Fragmentation characteristic of glutathione conjugates activated by high-energy collisions

Product ion spectra of fifteen monoglutathione and diglutathione conjugates have been measured using activation by 6000-eV collisions with helium in the third field-free region of a four-sector tandem mass spectrometer of EBEB configuration. Fragmentation patterns in the cation spectra have been analyzed for decompositions of the glutathione moiety that would permit recognition of an unknown as a glutathione conjugate. Five spectra from an earlier study of high-energy collisional activation on a BEEB four-sector instrument have also been included in this analysis. A suite of appropriate ions was found to occur consistently, including ions of m/z 307 comprising the glutathione tripeptide and the complementary ion [MH — 307]⁺ or the ion radical [MH — 306]^+’.     

Selectivity of elementary molecular processes in molecule-surface collisions

Excitation of internal vibrational modes of molecules scattered from surfaces in which charge transfer between collision partners occurs is considered. A mechanism is proposed which should lead to controllable selectivity in the fragmentation distributions of scattered polyatomic molecules.     

Fragmentation and reactivity in collisions of protonated diglycine with chemically modified perfluorinated alkylthiolate-self-assembled monolayer surfaces

Direct dynamics simulations are reported for quantum mechanical (QM)/molecular mechanical (MM) trajectories of N-protonated diglycine (gly(2)-H(+)) colliding with chemically modified perfluorinated octanethiolate self-assembled monolayer (SAM) surfaces. The RM1 semiempirical theory is used for the QM component of the trajectories. RM1 activation and reaction energies were compared with those determined from higher-level ab initio theories. Two chemical modifications are considered in which a head group (-COCl or -CHO) is substituted on the terminal carbon of a single chain of the SAM. These surfaces are designated as the COCl-SAM and CHO-SAM, respectively. Fragmentation, peptide reaction with the SAM, and covalent linkage of the peptide or its fragments with the SAM surface are observed. Peptide fragmentation via concerted CH(2)-CO bond breakage is the dominant pathway for both surfaces. HCl formation is the dominant species produced by reaction with the COCl-SAM, while for the CHO-SAM a concerted H-atom transfer from the CHO-SAM to the peptide combined with either a H-atom or radical transfer from the peptide to the surface to form singlet reaction products is the dominant pathway. A strong collision energy dependence is found for the probability of peptide fragmentation, its reactivity, and linkage with the SAM. Surface deposition, i.e., covalent linkage between the surface and the peptide, is compared to recent experimental observations of such bonding by Laskin and co-workers [Phys. Chem. Chem. Phys. 10, 1512 (2008)]. Qualitative differences in reactivity are seen between the COCl-SAM and CHO-SAM showing that chemical identity is important for surface reactivity. The probability of reactive surface deposition, which is most closely analogous to experimental observables, peaks at a value of around 20% for a collision energy of 50 eV.     

State-selective electron capture processes in collisions involving boron ions

A full theoretical treatment of electron capture processes using ab initio configuration interaction methods within, according to the collision energy range concerned, a semiclassical or a quantal collisional formalism including translation effects has been developed recently. An application for collisions involving boron, an important impurity in fusion reactors, is presented on examples of the ground state: B³⁺(1s²) + He, B⁴⁺(1s) + H, and the metastable ion B³⁺(1s2s) + H reactions. © 1996 John Wiley & Sons, Inc.     

Multiple-electron processes in 1.4 MeV/u ion-atom collisions

Simultaneous multiple-electron capture and multiple ionization is studied for collisions of highly stripped ionsA ^q+ with rare gas atomsB=He, Ne, Ar, Kr and Xe. At a specific energy of 1.4 MeV/u coincidence measurements were conducted distinguishing between pure ionization, stripping and capture of up to four electrons by projectiles in charge states fromq=6 up toq=48. The coincident charge-state distributions of target recoil ionsB ⁱ⁺ range fromi=1 up toi=19 (in few cases). For highly charged projectiles the relative fractions of recoil ions for concomitant electron capture and ionization are found to be nearly independent of projectile charge or species. Average charge states 〈i〉 of the recoil ions produced by loss respectively capture ofk electrons (k=?2, ?1, 0, 1, 2, 3, 4) from/into the projectile ion were determined. Their systematic dependences onk, on the target atomic number and the projectile ion charge are discussed. A calculation of partial cross sections for multi-electron collision processes in the He target atoms using unitarized first order perturbation theory for impact parameter dependent probabilities and an independent-electron picture is presented and discussed on the basis of the experimental data.     

Elastic and charge transfer processes in H+ + CO collisions

Proton and hydrogen atom time-of-flight spectra in collision energy range of E(trans) = 9.5-30 eV show that the endoergic charge transfer process in the H+ + CO system is almost an order of magnitude less probable than the elastic scattering [G. Niedner-Schatteburg and J. P. Toennies, Adv. Chem. Phys. LXXXII, 553 (1992)]. Ab initio computations at the multireference configuration interaction level have been performed to obtain the ground- and several low-lying excited electronic state potential energy curves in three different molecular orientations namely, H+ approaching the O-end and the C-end (collinear), and H+ approaching the CO molecule in perpendicular configuration with fixed CO internuclear distance. Nonadiabatic coupling terms between the ground electronic state (H+ + CO) and the three low-lying excited electronic states (H + CO+) have been computed and the corresponding diabatic potentials have been obtained. A time-dependent wavepacket dynamics study is modeled first involving only the ground and the first excited states and then involving the ground and the three lowest excited states at the collision energy of 9.5 eV. The overall charge transfer probability have been found to be approximately 20%-30% which is in qualitative agreement with the experimental findings.     

Unimolecular reaction kinetics in the high-pressure limit without collisions

Molecular activation by blackbody photons, first postulated in 1919 by Perrin, plays a dominant role in the unimolecular dissociation of large ions trapped at low pressure in a Fourier-transform mass spectrometer. Under readily achievable experimental conditions, molecular ions of the protein ubiquitin equilibrate with the blackbody radiation field inside the vacuum chamber. The internal energy of a population of these ions is given by a Boltzmann distribution. From the temperature dependence of unimolecular dissociation rate constants measured in the zero-pressure limit, Arrhenius activation parameters equal to those in the high-pressure limit are obtained.     

Fragmentation and rearrangement processes in the high resolution mass spectra of diphenylsilyl compounds

High resolution mass spectra of a series of diphenylsilyl compounds, Ph₂SiX₂(X=H, F, Cl) and Ph₂Si(oy)₂ (Y=Et, Me, H), were recorded. Results from selected metastable defocusing experiments showed that if X or OY can be readily lost stepwise, the relative abundance of the biphenyl radical rearrangement ion (d) is small; if neutral silicon species such as :SiX₂, SiX or :Si(OY)₂ are readily eliminated, the relative abundance of the ion d will be large. The ion d originates from both odd- and even-electron ions, thus making the radical site mechanism, which requires a phenyl radical to polarize the other phenyl group, rather unlikely to be an important general driving force. The condensation of phenyl groups could be more appropriately viewed in terms of bond liability and product stability. In the special case of diphenylsilyl catecholate, in addition to geminal cleavage of phenyl groups, complex fragmentation and rearrangement processes were also observed.     

Fragmentation and gas phase aggregation processes in the laser desorption ionization of chlorodiaminotriazines

Fragmentation and supramolecular aggregation induced during the laser desorption/ionization (LDI) of four chlorodiaminotriazines (simazine, atrazine, terbutylazine and propazine) have been investigated. The laser wavelength employed (266 nm) lies within the first absorption band of the four triazines. The main fragmentation channel observed involves the prompt cleavage of the Cl atom, followed by partial or total fragmentation of the side alkyl chains. Breakage of the triazinic ring becomes efficient at moderate laser powers; however, the deamination of the triazine is not observed to take place. In addition, the formation of both covalent and non-covalent triazinic aggregates in the desorption plume is found to be particularly efficient. Aggregates as large as heptamers are neatly detected, with the observation that those with the most intense signal involve the dechlorinated triazinic fragment. Both aggregation and fragmentation are largely suppressed upon dilution of the triazine under matrix-assisted laser desorption/ionization conditions.     

Electron transfer processes in potassium collisions with 5-fluorouracil and 5-chlorouracil

Electron transfer to uracil (U), 5-chlorouracil (5-ClU) and 5-fluorouracil (5-FU) yielding anion formation has been investigated in 30-100 eV potassium-molecule collisions. The rich fragmentation patterns of all three molecules suggest that electron transfer in collisions with electronegative neutrals may cause efficient damage to RNA. The main ring fragment anion in all the mass spectra was NCO(-) while the production of X(-) (X = F, Cl) was a strong decomposition of the halouracil temporary negative ions. Cl(-) was the most intense fragment anion in the 5-chlorouracil measurements, whereas NCO(-) production dominated in the U and 5-FU data. Arguments based on energetics and vibrational dynamics have been proposed to explain these differences. Electronic coupling between dipole- and valence-bound states may play a particularly important role in the fragmentation pathways of the 5-ClU parent anion. The stabilizing influence of the potassium cation following electron transfer (ionic scattering) on the observed fragmentation patterns is discussed, notably in the context of comparisons with free electron attachment processes.     

Spatial distributions and interstellar reaction processes

Methyl formate presents a challenge for the conventional chemical mechanisms assumed to guide interstellar organic chemistry. Previous studies of potential formation pathways for methyl formate in interstellar clouds ruled out gas-phase chemistry as a major production route, and more recent chemical kinetics models indicate that it may form efficiently from radical-radical chemistry on ice surfaces. Yet, recent chemical imaging studies of methyl formate and molecules potentially related to its formation suggest that it may form through previously unexplored gas-phase chemistry. Motivated by these findings, two new gas-phase ion-molecule formation routes are proposed and characterized using electronic structure theory with conformational specificity. The proposed reactions, acid-catalyzed Fisher esterification and methyl cation transfer, both produce the less stable trans-conformational isomer of protonated methyl formate in relatively high abundance under the kinetically controlled conditions relevant to interstellar chemistry. Gas-phase neutral methyl formate can be produced from its protonated counterpart through either a dissociative electron recombination reaction or a proton transfer reaction to a molecule with larger proton affinity. Retention (or partial retention) of the conformation in these neutralization reactions would yield trans-methyl formate in an abundance that exceeds predictions under thermodynamic equilibrium at typical interstellar temperatures of ≤100 K. For this reason, this conformer may prove to be an excellent probe of gas-phase chemistry in interstellar clouds. Motivated by new theoretical predictions, the rotational spectrum of trans-methyl formate has been measured for the first time in the laboratory, and seven lines have now been detected in the interstellar medium using the publicly available PRIMOS survey from the NRAO Green Bank Telescope.     

R-matrix theory of inelastic processes in low-energy electron collisions with HCl molecule

The processes of vibrational excitation and dissociative attachment in low-energy electron collisions with HCl molecule are considered. TheR matrix theory of these processes incorporating nuclear dynamics is developed. The input data of the theory are characteristics of the systeme-HCl calculated in the fixed-nuclei approximation. The comparison with experimental data and other theories is given. It is shown that the account of the nuclear motion leads to the significant increase of the vibrational excitation cross sections near threshold. However, in the present variant of the theory, the cross sections for the excitation of the first level are essentially lower than the experimental ones. The dissociative attachment cross sections are in good agreement with the experiment.     

Vibrational-translational energy transfer n atom-polyatomic molecule collisions in thermal reaction systems

Vibrational-translational energy transfer probabilities and collisional efficiencies are calculated for atom-polyatomic molecule collisions. It is assumed that a collision complex is formed and that the total internal vibrational energy is statistically distributed among all the modes of the complex. An attractive potential is assumed and account is taken of the centrifugal barrier. Conservation of system angular momentum is imposed. Convolution of the several thermal distribution functions is carried out and completeness and detailed balance are observed. Comparison of calculated quantum statistical quantities with experiment is made for the thermal isomerization of methyl and ethyl isocyanide in the presence of heavy atomic bath gases, such as Xe or Ar, and semiquantitative agreement is found.     

Fragmentation reaction via an ipso-attack in the multistep synthesis of regioselectively functionalized Calix

The acid-catalyzed convergent synthesis of a calix[8]arene containing a regioselectively functionalized upper rim has been investigated through the isolation and identification of cyclic and acyclic byproducts. Theoretical calculations demonstrated that the synthetic process involves two types of reaction mechanisms, one of which leads to the favorably constructed framework, while the other causes undesirable fragmentation via ipso-substitution. A possible rationale is proposed to explain the overall reaction pathways which derive the calix[8]arene along with the byproducts.     

Fragmentation processes of methylbutyl trifluoroacetates studied by tandem quadrupole mass spectrometry and isotope labeling

The fragmentation patterns of 3-methyl-2-butyl trifluoroacetate and 2-methyl-2-butyl trifluoroacetate were investigated by GC/MS/MS, with electron impact and collision-induced dissociation, on regular and isotope-labeled (deuterium and ¹⁸O) esters. The atoms found in various fragments could be traced back to specific positions in the parent molecules. In this way, molecular rearrangements potentially occurring during the formation of esters by trifluoroacetolysis of 3-methyl-2-butyl p-toluenesulfonate or trifluoroacetic acid addition to various 2-methylbutenes could be shown. Rearrangements also occurred during the fragmentation, particularly during the expulsion of the small fragments CO, C₂H₄ and F₂CO. For the decompositions of oxygen-containing ions these rearrangements were highly specific. By contrast, alkyl cations lead to fragments that are fully scrambled (statistical label distribution). Alkene radical cations ([C_nH_2n]^{+ ˙}) fragment to daughter ions that are extensively, but less than statistically scrambled. Hydrogen scrambling may also occur in fluoroalkyl cation fragments.     

Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Quantum mechanical reaction dynamics in collisions of chlorine atom with hydrogen molecule

We report the accurate determinations of quantum mechanical state-to-state probabilities tor reactions Cl H2 - HCl H and H' HCl - H'Cl H by the generalized Newton variational principle, on the most accurate available potential energy surface. We compare the results for three versions of realistic potential energy surfaces, and to those from hyperspherical close-coupling calculations.