Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation.

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2) n+, just like ionized acetylene clusters. The fragmentation products result from reactive ion-molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.

Probing Ionic Complexes of Ethylene and Acetylene with Vacuum-Ultraviolet Radiation.

Mixed complexes of acetylene-ethylene are studied using vacuum-ultraviolet (VUV) photoionization mass spectrometry and theoretical calculations. These complexes are produced and ionized at different distances from the exit of a continuous nozzle followed by reflectron time-of-flight mass spectrometry detection. Acetylene, with a higher ionization energy (11.4 eV) than ethylene (10.6 eV), allows for tuning the VUV energy and initializing reactions either from a C2H2(+) or a C2H4(+) cation. Pure acetylene and ethylene expansions are separately carried out to compare, contrast, and hence identify products from the mixed expansion: these are C3H3(+) (m/z = 39), C4H5(+) (m/z = 53), and C5H5(+) (m/z = 65). Intensity distributions of C2H2, C2H4, their dimers and reactions products are plotted as a function of ionization distance. These distributions suggest that association mechanisms play a crucial role in product formation closer to the nozzle. Photoionization efficiency (PIE) curves of the mixed complexes demonstrate rising edges closer to both ethylene and acetylene ionization energies. We use density functional theory (ωB97X-V/aug-cc-pVTZ) to study the structures of the neutral and ionized dimers, calculate their adiabatic and vertical ionization energies, as well as the energetics of different isomers on the potential energy surface (PES). Upon ionization, vibrationally excited clusters can use the extra energy to access different isomers on the PES. At farther ionization distances from the nozzle, where the number densities are lower, unimolecular decay is expected to be the dominant mechanism. We discuss the possible decay pathways from the different isomers on the PES and examine the ones that are energetically accessible.

Probing methanol cluster growth by vacuum ultraviolet ionization.

The ability to probe the formation and growth of clusters is key to answering fundamental questions in solvation and nucleation phenomena. Here, we present a mass spectrometric study of methanol cluster dynamics to investigate these two major processes. The clusters are produced in a molecular beam and ionized by vacuum ultraviolet (VUV) radiation at intermediate distances between the nozzle and the skimmer sampling different regimes of the supersonic expansion. The resulting cluster distribution is studied by time-of-flight mass spectrometry. Experimental conditions are optimized to produce intermediate size protonated methanol and methanol-water clusters and mass spectra and photoionization onsets and obtained. These results demonstrate that intensity distributions vary significantly at various nozzle to ionization distances. Ion-molecule reactions closer to the nozzle tend to dominate leading to the formation of protonated species. The protonated trimer is found to be the most abundant ion at shorter distances because of a closed solvation shell, a larger photoionization cross section compared to the dimer, and an enhanced neutral tetramer precursor. On the other hand, the protonated dimer becomes the most abundant ion at farther distances because of low neutral density and an enhanced charged protonated monomer-neutral methanol interaction. Thomson's liquid drop model is used to qualitatively explain the observed distributions.

Evolution of oxidation dynamics of histidine: non-reactivity in the gas phase, peroxides in hydrated clusters, and pH dependence in solution.

Oxidation of histidine by (1)O2 is an important process associated with oxidative damage to proteins during aging, diseases and photodynamic therapy of tumors and jaundice, and photochemical transformations of biological species in the troposphere. However, the oxidation mechanisms and products of histidine differ dramatically in these related environments which range from the gas phase through aerosols to aqueous solution. Herein we report a parallel gas- and solution-phase study on the (1)O2 oxidation of histidine, aimed at evaluating the evolution of histidine oxidation pathways in different media and at different ionization states. We first investigated the oxidation of protonated and deprotonated histidine ions and the same systems hydrated with explicit water molecules in the gas phase, using guided-ion-beam-scattering mass spectrometry. Reaction coordinates and potential energy surfaces for these systems were established on the basis of density functional theory calculations, Rice-Ramsperger-Kassel-Marcus modeling and direct dynamics simulations. Subsequently we tracked the oxidation process of histidine in aqueous solution under different pH conditions, using on-line UV-Vis spectroscopy and electrospray mass spectrometry monitoring systems. The results show that two different routes contribute to the oxidation of histidine depending on its ionization states. In each mechanism hydration is essential to suppressing the otherwise predominant dissociation of reaction intermediates back to reactants. The oxidation of deprotonated histidine in the gas phase involves the formation of 2,4-endoperoxide and 2-hydroperoxide of imidazole. These intermediates evolve to hydrated imidazolone in solution, and the latter either undergoes ring-closure to 6α-hydoxy-2-oxo-octahydro-pyrrolo[2,3-d]imidazole-5-carboxylate or cross-links with another histidine to form a dimeric product. In contrast, the oxidation of protonated histidine is mediated by 2,5-endoperoxide and 5-hydroperoxide, which convert to stable hydrated imidazolone end-product in solution. The contrasting mechanisms and reaction efficiencies of protonated vs. deprotonated histidine, which lead to pH dependence in the photooxidation of histidine, are interpreted in terms of the chemistry of imidazole with (1)O2. The biological implications of the results are also discussed.

Selective transport of amino acids into the gas phase: driving forces for amino acid solubilization in gas-phase reverse micelles.

We report a study on encapsulation of various amino acids into gas-phase sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) reverse micelles, using electrospray ionization guided-ion-beam tandem mass spectrometry. Collision-induced dissociation of mass-selected reverse micellar ions with Xe was performed to probe structures of gas-phase micellar assemblies, identify solute-surfactant interactions, and determine preferential incorporation sites of amino acids. Integration into gas-phase reverse micelles depends upon amino acid hydrophobicity and charge state. For examples, glycine and protonated amino acids (such as protonated tryptophan) are encapsulated within the micellar core via electrostatic interactions; while neutral tryptophan is adsorbed in the surfactant layer. As verified using model polar hydrophobic compounds, the hydrophobic effect and solute-interface hydrogen-bonding do not provide sufficient driving force needed for interfacial solubilization of neutral tryptophan. Neutral tryptophan, with a zwitterionic structure, is intercalated at the micellar interface between surfactant molecules through complementary effects of electrostatic interactions between tryptophan backbone and AOT polar heads, and hydrophobic interactions between tryptophan side chain and AOT alkyl tails. Protonation of tryptophan could significantly improve its incorporation capacity into gas-phase reverse micelles, and displace its incorporation site from the micellar interfacial zone to the core; protonation of glycine, on the other hand, has little effect on its encapsulation capacity. Another interesting observation is that amino acids of different isoelectric points could be selectively encapsulated into, and transported by, reverse micelles from solution to the gas phase, based upon their competition for protonation and subsequent encapsulation within the micellar core.

Reaction of protonated tyrosine with electronically excited singlet molecular oxygen (a1Delta(g)): an experimental and trajectory study.

Reaction of protonated tyrosine with the lowest electronically excited singlet state of molecular oxygen, (1)O(2) (a(1)Delta(g)), is reported over the center-of-mass collision energy (E(col)) range from 0.1 to 3.0 eV, using an electrospray-ionization, guided-ion-beam scattering instrument, in conjunction with ab initio electronic structure calculations and direct dynamics trajectory simulations. Only one product channel is observed, corresponding to generation of hydrogen peroxide via transfer of two hydrogen atoms from protonated tyrosine. Despite being exoergic, the reaction is in competition with physical quenching of (1)O(2) and is very inefficient. At low E(col), the reaction may be mediated by intermediate complexes and shows strong inhibition by collision energy. At high E(col), the reaction efficiency drops to approximately 1% and starts to have contribution from a direct mechanism. Quasi-classical trajectory simulations were performed to probe the mechanism at high collision energies. Analysis of trajectories shows that, at E(col) of 3.0 eV, a small fraction of hydrogen peroxide (25%) is produced via a direct, concerted mechanism where two hydrogen atoms are transferred simultaneously, but most hydrogen peroxide (75%) is formed by dissociation of hydroperoxide intermediates. According to ab initio calculations and trajectory simulations, collisions also lead to formation of various endoperoxides, and dissociation of endoperoxides may play a role in physical quenching of (1)O(2). The apparatus and experimental techniques are described in detail.

Mass spectrometry study of multiply negatively charged, gas-phase NaAOT micelles: how does charge state affect micellar structure and encapsulation?

We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na(n-z)AOT(n)](z-) (n = 1-18 and z = 1-2). Solvation by water was detected only for small aggregates [Na(n-1)AOT(n)H(2)O](-) of n = 3-9. Incorporation of glycine and tryptophan into [Na(n-z)AOT(n)](z-) aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na(n-z)AOT(n)](z-) of n ≥ 7, and at most two glycine molecules could be hosted in that of n ≥ 13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n ≥ 6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na(n+z)AOT(n)](z+) aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.

Guided-ion-beam scattering and direct dynamics trajectory study on the reaction of deprotonated cysteine with singlet molecular oxygen.

We present a study on the gas-phase reaction of deprotonated cysteine with the lowest electronically excited state of molecular oxygen O2[a(1)Δg], including the measurement of the effects of collision energy (E(col)) on reaction cross sections over a center-of-mass E(col) range from 0.1 to 1.0 eV. Deprotonated cysteine was generated using electrospray ionization, and has a carboxylate anionic structure (HSCH2CH(NH2)CO2(-)) in the gas phase. Three product ion channels were observed. The dissociation of HSCH2CH(NH2)CO2(-) to NH2CH2CO2(-) and neutral CH2S has the largest cross section over the entire E(col) range. This product channel is driven by the electronic excitation energy of (1)O2 (the so-called dissociative excitation transfer), and is strongly suppressed by E(col). Two minor channels correspond to the formation of HSCH2C(NH)CO2(-) + H2O2 via abstraction of two hydrogen atoms from HSCH2CH(NH2)CO2(-) by (1)O2, and the formation of OSCH2CH(NH2)CO2(-) radical via elimination of ·OH from an intermediate complex, respectively. Density functional theory calculations were used to locate various complexes, transition states, and products. Quasi-classical direct dynamics trajectory simulations were carried out at E(col) = 0.2 eV using the B3LYP/4-31G(d) level of theory. Trajectory results were used to guide the construction of a reaction coordinate, discriminate between different mechanisms, and provide additional mechanistic insights. Analysis of trajectories highlights the importance of complex mediation at the early stages of all reactions, and suggests a partially concerted mechanism for H2O2 elimination.

Reactions of deprotonated tyrosine and tryptophan with electronically excited singlet molecular oxygen (a1Δ(g)): a guided-ion-beam scattering, statistical modeling, and trajectory study.

The reactions of deprotonated tyrosine ([Tyr-H](-)) and tryptophan ([Trp-H](-)) with the lowest electronically excited state of molecular oxygen O(2)[a(1)Δ(g)] have been studied in the gas phase, including the measurement of the effects of collision energy (E(col)) on reaction cross sections over a center-of-mass E(col) range from 0.05 to 1.0 eV. [Tyr-H](-) and [Trp-H](-) were generated using electrospray ionization, and both have a pure carboxylate anion structure in the gas phase. Density functional theory calculations and RRKM modeling were used to examine properties of various complexes, transition states, and products that might be important along the reaction coordinate. It was found that deprotonation of Tyr and Trp results in a large effect on their (1)O(2)-mediated oxidation. For [Tyr-H](-), the reaction corresponds to the formation of a hydroperoxide intermediate, followed by intramolecular H transfer and subsequent dissociation to product ion 4-(2-aminovinyl)phenolate, and neutral H(2)O(2) and CO(2). Despite that the reaction is 1.83 eV exothermic, the reaction cross section shows a threshold-like behavior at low E(col) and increases with increasing E(col), suggesting that the reaction bears an activation barrier above the reactants. Quasi-classical, direct dynamics trajectory simulations were carried out for [Tyr-H](-) + (1)O(2) at E(col) = 0.75 eV, using B3LYP/4-31G* level of theory. Trajectories demonstrated the intermediacy of complexes at the early stage of the reaction. A similar product channel was observed in the reaction of [Trp-H](-) with (1)O(2), yielding product ion 3-(2-aminovinyl)indol-1-ide, H(2)O(2) and CO(2). However, the reaction cross section of [Trp-H](-) is strongly suppressed by E(col) and becoming negligible at E(col) > 1.0 eV, indicating that this reaction proceeds without energy barriers above the reactants.

Dissociative excitation energy transfer in the reactions of protonated cysteine and tryptophan with electronically excited singlet molecular oxygen (a1Δ(g)).

We report a study on the reactions of protonated cysteine (CysH(+)) and tryptophan (TrpH(+)) with the lowest electronically excited state of molecular oxygen (O(2), a(1)Δ(g)), including the measurement of the effects of collision energy (E(col)) on reaction cross sections over the center-of-mass E(col) range of 0.05 to 1.0 eV. Electronic structure calculations were used to examine properties of complexes, transition states and products that might be important along the reaction coordinate. For CysH(+) + (1)O(2), the product channel corresponds to C(α)-C(ß) bond rupture of a hydroperoxide intermediate CysOOH(+) accompanied by intramolecular H atom transfer, and subsequent dissociation to H(2)NCHCO(2)H(+), CH(3)SH and ground triplet state O(2). The reaction is driven by the electronic excitation energy of (1)O(2), the so-called dissociative excitation energy transfer. Quasi-classical direct dynamics trajectory simulations were calculated for CysH(+) + (1)O(2) at E(col) = 0.2 and 0.3 eV, using the B3LYP/6-21G method. Most trajectories formed intermediate complexes with significant lifetime, implying the importance of complex formation at the early stage of the reaction. Dissociative excitation energy transfer was also observed in the reaction of TrpH(+) with (1)O(2), leading to dissociation of a TrpOOH(+) intermediate. In contrast to CysOOH(+), TrpOOH(+) dissociates into a glycine molecule and charged indole side chain in addition to ground-state O(2) because this product charge state is energetically favorable. The reactions of CysH(+) + (1)O(2) and TrpH(+) + (1)O(2) present similar E(col) dependence, i.e., strongly suppressed by collision energy and becoming negligible at E(col) > 0.5 eV. This is consistent with a complex-mediated mechanism where a long-lived complex is critical for converting the electronic energy of (1)O(2) to the form of internal energy needed to drive complex dissociation.

Experimental and trajectory study on the reaction of protonated methionine with electronically excited singlet molecular oxygen (a1Δg): reaction dynamics and collision energy effects.

The reaction of protonated methionine with the lowest electronically excited state of molecular oxygen O(2)(a(1)Δ(g)) was studied in a guided ion beam apparatus, including the measurement of reaction cross sections over a center-of-mass collision energy (E(col)) range of 0.1-2.0 eV. A series of electronic structure and RRKM calculations were used to examine the properties of various complexes and transition states that might be important along the reaction coordinate. Only one product channel is observed, corresponding to generation of hydrogen peroxide via transfer of two hydrogen atoms (H2T) from protonated methionine to singlet oxygen. At low collision energies, the reaction approaches the collision limit and may be mediated by intermediate complexes. The reaction shows strong inhibition by collision energy, and becomes negligible at E(col) > 1.25 eV. A large set of quasi-classical direct dynamics trajectory simulations were calculated at the B3LYP/6-21G level of theory. Trajectories reproduced experimental results and provided insight into the mechanistic origin of the H2T reaction, how the reaction probability varies with impact parameter, and the suppressing effect of collision energy. Analysis of the trajectories shows that at E(col) = 1.0 eV the reaction is mediated by a precursor and/or hydroperoxide complex, and is sharply orientation-dependent. Only 20% of collisions have favorable reactant orientations at the collision point, and of those, less than half form precursor and hydroperoxide complexes which eventually lead to reaction. The narrow range of reactive collision orientations, together with physical quenching of (1)O(2) via intersystem crossing between singlet and triplet electronic states, may account for the low reaction efficiency observed at high E(col).