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

    2016-01-01

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

  3. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2004-10-01

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Lin, Yawei; Mayer, Paul M.

    2011-01-01

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

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

    PubMed

    Lin, Yawei; Mayer, Paul M

    2011-01-01

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

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

    PubMed

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

    2013-11-21

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

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1982-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2013-12-01

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

  14. 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.

  15. 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.

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

    PubMed

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

    1993-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Afonso, Carlos; Hathout, Yetrib; Fenselau, Catherine

    2004-02-01

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

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

    PubMed

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

    2015-01-01

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

  19. 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.

  20. 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

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

    PubMed

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

    2014-12-01

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

  2. 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

  3. 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.

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

    PubMed

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

    2010-08-01

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

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

    PubMed

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

    2015-04-23

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

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

    SciTech Connect

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

    2013-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

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

    PubMed

    Rožman, Marko

    2016-01-01

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

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

    PubMed

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

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Mihesan, Claudia; Glodić, Pavle; Velegrakis, Michalis

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  12. 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

  13. 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

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

    PubMed

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

    2016-05-14

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

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

    SciTech Connect

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

    2004-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Takayama, Mitsuo

    1994-09-01

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

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed Central

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

    2014-01-01

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

  20. 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

  1. 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.

  2. 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

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

    PubMed

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

    2011-03-15

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

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

    PubMed

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

    2016-03-18

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

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

    PubMed

    Shelley, Jacob T; Hieftje, Gary M

    2010-04-01

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

  6. 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

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

    PubMed

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

    2013-02-01

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

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

    PubMed

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

    2006-07-01

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

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

    PubMed

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

    2016-09-01

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

  10. 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.

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

    PubMed

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

    2011-05-15

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

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

    SciTech Connect

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

    2009-07-01

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

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

    SciTech Connect

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

    2014-01-15

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

  14. Products of Dissociative Recombination in the Ionosphere

    NASA Technical Reports Server (NTRS)

    Cosby, Philip

    1996-01-01

    SRI International undertook a novel experimental measurement of the product states formed by dissociative ro-combination (DR) of C2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and ro-vibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates.

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

    PubMed

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

    2011-03-15

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

  16. 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

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

    PubMed

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

    2016-02-25

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    PubMed

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

    2016-01-01

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

  20. 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

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

    SciTech Connect

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

    1996-09-26

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

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

    2016-09-01

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

  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.

    2016-06-01

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

  5. Products of Dissociative Recombination in the Ionosphere

    NASA Technical Reports Server (NTRS)

    Cosby, Philip

    1996-01-01

    SRI International undertook a novel experimental measurement of the product states formed by dissociative recombination (DR) of O2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and rovibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates. For a molecular ion such as O2(+), the dissociation recombination reaction is (1) O2(+) + e yields O + O + W. The atomic products of this reaction, in this case two oxygen atoms, can be produced in a variety of excited states and with a variety of kinetic energies, as represented by W in Eq. (1). These atoms are not only active in the neutral chemistry of the ionosphere, but are also especially important because their optical emissions are often used to infer in situ concentrations of the parent molecular ion and ambient electron densities. Many laboratory measurements have been made of DR reaction rates under a wide range of electron temperatures, but very little is known about the actual distributions among the final states of the atomic products. This lack of knowledge seriously limits the validity and effectiveness of efforts to model both natural and man-made ionospheric disturbances. Bates recently identified major deficiencies in the currently accepted branching ratios for O2(+) as they relate to blue and green line emission measurements in the nocturnal F-region. During our two-year effort, we partially satisfied our ambitious goals. We constructed and operated a variable pressure, electron-impact ion source and a high pressure, hollow-cathode discharge ion

  6. 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

  7. Dissociative Experiences, Creative Imagination, and Artistic Production in Students of Fine Arts

    ERIC Educational Resources Information Center

    Perez-Fabello, Maria Jose; Campos, Alfredo

    2011-01-01

    The current research was designed to assess the influence of dissociative experiences and creative imagination on the artistic production of Fine Arts students of the University of Vigo (Spain). The sample consisted of 81 students who were administered the Creative Imagination Scale and The Dissociative Experiences Scale. To measure artistic…

  8. Dissociative Ionization and Product Distributions of Benzene and Pyridine by Electron Impact

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Huo, Winifred M.; Fletcher, Graham D.

    2003-01-01

    We report a theoretical study of the dissociative ionization (DI) and product distributions of benzene (C6H6) and pyridine (C5H5N) from their low-lying ionization channels. Our approach 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 the electron-impact ionization resulting in an ion with the same nuclear geometry as the neutral molecule. In the second step, the nuclei relax from the initial geometry and undergo unimolecular dissociation. For the ionization process we use the improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64,042719-I (2001)]. For the unimolecular dissociation, we use multiconfigurational self-consistent field (MCSCF) methods to determine the steepest descent pathways to the possible product channels. More accurate methods are then used to obtain better energetics of the paths which are used to determine unimolecular dissociation probabilities and product distributions. Our analysis of the dissociation products and the thresholds of their productions for benzene are compared with the recent dissociative photoionization meausurements of benzene by Feng et al. [R. Feng, G. Cooper, C.E. Brion, J. Electron Spectrosc. Relat. Phenom. 123,211 (2002)] and the dissociative photoionization measurements of pyridine by Tixier et al. [S. Tixier, G. Cooper, R. Feng, C.E. Brion, J. Electron Spectrosc. Relat. Phenom. 123,185 (2002)] using dipole (e,e+ion) coincidence spectroscopy.

  9. Thermal regulation of methane hydrate dissociation: Implications for gas production models

    USGS Publications Warehouse

    Circone, S.; Kirby, S.H.; Stern, L.A.

    2005-01-01

    Thermal self-regulation of methane hydrate dissociation at pressure, temperature conditions along phase boundaries, illustrated by experiment in this report, is a significant effect with potential relevance to gas production from gas hydrate. In surroundings maintained at temperatures above the ice melting point, the temperature in the vicinity of dissociating methane hydrate will decrease because heat flow is insufficient to balance the heat absorbed by the endothermic reaction: CH4??nH2O (s) = CH4 (g) + nH2O (l). Temperature decreases until either all of the hydrate dissociates or a phase boundary is reached. At pressures above the quadruple point, the temperature-limiting phase boundary is that of the dissociation reaction itself. At lower pressures, the minimum temperature is limited by the H2O solid/liquid boundary. This change in the temperature-limiting phase boundary constrains the pressure, temperature conditions of the quadruple point for the CH4-H2O system to 2.55 ?? 0.02 MPa and 272.85 ?? 0.03 K. At pressures below the quadruple point, hydrate dissociation proceeds as the liquid H2O produced by dissociation freezes. In the laboratory experiments, dissociation is not impeded by the formation of ice byproduct per se; instead rates are proportional to the heat flow from the surroundings. This is in contrast to the extremely slow dissociation rates observed when surrounding temperatures are below the H2O solid/liquid boundary, where no liquid water is present. This "anomalous" or "self" preservation behavior, most pronounced near 268 K, cannot be accessed when surrounding temperatures are above the H2O solid/liquid boundary. ?? 2005 American Chemical Society.

  10. The contribution of dissociative processes to the production of atomic lines in hydrogen plasmas

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1985-01-01

    The contribution of molecular dissociative processes to the production of atomic lines is considered for a steady-state hydrogen plasma. If the contribution of dissociative processes is dominant, a substantial simplification in plasma diagnostics can be achieved. Numerical calculations have been performed for the production of Balmer alpha, beta, and gamma lines in hydrogen plasmas with medium and large degrees of ionization (x greater than about 0.0001) and for electron temperatures of 5000-45,000 K and electron densities of 10 to the 10th to 10 to the 16th/cu cm.

  11. Parameterization for light ion production from electromagnetic dissociation

    NASA Astrophysics Data System (ADS)

    Norbury, John

    2014-09-01

    Light ion (hydrogen and helium isotopes) production from relativistic nucleus-nucleus collisions is important in space radiation protection problems, when galactic cosmic rays interact with spacecraft. In fact, for thick spacecraft shields, such as the International Space Station, light ion and neutron production can dominate the contribution to dose equivalent. Both strong and electromagnetic interactions can contribute to light ion production. The present work extends a previous parameterization of electromagnetically produced light ions, so that particle branching ratios are described more realistically.

  12. 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

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

    PubMed

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

    2006-09-01

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

  14. 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.

  15. A Dissociation between Orthographic Awareness and Spelling Production.

    ERIC Educational Resources Information Center

    Perry, Conrad; Ziegler, Johannes C.; Coltheart, Max

    2002-01-01

    Two nonword spelling and two orthographic awareness experiments examined production and awareness of sound-spelling relationships. Results of the nonword spelling experiments suggest people use phoneme-grapheme sized relationships when spelling nonwords. Orthographic awareness experiments suggest, under some circumstances, people can use larger…

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

    PubMed

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

    2016-06-01

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

  17. Hydrogen production by water dissociation using ceramic membranes - annual report for FY 2010.

    SciTech Connect

    Balachandran, U.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Lu, Y.; Park, C. Y.; Picciolo, J. J.

    2011-03-14

    The objective of this project is to develop dense ceramic membranes that can produce hydrogen via coal/coal gas-assisted water dissociation without using an external power supply or circuitry. This project grew from an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen production by two methods. In one method, a hydrogen transport membrane (HTM) selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen using OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  18. Hydrogen production by water dissociation using ceramic membranes. Annual report for FY 2009.

    SciTech Connect

    Balachandran, U.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Lu, Y.; Park, C. Y.; Picciolo, J. J.; Energy Systems

    2010-04-20

    The objective of this project is to develop dense ceramic membranes that can produce hydrogen via coal/coal gas-assisted water dissociation without using an external power supply or circuitry. This project grew from an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen production by two methods. In one method, a hydrogen transport membrane selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen by means of OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  19. Hydrogen production by water dissociation using ceramic membranes - annual report for FY 2008.

    SciTech Connect

    Balachandran, U.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Lu, Y.; Park, C. Y.; Picciolo, J. J.; Energy Systems

    2009-03-25

    The objective of this project is to develop dense ceramic membranes that, without using an external power supply or circuitry, can produce hydrogen via coal/coal gas-assisted water dissociation. This project grew from an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen production by two methods. In one method, a hydrogen transport membrane (HTM) selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen by means of OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

  20. Dissociation and product formation in NF sub 3 radio-frequency glow discharges

    SciTech Connect

    Hargis, P.J. Jr.; Greenberg, K.E. )

    1990-03-15

    Laser Raman spectroscopy was used to measure NF{sub 3} dissociation and N{sub 2} formation in the active volume of 13.56-MHz NF{sub 3} radio-frequency (rf) discharges. Gating the rf discharge suppressed optical emission, allowing NF{sub 3} and N{sub 2} Raman measurements at rf powers where N{sub 2} production was expected to be significant. Greater than 90% dissociation of the NF{sub 3} was observed in a 750 mTorr discharge at rf power densities on the order of 1 W/cm{sup 2} , yet less than 50 mTorr of N{sub 2} was produced. NF was the only other nitrogen containing species detected in the active volume of the discharge.

  1. 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.

  2. Research on the production of hydrogen by direct thermal dissociation of water vapor

    SciTech Connect

    Lapicque, F.; Abdul-Aziz, G.; Anthony, A.M.; Baumard, B.; Cales, B.; Lede, J.; Ledoux, M.; Puechberty, D.; Villermaux, J.

    1985-04-01

    The partial dissociation of steam to the extent of a few percent at temperatures above 2000K is predicted thermodynamically. Dissociation probably occurs by a partially heterogeneous mechanism between 1,700 K and 1,900 K, and by a homogeneous mechanism above 2,000 K. The kinetic constants for the corresponding elementary processes are presented. These thermal splitting reactions can be utilized either by separating oxygen across a semipermeable membrane or by rapid cooling of the reacting mixture. In order to use the first method, materials based on solid solutions of the ternary system ZrO/sub 2/-CeO/sub 2/-Y/sub 2/O/sub 3/ were developed. Their properties were studied and taken advantage of to make membranes semipermeable to oxygen. The second method uses a dissociation reactor (a zirconia nozzle heated by concentrated thermal radiation followed by a quenching zone (mixing with cold gas). After optimizing the nozzle shape and the process of quenching, an appreciable production of hydrogen was achieved (two liters per hour per 700 W of thermal input). The reactor was tested successfully at the 2-kW Odeillo solar furnace.

  3. Unimolecular dissociation dynamics of vibrationally activated CH3CHOO Criegee intermediates to OH radical products.

    PubMed

    Kidwell, Nathanael M; Li, Hongwei; Wang, Xiaohong; Bowman, Joel M; Lester, Marsha I

    2016-05-01

    The hydroxyl radical is an important atmospheric oxidant, and a significant source of its production occurs through alkene ozonolysis. This takes place via a cycloaddition reaction and subsequent fragmentation to form an energized carbonyl oxide (for example, CH3CHOO), known as a Criegee intermediate, which can then either react with another atmospheric species or decay and, in doing so, produce the hydroxyl radical. Here, we examine the dissociation dynamics of a prototypical Criegee intermediate by characterizing the translational and internal energy distributions of the OH radical products, which reflect critical configurations along the reaction pathway. Experimentally, the kinetic energy release to OH products is ascertained through velocity map imaging. Theoretically, quasi-classical trajectories are performed on a new full-dimensional, ab initio potential energy surface. Both experiment and theory show that most of the available energy flows into internal excitation of the vinoxy products. The isotropic angular distribution of OH fragments indicates that dissociation occurs in ≥2 ps, in agreement with theory. PMID:27102686

  4. Unimolecular dissociation dynamics of vibrationally activated CH3CHOO Criegee intermediates to OH radical products

    NASA Astrophysics Data System (ADS)

    Kidwell, Nathanael M.; Li, Hongwei; Wang, Xiaohong; Bowman, Joel M.; Lester, Marsha I.

    2016-05-01

    The hydroxyl radical is an important atmospheric oxidant, and a significant source of its production occurs through alkene ozonolysis. This takes place via a cycloaddition reaction and subsequent fragmentation to form an energized carbonyl oxide (for example, CH3CHOO), known as a Criegee intermediate, which can then either react with another atmospheric species or decay and, in doing so, produce the hydroxyl radical. Here, we examine the dissociation dynamics of a prototypical Criegee intermediate by characterizing the translational and internal energy distributions of the OH radical products, which reflect critical configurations along the reaction pathway. Experimentally, the kinetic energy release to OH products is ascertained through velocity map imaging. Theoretically, quasi-classical trajectories are performed on a new full-dimensional, ab initio potential energy surface. Both experiment and theory show that most of the available energy flows into internal excitation of the vinoxy products. The isotropic angular distribution of OH fragments indicates that dissociation occurs in ≥2 ps, in agreement with theory.

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

    NASA Astrophysics Data System (ADS)

    Vigasin, A. A.

    2014-11-01

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

  6. 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.

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

    PubMed Central

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

    1980-01-01

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

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

    PubMed

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

    2016-03-01

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

  9. Hydrogen production by water dissociation using ceramic membranes. Annual report for FY 2007.

    SciTech Connect

    Balachandran, U.; Chen, L.; Dorris, S. E.; Emerson, J. E.; Lee, T. H.; Park, C. Y.; Picciolo, J. J.; Song, S. J.; Energy Systems

    2008-03-04

    The objective of this project is to develop dense ceramic membranes that, without using an external power supply or circuitry, can produce hydrogen via coal/coal gas-assisted water dissociation. This project grew out of an effort to develop a dense ceramic membrane for separating hydrogen from gas mixtures such as those generated during coal gasification, methane partial oxidation, and water-gas shift reactions [1]. That effort led to the development of various cermet (i.e., ceramic/metal composite) membranes that enable hydrogen to be produced by two methods. In one method, a hydrogen transport membrane (HTM) selectively removes hydrogen from a gas mixture by transporting it through either a mixed protonic/electronic conductor or a hydrogen transport metal. In the other method, an oxygen transport membrane (OTM) generates hydrogen mixed with steam by removing oxygen that is generated through water splitting [1, 2]. This project focuses on the development of OTMs that efficiently produce hydrogen via the dissociation of water. Supercritical boilers offer very high-pressure steam that can be decomposed to provide pure hydrogen by means of OTMs. Oxygen resulting from the dissociation of steam can be used for coal gasification, enriched combustion, or synthesis gas production. Hydrogen and sequestration-ready CO{sub 2} can be produced from coal and steam by using the membrane being developed in this project. Although hydrogen can also be generated by high-temperature steam electrolysis, producing hydrogen by water splitting with a mixed-conducting membrane requires no electric power or electrical circuitry.

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

    PubMed

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

    2010-02-01

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

  11. Dissociation of alpha-macrofetoprotein and alpha-fetoprotein production during experimental injury.

    PubMed

    Hudig, D; Sell, S; Newell, L; Smuckler, E A

    1979-02-01

    The concentrations of two major fetal serum proteins of the rat, alpha-macrofetoprotein (AMF) and alpha-fetoprotein (AFP) are measured following administration of croton oil, carbon tetrachloride, galactosamine or ethionine, and after partial hepatectomy. Greatly elevated serum concentrations of AMF are found after croton oil injection, following oral administration of CCl4, and after partial hepatectomy, but not after ethionine or galactosamine. Elevations of AFP occur after administration of hepatotoxic agents during the stage of restitutive proliferation and after exposure to the hepatocarcinogen ethionine, but not after croton oil. Therefore, elevations of AMF and AFP are clearly dissociated under certain conditions. In situations such as partial hepatectomy, after which elevations in both AMF and AFP occur, AMF appears before AFP. Therefore, the production of AMF and AFP appear to be under completely independent regulation in the adult. PMID:85804

  12. Apparatus for hydrogen and carbon production via carbon aerosol-catalyzed dissociation of hydrocarbons

    NASA Technical Reports Server (NTRS)

    Muradov, Nazim Z. (Inventor); Smith, Franklyn (Inventor); Tabatabaie-Raissi, Ali (Inventor)

    2012-01-01

    A novel process and apparatus is disclosed for sustainable, continuous production of hydrogen and carbon by catalytic dissociation or decomposition of hydrocarbons at elevated temperatures using in-situ generated carbon particles. Carbon particles are produced by decomposition of carbonaceous materials in response to an energy input. The energy input can be provided by at least one of a non-oxidative and oxidative means. The non-oxidative means of the energy input includes a high temperature source, or different types of plasma, such as, thermal, non-thermal, microwave, corona discharge, glow discharge, dielectric barrier discharge, or radiation sources, such as, electron beam, gamma, ultraviolet (UV). The oxidative means of the energy input includes oxygen, air, ozone, nitrous oxide (NO.sub.2) and other oxidizing agents. The method, apparatus and process of the present invention is applicable to any gaseous or liquid hydrocarbon fuel and it produces no or significantly less CO.sub.2 emissions compared to conventional processes.

  13. 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

  14. Standard enthalpies of formation of α-aminobutyric acid and products of its dissociation in an aqueous solution

    NASA Astrophysics Data System (ADS)

    Lytkin, A. I.; Chernikov, V. V.; Krutova, O. N.

    2016-08-01

    Heats of solution of crystalline α-aminobutyric acid in water and in aqueous solutions of potassium hydroxide at 298.15 K are measured by means of direct calorimetry. Standard enthalpies of formation of the amino acid and products of its dissociation in an aqueous solution are calculated.

  15. Standard enthalpy of formation of L-glutamine and the products of its dissociation in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Kochergina, L. A.; Lytkin, A. I.; Krutova, O. N.; Damrina, K. V.

    2014-03-01

    Heat effects of the dissolution of crystalline L-glutamine in water and lithium hydroxide solutions were determined by direct calorimetry at 298.15 K. Standard enthalpies of formation of L-glutamine and the products of its dissociation in aqueous solution were calculated.

  16. Interference between dissociating states in H{sub 2}O{sub 2} and HOCl causes orientation of OH diatomic products

    SciTech Connect

    Alexander, Andrew J.

    2002-12-01

    H{sub 2}O{sub 2} and HOCl were dissociated using circularly polarized light at wavelengths 330-370 nm, and angular-momentum polarization of OH ({sup 2}{pi}) products was measured using laser induced fluorescence. The OH (J=0.5) products exhibit orientation of angular momenta resulting from interference between excited dissociating states of the parent molecules.

  17. 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.

  18. 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

  19. Dissociation between distortion-product and click-evoked otoacoustic emissions in sheep (Ovis aries)

    PubMed Central

    McFadden, Dennis; Pasanen, Edward G.; Valero, Michelle D.; Roberts, Eila K.; Lee, Theresa M.

    2008-01-01

    Distortion-product otoacoustic emissions (DPOAEs) were weak or absent in about one-third of sheep (Ovis aries) of both sexes tested for otoacoustic emissions (OAEs) even though their click-evoked OAEs (CEOAEs) seemingly were typical of other sheep of the same sex. Various pieces of evidence suggest that the absence of measurable DPOAEs was unlikely to be attributable to anesthetic effects, a poorly located probe tip, a pressure differential between middle and outer ears, season of the year, body position during testing, temperature effects, or previous medical history. Sheep apparently can exhibit a marked dissociation between DPOAEs and CEOAEs. In those sheep having measurable DPOAEs, the DPOAEs were stronger in males than in females, which is the opposite direction of effect from the CEOAEs measured in these same sheep and in humans. In female sheep exposed to higher-than-normal levels of androgens during gestation, the measurable DPOAEs were stronger than in untreated females. Although this also was the opposite direction of effect from expected, it still was a shift in the male direction, in accord with past findings about the masculinizing effects of androgens on OAEs. In sheep, androgen exposure appears to have different effects on the mechanisms underlying DPOAEs from those underlying CEOAEs. PMID:19206800

  20. Major Effects in the Thermodynamics of Detonation Products: Phase Segregation versus Ionic Dissociation

    SciTech Connect

    Bastea, S; Fried, L E

    2010-03-09

    Water (H{sub 2}O) and nitrogen (N{sub 2}) are major detonation products of high explosives and it has long been conjectured that they may phase segregate at high enough temperatures and pressures to influence detonation properties of common explosives. We analyze the phase diagram of H{sub 2}O-N{sub 2} mixtures using a thermodynamic theory for polar-nonpolar mixtures and find that phase segregation is unlikely to occur above approximately 1600K. Therefore, H{sub 2}O-N{sub 2} immiscibility is not likely to be relevant for detonation predictions. We propose instead that the high pressure ionic dissociation of water plays an important role in detonation, and model it using a new ionic thermodynamics. We employ this model in chemical equilibrium calculations of standard high explosives, e.g. PETN, HMX and RDX, and find that it performs very well under a wide range of conditions. Thus, although it may require further development, it is likely that explicitly ionic thermodynamics will become a standard tool for explosives modeling.

  1. 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.

  2. Infrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexes.

    PubMed

    Verkerk, Udo H; Zhao, Junfang; Saminathan, Irine S; Lau, Justin Kai-Chi; Oomens, Jos; Hopkinson, Alan C; Siu, K W Michael

    2012-04-16

    Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative. PMID:22455512

  3. 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.

  4. Reaction of Cu+ with dimethoxyethane: Competition between association and multiple dissociation channels

    NASA Astrophysics Data System (ADS)

    Koizumi, Hideya; Muntean, Felician; Armentrout, P. B.

    2004-01-01

    The reaction of Cu+ with dimethoxyethane (DXE) is studied using kinetic-energy dependent guided ion beam mass spectrometry. The bimolecular reaction forms an associative Cu+(DXE) complex that is long-lived and dissociates into several competitive channels: C4H9O2++CuH, Cu+(C3H6O)+CH3OH, back to reactants, and other minor channels. The kinetic-energy dependences of the cross sections for the three largest product channels are interpreted with several different models (including rigorous phase space theory) to yield 0 K bond energies after accounting for the effects of multiple ion-molecule collisions, internal energy of the reactant ions, Doppler broadening, and dissociation lifetimes. These values are compared with bond energies obtained from collision-induced dissociation (CID) studies of the Cu+(DXE) complex and found to be self-consistent. Although all models provide reasonable thermochemistry, phase space theory reproduces the details of the cross sections most accurately. We also examine the dynamics of this reaction using time-of-flight methods and a retarding potential analysis. This provides additional insight into the unimolecular decay of the long-lived Cu+(DXE) association complex. Comparison of results from this study with those from the complementary CID study, thus forming the same energized Cu+(DXE) complex in two distinct ways, allows an assessment of the models used to interpret CID thresholds.

  5. Strong-field control over the product branching ratios in molecular dissociation

    NASA Astrophysics Data System (ADS)

    Rigsbee, Brandon; Zohrabi, Mohammad; Ablikim, Utuq; Guevara, Nicolais; Carnes, Kevin; Ben-Itzhak, Itzik; Esry, Brett

    2012-06-01

    We present a theoretical and experimental study of strong-field control over the fragmentation channel in molecular dissociation by intense, single-color laser fields with emphasis on the effect of chirped pulses. In particular, the branching ratio between H+D^+ and H^++D from an HD^+ target is examined as a function of kinetic energy release for 790 nm pulses with intensities on the order of 10^14 W/cm^2 and pulse lengths ranging from 25 to 65 fs. Theoretical calculations based on numerical solutions of the time-dependent Schr"odinger equation in the Born-Oppenheimer approximation are compared to measurements using a coincidence 3-D momentum imaging technique. Both demonstrate that control is indeed possible and depends, as expected, on details of the laser pulse such as its chirp.

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

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Courtenay Lewis, John

    2014-11-01

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

  9. 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.

  10. 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.

  11. Dynamics of production of iodine atoms by dissociation of iodides in a pulsed self-sustained discharge

    SciTech Connect

    Vagin, Nikolai P; Kochetov, Igor' V; Napartovich, A P; Yuryshev, Nikolai N

    2013-07-31

    Absorption at the laser transition has been used for the first time to assess the evolution of concentration of iodine atoms in a pulsed self-sustained discharge in mixtures of iodides with a buffer gas such as molecular nitrogen and helium. Dynamics of the iodine atom production is studied by the method of absorption spectroscopy. The dissociation of C{sub n}F{sub 2n+1}I and CnH{sub 2n+1}I (n = 1, 2) iodides is investigated. The energy required to produce atomic iodine is evaluated. The experimental data obtained for CF{sub 3}I are compared with the results of numerical simulations, their reasonable agreement being demonstrated. (active media)

  12. 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.

  13. The Harvard Beat Assessment Test (H-BAT): a battery for assessing beat perception and production and their dissociation

    PubMed Central

    Fujii, Shinya; Schlaug, Gottfried

    2013-01-01

    Humans have the abilities to perceive, produce, and synchronize with a musical beat, yet there are widespread individual differences. To investigate these abilities and to determine if a dissociation between beat perception and production exists, we developed the Harvard Beat Assessment Test (H-BAT), a new battery that assesses beat perception and production abilities. H-BAT consists of four subtests: (1) music tapping test (MTT), (2) beat saliency test (BST), (3) beat interval test (BIT), and (4) beat finding and interval test (BFIT). MTT measures the degree of tapping synchronization with the beat of music, whereas BST, BIT, and BFIT measure perception and production thresholds via psychophysical adaptive stair-case methods. We administered the H-BAT on thirty individuals and investigated the performance distribution across these individuals in each subtest. There was a wide distribution in individual abilities to tap in synchrony with the beat of music during the MTT. The degree of synchronization consistency was negatively correlated with thresholds in the BST, BIT, and BFIT: a lower degree of synchronization was associated with higher perception and production thresholds. H-BAT can be a useful tool in determining an individual's ability to perceive and produce a beat within a single session. PMID:24324421

  14. Effects of Carbonyl Bond and Metal Cluster Dissociation and Evaporation Rates on Predictions of Nanotube Production in HiPco

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Smalley, Richard E.

    2002-01-01

    The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNT) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the co-formation of CO2. It is shown that the production of CO2 is significantly greater for FeCO due to its lower bond energy as compared with that ofNiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

  15. The Harvard Beat Assessment Test (H-BAT): a battery for assessing beat perception and production and their dissociation.

    PubMed

    Fujii, Shinya; Schlaug, Gottfried

    2013-01-01

    Humans have the abilities to perceive, produce, and synchronize with a musical beat, yet there are widespread individual differences. To investigate these abilities and to determine if a dissociation between beat perception and production exists, we developed the Harvard Beat Assessment Test (H-BAT), a new battery that assesses beat perception and production abilities. H-BAT consists of four subtests: (1) music tapping test (MTT), (2) beat saliency test (BST), (3) beat interval test (BIT), and (4) beat finding and interval test (BFIT). MTT measures the degree of tapping synchronization with the beat of music, whereas BST, BIT, and BFIT measure perception and production thresholds via psychophysical adaptive stair-case methods. We administered the H-BAT on thirty individuals and investigated the performance distribution across these individuals in each subtest. There was a wide distribution in individual abilities to tap in synchrony with the beat of music during the MTT. The degree of synchronization consistency was negatively correlated with thresholds in the BST, BIT, and BFIT: a lower degree of synchronization was associated with higher perception and production thresholds. H-BAT can be a useful tool in determining an individual's ability to perceive and produce a beat within a single session. PMID:24324421

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

    PubMed Central

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

    2010-01-01

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

  17. 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.

  18. 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.

  19. 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

  20. Spondylopelvic dissociation.

    PubMed

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

    2014-01-01

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

  1. 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

  2. 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.

  3. 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.

  4. 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.

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

    SciTech Connect

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

    2014-07-15

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

  6. 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.

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

    SciTech Connect

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

    1981-05-01

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

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

    SciTech Connect

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

    2004-06-01

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

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

    SciTech Connect

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

    1981-09-01

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

  10. Dissociation products and structures of solid H2S at strong compression

    NASA Astrophysics Data System (ADS)

    Li, Yinwei; Wang, Lin; Liu, Hanyu; Zhang, Yunwei; Hao, Jian; Pickard, Chris J.; Nelson, Joseph R.; Needs, Richard J.; Li, Wentao; Huang, Yanwei; Errea, Ion; Calandra, Matteo; Mauri, Francesco; Ma, Yanming

    2016-01-01

    Hydrogen sulfides have recently received a great deal of interest due to the record high superconducting temperatures of up to 203 K observed on strong compression of dihydrogen sulfide (H2S ). A joint theoretical and experimental study is presented in which decomposition products and structures of compressed H2S are characterized, and their superconducting properties are calculated. In addition to the experimentally known H2S and H3S phases, our first-principles structure searches have identified several energetically competitive stoichiometries that have not been reported previously: H2S3 , H3S2 , HS2, and H4S3 . In particular, H4S3 is predicted to be thermodynamically stable within a large pressure range of 25-113 GPa. High-pressure x-ray diffraction measurements confirm the presence of H3S and H4S3 through decomposition of H2S that emerges at 27 GPa and coexists with residual H2S , at least up to the highest pressure of 140 GPa studied in our experiments. Electron-phonon coupling calculations show that H4S3 has a small T c of below 2 K, and that H2S is mainly responsible for the observed superconductivity of samples prepared at low temperature (<100 K).

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2008-02-21

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

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

    NASA Astrophysics Data System (ADS)

    Zheng, Chunguang

    1997-08-01

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

  14. 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).

  15. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes

    NASA Astrophysics Data System (ADS)

    Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2016-04-01

    Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes.

  16. 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.

  17. 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

  18. High-energy collision-activated and electron-transfer dissociation of gas-phase complexes of tryptophan with Na+, K+, and Ca2+

    NASA Astrophysics Data System (ADS)

    Fujihara, Akimasa; Sha, Yuki; Matsuo, Sou; Toyoda, Michisato; Hayakawa, Shigeo

    2014-10-01

    The structure and reactivity of gas-phase complexes of tryptophan (Trp) with Na+, K+, and Ca2+ were examined by high-energy collision-activated dissociation (CAD) and electron transfer dissociation (ETD) using alkali metal targets. In the CAD spectra of M+Trp (M = Na and K), neutral Trp loss was the primary dissociation pathway, and the product ion of collision-induced intracomplex electron transfer from the indole π ring of Trp to the alkali metal ion was observed, indicating a charge-solvated structure in which Trp is non-zwitterionic. The NH3 loss observed in the CAD spectrum of Ca2+Trp2 is ascribed to a CZ (mixed charge-solvated/zwitterionic)-type structure, in which one Trp is non-zwitterionic and the other Trp adopts a zwitterionic structure with an NH3+ moiety. The H atom and NH3 losses observed in the ETD spectrum of Ca2+Trp2 indicate the formation of a hypervalent radical in the complex, R-NH3, via electron transfer from the alkali metal target to the NH3+ group of the CZ-type structure. Ca2+ attachment to Trp cluster induces the zwitterionic structure of Trp in the gas phase, and an electron transfer to the zwitterionic Trp forms the hypervalent radical as a reaction intermediate.

  19. Ozone-Induced Dissociation of Conjugated Lipids Reveals Significant Reaction Rate Enhancements and Characteristic Odd-Electron Product Ions

    NASA Astrophysics Data System (ADS)

    Pham, Huong T.; Maccarone, Alan T.; Campbell, J. Larry; Mitchell, Todd W.; Blanksby, Stephen J.

    2013-02-01

    Ozone-induced dissociation (OzID) is an alternative ion activation method that relies on the gas phase ion-molecule reaction between a mass-selected target ion and ozone in an ion trap mass spectrometer. Herein, we evaluated the performance of OzID for both the structural elucidation and selective detection of conjugated carbon-carbon double bond motifs within lipids. The relative reactivity trends for [M + X]+ ions (where X = Li, Na, K) formed via electrospray ionization (ESI) of conjugated versus nonconjugated fatty acid methyl esters (FAMEs) were examined using two different OzID-enabled linear ion-trap mass spectrometers. Compared with nonconjugated analogues, FAMEs derived from conjugated linoleic acids were found to react up to 200 times faster and to yield characteristic radical cations. The significantly enhanced reactivity of conjugated isomers means that OzID product ions can be observed without invoking a reaction delay in the experimental sequence (i.e., trapping of ions in the presence of ozone is not required). This possibility has been exploited to undertake neutral-loss scans on a triple quadrupole mass spectrometer targeting characteristic OzID transitions. Such analyses reveal the presence of conjugated double bonds in lipids extracted from selected foodstuffs. Finally, by benchmarking of the absolute ozone concentration inside the ion trap, second order rate constants for the gas phase reactions between unsaturated organic ions and ozone were obtained. These results demonstrate a significant influence of the adducting metal on reaction rate constants in the fashion Li > Na > K.

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  1. Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes.

    PubMed

    Quintyn, Royston S; Zhou, Mowei; Yan, Jing; Wysocki, Vicki H

    2015-12-01

    One attractive feature of ion mobility mass spectrometry (IM-MS) lies in its ability to provide experimental collision cross section (CCS) measurements, which can be used to distinguish different conformations that a protein complex may adopt during its gas-phase unfolding. However, CCS values alone give no detailed information on subunit structure within the complex. Consequently, structural characterization typically requires molecular modeling, which can have uncertainties without experimental support. One method of obtaining direct experimental evidence on the structures of these intermediates is utilizing gas-phase activation techniques that can effectively dissociate the complexes into substructures while preserving the native topological information. The most commonly used activation method, collision-induced dissociation (CID) with low-mass target gases, typically leads to unfolding of monomers of a protein complex. Here, we describe a method that couples IM-MS and surface-induced dissociation (SID) to dissociate the source-activated precursors of three model protein complexes: C-reactive protein (CRP), transthyretin (TTR), and concanavalin A (Con A). The results of this study confirm that CID involves the unfolding of the protein complex via several intermediates. More importantly, our experiments also indicate that retention of similar CCS between different intermediates does not guarantee retention of structure. Although CID spectra (at a given collision energy) of source-activated, mass-selected precursors do not distinguish between native-like, collapsed, and expanded forms of a protein complex, dissociation patterns and/or average charge states of monomer products in SID of each of these forms are unique. PMID:26499904

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

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

    PubMed

    Nikitin, E E; Troe, J

    2006-05-01

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

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

    SciTech Connect

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

    1997-06-01

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

  6. The Generation of Hot Galactic Halos: Multi-Phase Simulations including Collision-Induced Shock Heating, and Comparisons with Observations

    NASA Astrophysics Data System (ADS)

    Hearn, Nathan C.; Lamb, Susan A.

    2001-09-01

    The presence of hot halos around some colliding and supposed merging galaxies, as detected in X-rays, suggests that galaxy interactions may be responsible for the production of significant amounts of hot-phase interstellar gas in some systems. Possible mechanisms for producing this hot material are large-scale shock heating due to the collision itself, as well as the subsequent supernova explosions and intense stellar winds from the massive stars that are formed in collision-induced starbursts. We are using numerical simulations of galaxy collisions and mergers to explore the possible contribution of these various physical mechanisms. These simulations are compared with observations of real systems. Here we report on results from the application of a new N-body/smoothed particle hydrodynamics simulation code that has been constructed to allow the representation of multiple phases in the interstellar medium (Hearn et al, in preparation). This simulation code has been used to explore the generation of hot interstellar gas due to the large-scale shock heating that occurs during the collision and merger of two gas-rich disk galaxies. This current study allows us to place limits on the effect of the collision itself (as opposed to the results of subsequent star formation) on the generation of hot halos. We compare our numerical results to the extensive observations of the collisional merging system Arp 220 and, in particular, with our recent Chandra observations of its extended X-ray halo (McDowell et al, in preparation).

  7. 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.

  8. 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.

  9. 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

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

    PubMed

    Knyazev, Vadim D; Stein, Stephen E

    2010-03-01

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

  11. 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.

  12. Cross sections for production of H(2p, 2s, 1s) by electron collisional dissociation of H2

    NASA Technical Reports Server (NTRS)

    Ajello, J. M.; James, G. K.; Shemansky, D. E.

    1991-01-01

    The excitation function of H Ly-alpha from the astrophysically important dissociation of electron-excited H2 over the range 10-700 eV has been measured. The analysis predicts the cross section to energies higher than the present experimental limit, and it is found that the predicted shape is in close agreement with measured results. At 6 eV the cross section is dominated by the electric dipole first Born component, while at 100 eV the electric dipole component constitutes 73 percent of the total H(2p) cross section. The cross sections of the H(2s) and H(1s) components are calculated.

  13. 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.

  14. 2D laser-collision induced fluorescence in low-pressure argon discharges

    DOE PAGESBeta

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

    2015-09-25

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

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Martin, A. D.

    2016-02-01

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed

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

    2015-02-28

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

  1. Hybrid quadrupole mass filter/quadrupole ion trap/time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions

    SciTech Connect

    Gulyuz, Kerim; Stedwell, Corey N.; Wang Da; Polfer, Nick C.

    2011-05-15

    We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator/amplifier (OPO/A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure ({approx}10{sup -5} Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH{sup +}, as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.

  2. Monte Carlo/RRKM/classical trajectories modeling of collisional excitation and dissociation of n-butylbenzene ion in multipole collision cells of tandem mass spectrometers.

    PubMed

    Knyazev, Vadim D; Stein, Stephen E

    2010-06-10

    The two-channel reaction of collision-induced dissociation (CID) of the n-butylbenzene cation under the conditions of multipole collision cells of tandem mass spectrometers was studied computationally. The results were compared with the experimental data from earlier CID studies. The Monte Carlo method used includes simulation of the trajectories of flight of the parent (n-C(4)H(9)C(6)H(5)(+)) and the product (C(7)H(7)(+) and C(7)H(8)(+)) ions in the electromagnetic field of multipole ion guides and collision cells, classical trajectory modeling of collisional activation and scattering of ions, and RRKM modeling of the parent ion decomposition. Experimental information on the energy dependences of the rates of the n-butylbenzene cation dissociation via two channels was used to create an RRKM model of the reaction. Effects of uncertainties in the critical parameters of the model of the reaction and the collision cells on the results of calculations were evaluated and shown to be minor. The results of modeling demonstrate a good agreement with experiment, providing support for the applied computational method in general and the use of classical trajectory modeling of collisional activation of ions in particular. PMID:20481494

  3. Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides

    PubMed Central

    Liu, Jian; McLuckey, Scott A.

    2012-01-01

    The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation. PMID:23264749

  4. Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides.

    PubMed

    Liu, Jian; McLuckey, Scott A

    2012-12-15

    The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation. PMID:23264749

  5. Sub-part-per-million precursor and product mass accuracy for high-throughput proteomics on an electron transfer dissociation-enabled orbitrap mass spectrometer.

    PubMed

    Wenger, Craig D; McAlister, Graeme C; Xia, Qiangwei; Coon, Joshua J

    2010-05-01

    We demonstrate a new approach for internal mass calibration on an electron transfer dissociation-enabled linear ion trap-orbitrap hybrid mass spectrometer. Fluoranthene cations, a byproduct of the reaction used for generation of electron transfer dissociation reagent anions, are co-injected with the analyte cations in all orbitrap mass analysis events. The fluoranthene cations serve as a robust internal calibrant with minimal impact on scan time (<20 ms) or spectral quality. Following external mass calibration, 60 replicate LC-MS/MS runs of a complex peptide mixture were collected over the course of approximately 136 h (almost 6 days). Using only standard external mass calibration, the mass accuracy for a typical analysis was -3.31 +/- 0.93 ppm (sigma) for precursors and -2.32 +/- 0.89 ppm for products. After application of internal recalibration, mass accuracy improved to +0.77 +/- 0.71 ppm for precursors and +0.17 +/- 0.67 ppm for products. When all 60 replicate runs were analyzed together without internal mass recalibration, the mass accuracy was -1.23 +/- 1.54 ppm for precursors and -0.18 +/- 1.42 ppm for products, nearly a 2-fold drop in precision relative to an individual run. After internal mass recalibration, this improved to +0.80 +/- 0.70 ppm for precursors and +0.16 +/- 0.67 ppm for products, roughly equivalent to that obtained in a single run, demonstrating a near complete elimination of mass calibration drift. PMID:20124352

  6. Sub-part-per-million Precursor and Product Mass Accuracy for High-throughput Proteomics on an Electron Transfer Dissociation-enabled Orbitrap Mass Spectrometer*

    PubMed Central

    Wenger, Craig D.; McAlister, Graeme C.; Xia, Qiangwei; Coon, Joshua J.

    2010-01-01

    We demonstrate a new approach for internal mass calibration on an electron transfer dissociation-enabled linear ion trap-orbitrap hybrid mass spectrometer. Fluoranthene cations, a byproduct of the reaction used for generation of electron transfer dissociation reagent anions, are co-injected with the analyte cations in all orbitrap mass analysis events. The fluoranthene cations serve as a robust internal calibrant with minimal impact on scan time (<20 ms) or spectral quality. Following external mass calibration, 60 replicate LC-MS/MS runs of a complex peptide mixture were collected over the course of ∼136 h (almost 6 days). Using only standard external mass calibration, the mass accuracy for a typical analysis was −3.31 ± 0.93 ppm (σ) for precursors and −2.32 ± 0.89 ppm for products. After application of internal recalibration, mass accuracy improved to +0.77 ± 0.71 ppm for precursors and +0.17 ± 0.67 ppm for products. When all 60 replicate runs were analyzed together without internal mass recalibration, the mass accuracy was −1.23 ± 1.54 ppm for precursors and −0.18 ± 1.42 ppm for products, nearly a 2-fold drop in precision relative to an individual run. After internal mass recalibration, this improved to +0.80 ± 0.70 ppm for precursors and +0.16 ± 0.67 ppm for products, roughly equivalent to that obtained in a single run, demonstrating a near complete elimination of mass calibration drift. PMID:20124352

  7. 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

  8. Dissociated Vertical Deviation

    MedlinePlus

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

  9. 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.

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

    PubMed

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

    2015-01-28

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

  11. Protonation Sites and Dissociation Mechanisms of t-Butylcarbamates in Tandem Mass Spectrometric Assays for Newborn Screening

    PubMed Central

    Spáčil, Zdeněk; Hui, Renjie; Gelb, Michael H.; Tureček, František

    2011-01-01

    Structures of tert-butylcarbamate ions in the gas phase and methanol solution were studied for simple secondary and tertiary carbamates as well as for carbamate-containing products and internal standards for lysosomal enzyme assays used in newborn screening of a α-galactosidase A deficiency (GLA, Fabry disease), mucopolysaccharidosis I (Hurler disease), and mucopolysaccharidosis II (Hunter disease). Protonation of simple t-butylcarbamates can occur at the carbonyl group which is the preferred site in the gas phase. Protonation in methanol solution is more favorable if occurring at the carbamate nitrogen atom. Protonation of more complex t-butylcarbamates occurs at amide and carbamate carbonyl groups, and the ions are stabilized by intramolecular hydrogen bonding which is affected by solvation. Tertiary carbamates containing aminophenol amide groups were calculated to have substantially greater gas-phase basicities than secondary carbamates containing coumarin amide groups. The main diagnostically important ion dissociation by elimination of 2-methylpropene (isobutylene, i-C4H8) and carbon dioxide is shown by experiment and theory to proceed in two steps. Energy-resolved collision-induced dissociation of the Hurler’s disease enzymatic product ion, which is a coumarin-diamine linker-t-butylcarbamate conjugate (3a+), indicated separate energy thresholds for the loss of i-C4H8 and CO2. Computational investigation of the potential energy surface along two presumed reaction pathways indicated kinetic preference for the migration of a t-butyl hydrogen atom to the carbamate carbonyl resulting in the isobutylene loss. The consequent loss of CO2 required further proton migrations that had to overcome energy barriers. PMID:22012676

  12. Effects of carbonyl bond, metal cluster dissociation, and evaporation rates on predictions of nanotube production in high-pressure carbon monoxide

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Smalley, Richard E.

    2003-01-01

    The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNTs) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the conformation of CO2. It is shown that the production of CO2 is significantly greater for FeCO because of its lower bond energy as compared with that of NiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

  13. 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.

  14. State-resolved unimolecular dissociation of cis-cis HOONO: Product state distributions and action spectrum in the 2νOH band region

    NASA Astrophysics Data System (ADS)

    Matthews, Jamie; Sinha, Amitabha

    2005-03-01

    Nascent OH fragment product state distributions arising from unimolecular dissociation of room temperature HOONO, initiated by excitation in the region of the 2νOH band, are probed using laser-induced fluorescence at sub-Doppler resolution. Phase-space simulations of the measured OH rotational distributions are consistent with the dissociation dynamics being statistical and confirm that all major features in the room temperature action spectrum belong to the cis-cis conformer. The phase-space simulations also allow us to estimate the HO-ONO bond dissociation energy of cis-cis HOONO to be D0=19.9±0.5kcal /mol, which when combined with the known heat-of-formation data for the OH and NO2 fragments gives ΔHf0(cis-cisHOONO )=-2.5kcal/mol. In addition to fragment energy release, spectral features in the cis-cis HOONO action spectrum are examined with respect to their shifts upon N15 isotope substitution and through ab initio spectral simulation using a two-dimensional dipole surface that takes into account the influence of HOON torsional motion on the OH stretching overtone. The two-dimensional spectral simulations, using CCSD(T)/cc-pVTZ dipole surface, qualitatively reproduces features appearing in the action spectrum and suggest that the strong broad feature occurring ˜570cm-1 to the blue of the cis-cis HOONO 2νOH peak, likely involve excitation of HOON-torsion/OH-stretch combination bands originating from thermally populated excited torsional states. A closer examination of the predictions of the two-dimensional model with experiments also reveals its limitations and suggests that a more elaborate treatment, one which includes several additional modes, will likely be required in order to fully explain the room temperature action spectrum. Ab initio calculations of the HOON torsional potential at the CCSD(T)/cc-pVTZ level of theory are also presented and confirm that cis-perp configuration does not correspond to a bound localized minimum on the HOONO potential

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

    PubMed

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

    2012-08-28

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

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

    NASA Astrophysics Data System (ADS)

    Bussery-Honvault, Béatrice; Hartmann, Jean-Michel

    2014-02-01

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

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

    PubMed

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

    2015-11-17

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

  18. 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.

  19. 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.

  20. 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.

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

    PubMed

    Bussery-Honvault, Béatrice; Hartmann, Jean-Michel

    2014-02-01

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

  2. 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

  3. 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.

  4. Neural Dissociation in the Production of Lexical versus Classifier Signs in ASL: Distinct Patterns of Hemispheric Asymmetry

    ERIC Educational Resources Information Center

    Hickok, Gregory; Pickell, Herbert; Klima, Edward; Bellugi, Ursula

    2009-01-01

    We examine the hemispheric organization for the production of two classes of ASL signs, lexical signs and classifier signs. Previous work has found strong left hemisphere dominance for the production of lexical signs, but several authors have speculated that classifier signs may involve the right hemisphere to a greater degree because they can…

  5. 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.

  6. Structural elucidation of sulfaquinoxaline metabolism products and their occurrence in biological samples using high-resolution Orbitrap mass spectrometry.

    PubMed

    Hoff, Rodrigo Barcellos; Meneghini, Leonardo; Pizzolato, Tânia Mara; Peralba, Maria do Carmo Ruaro; Díaz-Cruz, M Silvia; Barceló, Damià

    2014-06-01

    Four previously unreported metabolism products of sulfaquinoxaline (SQX), a widely used veterinary medicine, were isolated and analyzed using liquid chromatography coupled to high-resolution Orbitrap mass spectrometry. Metabolites were structurally elucidated, and a fragmentation pathway was proposed. The combination of high-resolution MS(2) spectra, linear ion trap MS(2), in-source collision-induced dissociation (CID) fragmentation, and photolysis were used to analyze SQX and its metabolites. All metabolism products identified showed a similar fragmentation pattern to that of the original drug. Differential product ions were produced at m/z 162 and 253 which contain the radical moiety with more 16 Da units than sulfaquinoxaline. This occurs by a hydroxyl attachment to the quinoxaline moiety. With the exception of two low-intensity compounds, all the mass errors were below 5.0 ppm. The distribution of these metabolites in some animal species are also presented and discussed. PMID:24796379

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

    PubMed

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

    2014-09-11

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

  8. Thermal device and method for production of carbon monoxide and hydrogen by thermal dissociation of hydrocarbon gases

    DOEpatents

    Detering, Brent A.; Kong, Peter C.

    2001-01-01

    Carbon monoxide is produced in a fast quench reactor. The production of carbon monoxide includes injecting carbon dioxide and some air into a reactor chamber having a high temperature at its inlet and a rapidly expanding a reactant stream, such as a restrictive convergent-divergent nozzle at its outlet end. Carbon dioxide and other reactants such as methane and other low molecular weight hydrocarbons are injected into the reactor chamber. Other gas may be added at different stages in the process to form a desired end product and prevent back reactions. The resulting heated gaseous stream is then rapidly cooled by expansion of the gaseous stream.

  9. Influence of discharge production conditions, gas pressure, current intensity and voltage type, on SF6 dissociation under point-plane corona discharges

    NASA Astrophysics Data System (ADS)

    Belarbi, A.; Pradayrol, C.; Casanovas, J.; Casanovas, A. M.

    1995-02-01

    The study of the formation of Sulfur Hexafluoride (SF6) dissociation products under point to plane corona discharges was carried out at P(sub SF(6)) = 300 kPa using different discharges production conditions (50 Hz ac voltage, dc negative polarity voltage, mean discharge current intensity bar-I varying between 2 and 45 micro-A for dc negative polarity voltage), for two plane electrode materials (aluminum and stainless steel), and moisture levels (200 and 2000 ppm(sub v) H2O). The stable gaseous by-products formed (SO2F2, SOF4, SOF2, and S2F10) were assayed by gas-phase chromatography. The results indicate an important effect of the metal constituting the plane electrode and of the moisture conditions whatever the SF6 pressure (100-300 kPa), discharges intensity (bar-I) and voltage type studied. An effect of the increase of SF6 pressure up to 300 kPa was mainly observed for S2F10 and corresponds to a greater formation of this compound with P(sub SF(6)). The influence of the mean discharge current intensity on SF6 by-product formation carried out for a transported charge of 1 C showed that for I less than or equal to 10 micro-A, the effect varies according to the compound considered and depends on the water content of the SF6 and/or on the plane electrode material, whereas for bar-I greater than 10 micro-A, the levels of the four compound studied hardly vary with the current. Comparison of results obtained under ac and dc voltage for a cumulated charge of between 0.5 and 11 C showed that (SO2F2+SOF4) and SOF2 were formed in larger quantities with ac than with dc, unlike S2F10 for which the opposite effect was observed.

  10. 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.

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

    PubMed

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

    2016-03-01

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

  12. Production of e+e- Pairs Accompanied by Nuclear Dissociation in Ultra-peripheral Heavy Ion Collisions

    SciTech Connect

    Adams, J.; Adler, C.; Aggarwal, M.M.; Ahammed, Z.; Allgower, C.; Amonett, J.; Anderson, B.D.; Anderson, M.; Arkhipkin, D.; Averichev, G.S.; Bai, Y.; Balewski, J.; Barannikova, O.; Barnby, L.S.; Baudot, J.; Bekele, S.; Belaga, V.V.; Bellwied, R.; Berger, J.; Bichsel, H.; Billmeier, A.; Bland, L.C.; Blyth, C.O.; Bonner, B.E.; Boucham, A.; Brandin, A.; Bravar, A.; Cadman, R.V.; Caines, H.; Calderon de la Barca Sanchez, M.; Cardenas, A.; Carroll, J.; Castillo, J.; Castro, M.; Cebra, D.; Chaloupka, P.; Chattopadhyay, S.; Chen, Y.; Chernenko, S.P.; Cherney, M.; Chikanian, A.; Choi, B.; Christie, W.; Coffin, J.P.; Cormier, T.M.; Corral, M.M.; Cramer, J.G.; Crawford, H.J.; Deng, W.S.; Derevschikov, A.A.; Didenko, L.; Dietel, T.; Draper, J.E.; Dunin, V.B.; Dunlop, J.C.; Eckardt, V.; Efimov, L.G.; Emelianov, V.; Engelage, J.; Eppley, G.; Erazmus, B.; Fachini, P.; Faine, V.; Faivre, J.; Fatemi, R.; Filimonov, K.; Finch, E.; Fisyak, Y.; Flierl, D.; Foley, K.J.; Fu, J.; Gagliardi, C.A.; Gagunashvili, N.; Gans, J.; Gaudichet, L.; Germain, M.; Geurts, F.; Ghazikhanian, V.; Grachov, O.; Grigoriev, V.; Guedon, M.; Guertin, S.M.; Gushin, E.; Hallman, T.J.; Hardtke, D.; Harris, J.W.; Heinz, M.; Henry, T.W.; Heppelmann, S.; Herston, T.; Hippolyte, B.; Hirsch, A.; Hjort, E.; Hoffmann, G.W.; Horsley, M.; Huang, H.Z.; Humanic, T.J.; Igo, G.; Ishihara, A.; Ivanshin, Yu.I.; Jacobs, P.; Jacobs, W.W.; Janik, M.; Johnson, I.; Jones, P.G.; Judd, E.G.; Kaneta, M.; Kaplan, M.; Keane, D.; Kiryluk, J.; Kisiel, A.; Klay, J.; Klein, S.R.; Klyachko, A.; Kollegger, T.; Konstantinov, A.; Kopytine, S.M.; Kotchenda, L.; Kovalenko, A.D.; Kramer, M.; Kravtsov, P.; Krueger, K.; Kuhn, C.; Kulikov, A.I.; Kunde, G.J.; Kunz, C.L.; Kutuev, R.K.; Kuznetsov, A.A.; Lamont, M.A.C.; Landgraf, J.M.; Lange, S.; Lansdell, C.P.; Lasiuk, B.; Laue, F.; Lauret, J.; Lebedev, A.; Lednicky, R.; Leontiev, V.M.; LeVine, M.J.; Li, Q.; Lindenbaum, S.J.; Lisa, M.A.; Liu, F.; Liu, L.; Liu, Z.; et al.

    2004-04-07

    We present the first data on e{sup +}e{sup -} pair production accompanied by nuclear breakup in ultra-peripheral gold-gold collisions at a center of mass energy of 200 GeV per nucleon pair. The nuclear breakup requirement selects events at small impact parameters, where higher-order corrections to the pair production cross section should be enhanced. We compare the pair kinematic distributions with two calculations: one based on the equivalent photon approximation, and the other using lowest-order quantum electrodynamics (QED); the latter includes the photon virtuality. The cross section, pair mass, rapidity and angular distributions are in good agreement with both calculations. The pair transverse momentum, p{sub T}, spectrum agrees with the QED calculation, but not with the equivalent photon approach. We set limits on higher-order contributions to the cross section. The e{sup +} and e{sup -} p{sub T} spectra are similar, with no evidence for interference effects due to higher-order diagrams.

  13. 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.

  14. Dissociative Ionization of Pyridine by Electron Impact

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher; Huo, Winifred; Kwak, Dochan (Technical Monitor)

    2002-01-01

    In order to understand the damage of biomolecules by electrons, a process important in radiation damage, we undertake a study of the dissociative ionization (DI) of pyridine (C5H5N) from the low-lying ionization channels. The methodology used is the same as in the benzene study. While no experimental DI data are available, we compare the dissociation products from our calculations with the dissociative photoionization measurements of Tixier et al. using dipole (e, e(+) ion) coincidence spectroscopy. Comparisons with the DI of benzene is also made so as to understand the difference in DI between a heterocyclic and an aromatic molecule.

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  16. 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

  17. Dissociative Ionization of Benzene by Electron Impact

    NASA Technical Reports Server (NTRS)

    Huo, Winifred; Dateo, Christopher; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We report a theoretical study of the dissociative ionization (DI) of benzene from the low-lying ionization channels. Our approach makes use of the fact that electron motion is much faster than nuclear motion and DI is treated as a two-step process. The first step is electron-impact ionization resulting in an ion with the same nuclear geometry as the neutral molecule. In the second step the nuclei relax from the initial geometry and undergo unimolecular dissociation. For the ionization process we use the improved binary-encounter dipole (iBED) model. For the unimolecular dissociation step, we study the steepest descent reaction path to the minimum of the ion potential energy surface. The path is used to analyze the probability of unimolecular dissociation and to determine the product distributions. Our analysis of the dissociation products and the thresholds of the productions are compared with the result dissociative photoionization measurements of Feng et al. The partial oscillator strengths from Feng et al. are then used in the iBED cross section calculations.

  18. Detailed glycan structural characterization by electronic excitation dissociation.

    PubMed

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

    2013-11-01

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

  19. Thermal dissociation behavior and dissociation enthalpies of methane-carbon dioxide mixed hydrates.

    PubMed

    Kwon, Tae-Hyuk; Kneafsey, Timothy J; Rees, Emily V L

    2011-06-30

    Replacement of methane with carbon dioxide in hydrate has been proposed as a strategy for geologic sequestration of carbon dioxide (CO(2)) and/or production of methane (CH(4)) from natural hydrate deposits. This replacement strategy requires a better understanding of the thermodynamic characteristics of binary mixtures of CH(4) and CO(2) hydrate (CH(4)-CO(2) mixed hydrates), as well as thermophysical property changes during gas exchange. This study explores the thermal dissociation behavior and dissociation enthalpies of CH(4)-CO(2) mixed hydrates. We prepared CH(4)-CO(2) mixed hydrate samples from two different, well-defined gas mixtures. During thermal dissociation of a CH(4)-CO(2) mixed hydrate sample, gas samples from the head space were periodically collected and analyzed using gas chromatography. The changes in CH(4)-CO(2) compositions in both the vapor phase and hydrate phase during dissociation were estimated based on the gas chromatography measurements. It was found that the CO(2) concentration in the vapor phase became richer during dissociation because the initial hydrate composition contained relatively more CO(2) than the vapor phase. The composition change in the vapor phase during hydrate dissociation affected the dissociation pressure and temperature; the richer CO(2) in the vapor phase led to a lower dissociation pressure. Furthermore, the increase in CO(2) concentration in the vapor phase enriched the hydrate in CO(2). The dissociation enthalpy of the CH(4)-CO(2) mixed hydrate was computed by fitting the Clausius-Clapeyron equation to the pressure-temperature (PT) trace of a dissociation test. It was observed that the dissociation enthalpy of the CH(4)-CO(2) mixed hydrate lays between the limiting values of pure CH(4) hydrate and CO(2) hydrate, increasing with the CO(2) fraction in the hydrate phase. PMID:21604671

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

    DOE PAGESBeta

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

    2015-05-29

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

  1. 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.

  2. 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.

  3. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2011-11-01

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

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

    PubMed

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

    2015-08-01

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

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

    SciTech Connect

    Kouzov, A. P.; Chrysos, M.

    2009-10-15

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

  8. 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.

  9. The role of water in gas hydrate dissociation

    USGS Publications Warehouse

    Circone, S.; Stern, L.A.; Kirby, S.H.

    2004-01-01

    When raised to temperatures above the ice melting point, gas hydrates release their gas in well-defined, reproducible events that occur within self-maintained temperature ranges slightly below the ice point. This behavior is observed for structure I (carbon dioxide, methane) and structure II gas hydrates (methane-ethane, and propane), including those formed with either H2O- or D2O-host frameworks, and dissociated at either ambient or elevated pressure conditions. We hypothesize that at temperatures above the H2O (or D2O) melting point: (1) hydrate dissociation produces water + gas instead of ice + gas, (2) the endothermic dissociation reaction lowers the temperature of the sample, causing the water product to freeze, (3) this phase transition buffers the sample temperatures within a narrow temperature range just below the ice point until dissociation goes to completion, and (4) the temperature depression below the pure ice melting point correlates with the average rate of dissociation and arises from solution of the hydrate-forming gas, released by dissociation, in the water phase at elevated concentrations. In addition, for hydrate that is partially dissociated to ice + gas at lower temperatures and then heated to temperatures above the ice point, all remaining hydrate dissociates to gas + liquid water as existing barriers to dissociation disappear. The enhanced dissociation rates at warmer temperatures are probably associated with faster gas transport pathways arising from the formation of water product.

  10. Dissociation of diatomic gases

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1991-01-01

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