Ion-molecule Collisions Research Articles

Elucidating Potential Energy Surfaces for Singlet O2 Reactions with Protonated, Deprotonated, and Di-Deprotonated Cystine Using a Combination of Approximately Spin-Projected Density Functional Theory and Guided-Ion-Beam Mass Spectrometry

The reactivity of cystine toward electronically excited singlet O2 (a1Δg) has been long debated, despite the fact that most organic disulfides are susceptible to oxidation by singlet O2. We report a combined experimental and computational study on reactions of singlet O2 with gas-phase cystine at different ionization and hydration states, aimed to determine reaction outcomes, mechanisms, and potential energy surfaces (PESs). Ion-molecule collisions of protonated and di-deprotonated cystine ions with singlet O2, in both the absence and the presence of a water ligand, were measured over a center-of-mass collision energy (Ecol) range from 0.1 to 1.0 eV, using a guided-ion-beam scattering tandem mass spectrometer. No oxidation was observed for these reactant ions except collision-induced dissociation at high energies. Guided by density functional theory (DFT)-calculated PESs, reaction coordinates were established to unravel the origin of the nonreactivity of cystine ions toward singlet O2. To account for mixed open- and closed-shell characters, singlet O2 and critical structures along reaction coordinates were evaluated using broken-symmetry, open-shell DFT with spin contamination errors removed by an approximate spin-projection method. It was found that collision of protonated cystine with singlet O2 follows a repulsive potential surface and possesses no chemically significant interaction and that collision-induced dissociation of protonated cystine is dominated by loss of water and CO. Collision of di-deprotonated cystine with singlet O2, on the other hand, forms a short-lived electrostatically bonded precursor complex at low Ecol. The latter may evolve to a covalently bonded persulfoxide, but the conversion is blocked by an activation barrier lying 0.39 eV above reactants. At high Ecol, C-S bond cleavage dominates the collision-induced dissociation of di-deprotonated cystine, leading to charge-separated fragmentation. Cross section for the ensuing fragment ion H2NCH(CO2-)CH2SS• was measured as a function of Ecol, and the mechanism of charge-separated fragmentation was discussed. It was also found that the reaction of deprotonated cystine with singlet O2 follows a similar mechanism as that of di-deprotonated cystine, but with an even higher activation barrier (0.72 eV).

Calculation of the sensitivity of proton-transfer-reaction mass spectrometry (PTR-MS) for organic trace gases using molecular properties

Proton-transfer-reaction mass spectrometry (PTR-MS) allows the detection of a large number of trace gases in air through proton-transfer reaction with H3O+ reagent ions and detection by a mass spectrometer. Measurement sensitivities can be experimentally determined using calibration gases or calculated using the rate constant for the proton-transfer reaction, but rate constants have only been measured for a subset of compounds. Numerous theoretical approaches that describe the ion-molecule collision processes have shown how to accurately calculate capture collision rate constants between an ion and neutral molecules using the polarizability and permanent dipole moment of the molecule. Here we show that polarizability, dipole moment, and resulting capture rate constants for proton-transfer reactions of H3O+ with various different volatile organic compounds (VOCs) can be obtained using the molecular mass, elemental composition, and functionality of VOCs. The polarizabilities of a class of VOCs possessing a specific number of electronegative atoms were linearly correlated with their molecular mass. The dipole moments in a series of VOCs, in which VOCs contain a specific functional group and arbitrary residual hydrocarbon parts, can be approximated as a constant value. The capture rate constants calculated using polarizability and dipole moment, as estimated from molecular mass, elemental composition, and functional group, agreed within 10% with measured values for most VOCs. Those capture rate constants were applied to the calculation of the sensitivities of VOCs detected by our PTR-MS, taking into account the ion transmission efficiency and the degree of fragmentation of protonated VOCs observed in that instrument as well as chemical properties of the VOCs. The resulting calculated sensitivities agreed within 20–50% of those measured by PTR-MS, but several notable exceptions exist. This result shows that the neutral concentration of a VOC detected as a protonated molecule in PTR-MS can be approximated using only molecular mass, elemental composition, and functionality of the VOC. The present study is useful for all PTR-MS instruments regardless of the type of mass analyzer; however, the identification of elemental composition by high mass resolution instrumentation is important.

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.

SOLPS-ITER Study of neutral leakage and drift effects on the alcator C-Mod divertor plasma

As part of an effort to validate the edge plasma model in the SOLPS-ITER code suite under ITER-relevant divertor plasma and neutral conditions, we report on progress in the modeling of the Alcator C-Mod divertor plasma with the new code. We perform simulations with a complete drifts model and kinetic neutrals, including effects of neutral viscosity, ion-molecule collisions and Lyα-opaque conditions, but assuming a pure deuterium plasma. Through a series of simulations with varying divertor geometries, we show the importance of including neutal leakage paths through the divertor substructure on the divertor plasma solution. Moreover, the impact of drifts on inner-outer target asymmetries is assessed. Including both effects, we achieve excellent agreement between simulations and upstream and outer target Langmuir Probe data. In absence of strong volumetric losses due to e.g. impurity radiation in our simulations, the strong inner target detachment observed experimentally remains elusive in our modeling at present.

Thermodynamics and Reaction Mechanisms of Decomposition of the Simplest Protonated Tripeptide, Triglycine: A Guided Ion Beam and Computational Study.

We present a thorough characterization of fragmentations observed in threshold collision-induced dissociation (TCID) experiments of protonated triglycine (H+GGG) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Kinetic energy-dependent cross-sections for 10 ionic products are observed and analyzed to provide 0 K barriers for six primary products: [b2]+, [y1 + 2H]+, [b3]+, CO loss, [y2 + 2H]+, and [a1]+; three secondary products: [a2]+, [a3]+, and [y2 + 2H - CO]+; and two tertiary products: high energy [y1 + 2H]+ and [a2 - CO]+ after accounting for multiple ion-molecule collisions, internal energy of reactant ions, unimolecular decay rates, competition between channels, and sequential dissociations. Relaxed potential energy surface scans performed at the B3LYP-D3/6-311+G(d,p) level of theory are used to identify transition states (TSs) and intermediates of the six primary and one secondary products. Geometry optimizations and single point energy calculations were performed at several levels of theory. These theoretical energies are compared with experimental energies and are found to give reasonably good agreement, in particular for the M06-2X level of theory. This good agreement between experiment and theory validates the reaction mechanisms explored computationally here and elsewhere and allows identification of the product structures formed at threshold energies. The present work presents the first measurement of absolute experimental threshold energies of important sequence ions and non-sequence ions: [y1 + 2H]+, [b3]+, CO loss, [a1]+, and [a3]+, and refines those for [b2]+ and [y2 + 2H]+ previously measured. Graphical Abstract ᅟ.

Evolution of the energy-loss-spectrum profile with the projectile mass in impulsive ion-molecule collisions

Systematic analysis is made for illuminating the mechanism of rotational and vibrational excitations in an impulsive ion-molecule collision from the viewpoint of its sudden nature. Variation of the energy-loss spectrum with the projectile mass is examined in the collision system of an alkali-metal ion with a nitrogen molecule at a hyperthermal energy of 27 eV using a common interaction potential. The spectra are obtained by the classical trajectory calculation and compared with two sudden-limit models---the hard-shell model for rigid-rotor molecules and the hard-potential model for vibrating-rotor molecules [A. Ichimura and M. Nakamura, Phys. Rev. A 69, 022716 (2004)]. For a projectile much lighter than the target, the vibrational and rotational excitation occurs in such a way that the hard-potential model predicts, producing a spectral profile with double peaks. As the projectile mass increases, the vibrational suddenness is degraded so that the vibrational excitation becomes quenched, while the spectral profile still shows a double-peak structure explainable with the hard-shell model. Subsequently, as the projectile mass further increases, the rotational suddenness is also degraded so that the spectrum indicates a profile departing far from the prediction of the hard-shell model; the deeply inelastic peak is suppressed and the nearly elastic peak is enhanced. Such spectral deformation actually occurs in an experimental result reported for ${\mathrm{Na}}^{+}--{\mathrm{N}}_{2}$ collisions [M. Nakamura, S. Kita, and T. Hasegawa, J. Phys. Soc. Jpn. 56, 3161 (1987)]. Eventually, the deeply inelastic peak disappears due to temporary excitation during a collision.

Determination of Energy-Transfer Distributions in Ionizing Ion-Molecule Collisions.

The ionization and fragmentation of the nucleoside thymidine in the gas phase has been investigated by combining ion collision with state-selected photoionization experiments and quantum chemistry calculations. The comparison between the mass spectra measured in both types of experiments allows us to accurately determine the distribution of the energy deposited in the ionized molecule as a result of the collision. The relation of two experimental techniques and theory shows a strong correlation between the excited states of the ionized molecule with the computed dissociation pathways, as well as with charge localization or delocalization.

An independent-atom-model description of ion-molecule collisions including geometric screening corrections

A new model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is introduced. The ion-molecule cross sections for net capture and net ionization are represented as weighted sums of atomic cross sections with weight factors that are determined from a geometric model of overlapping cross section areas. Results are presented for proton collisions with targets ranging from diatomic to complex polyatomic molecules. Significant improvement compared to simple additivity rule results and in general good agreement with experimental data are found. The flexibility of the approach opens up the possibility to study more detailed observables such as orientation-dependent and charge-state-correlated cross sections for a large class of complex targets ranging from biomolecules to atomic clusters.

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine.

The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies.

Coherent electron emission beyond Young-type interference from diatomic molecules

It has been known for more than 15 years that the differential cross section of electrons emitted from diatomic molecules during interaction with energetic charged particles oscillates as a function of electron momentum. The origin of the phenomenon is two-center interference, which naturally relates it back to the Young double-slit experiment. In addition to a characteristic frequency which can be described by lowest-order perturbation theories, the observation and origin of higher-order harmonics of the basic oscillation frequency has been much discussed. Here, we show that high harmonics of the fundamental Young-type oscillation frequency observed in electron spectra in fast ion-molecule collisions can be clearly exposed in numerical solutions of the time-dependent Schr\odinger equation within a one-dimensional model. Momentum distribution of the ejected electron is analyzed and shows that the phenomenon emerges when the charged particle beam collides with diatomic molecules with substantial large internuclear distance. Frequency spectra from nonperturbative calculations for electron emission from ${\text{Rb}}_{2}{}^{+}$ and ${\text{Cs}}_{2}{}^{+}$ exhibit a pronounced high-order oscillation in contrast to similar close-coupling calculations performed on ${\text{H}}_{2}$ targets. The electron emission from these heavy molecules contains second- and third-order harmonics which are fully reproduced in an analytic model based on the Born series. Extending to triatomic molecular targets displays an increased range of harmonics. This suggests that electron emission spectra from new experiments on heavy diatomic and linear polyatomic molecular targets may provide a unique insight into competing coherent emission mechanisms and their relative strength.

Velocity-selected magnetic guiding of Zeeman-decelerated hydrogen atoms

An original design of magnetic guide is presented, suitable for use with Zeeman-decelerated supersonic beams of ground-state hydrogen atoms and other light paramagnetic species. Three-dimensional particle trajectory simulations show that, by combining a series of permanent-magnet Halbach arrays with pulsed high-current wire electromagnets, this guide can be used to efficiently transmit the slow, decelerated atoms and discard the faster, undecelerated atoms and other species in the gas beam. The curved guide would be suitable for guiding hydrogen atoms into an ion trap to investigate low temperature ion-molecule collisions. It is also shown that the device could be used for the guiding or velocity selection from an undecelerated supersonic or effusive beam.

Results of the Ion–Neutral Collision Frequency Measurements in the Lower Thermosphere by the Method of Resonance Scattering of the Radio Waves by Artificial Periodic Irregularities

UDC 550.388.2+551.510.536 We present for the first time the experimental data on the frequency of ion–neutral collisions at the altitudes of the ionospheric E layer, which were obtained by the method of resonance scattering of the radio waves by artificial periodic irregularities of the ionospheric plasma. The measurements were carried out in different time periods from 1990 to 2012. Time and altitude dependences of the collision frequency are given. The dependence of the collision frequency on the solar and geomagnetic activity has been analyzed. Collisions of electrons and ions with atoms and molecules play an important role in physics of the ionosphere and atmosphere. In particular, they determine the friction force and should be taken into account in the equations of motion of a medium when its viscosity increases. The frequency of ion–neutral collisions affects the energy and momentum transfer processes [1–4]. When propagation of internal gravity waves above 100 km is considered, it is needed to allow for dissipation due to increasing viscosity of the medium [4–7], which is directly related to collisions. The frequency νin of collisions between ions and neutral molecules should also be taken into account when the low-frequency processes associated with the plasma conductivity are analyzed (see, e. g., [8]). However, the experimental data on νin are fairly scarce. Meanwhile, considerable variations in the ion–neutral collision frequency can be observed in the upper ionosphere. These variations are due most frequently to the neutral atmosphere density variations caused by the transmission of internal gravity and tidal waves. Variations from day to day can be due to propagation of planetary waves. At the altitudes of the upper mesosphere and lower thermosphere, the neutral atmosphere density variations according to the lidar data can exceed 20%, while the temperature variations can reach 70 K [9, 10]. Observations suggest that during propagation of gravity waves the collision frequency can be changed by a factor of 1.5–2 for half an hour [9, 11]. The collision frequency variations can also be a consequence of variations in the composition of both the ion component and the neutral atoms and molecules. In particular, in the ionospheric E region, variations in the ion–neutral collision frequency can be caused by the penetration of metal meteor particles and ions that contribute to the formation of both the sporadic layers of the electron density and the layer with increased content of Na, K, Fe, etc. atoms [12–15]. In this paper, we present the results of determining the ion–molecule collision frequency obtained by the method of resonant scattering of radio waves by artificial periodic irregularities of the plasma at the altitudes of the ionospheric E region.

Primary processes: from atoms to diatomic molecules and clusters

This article presents a short review of the main progresses achieved at the GANIL facilities during the last thirty years in the field of ion-atom and ion-diatomic molecule collisions. Thanks to the wide range of projectile energies and species available on the different beam lines of the facility, elementary processes such as electron capture, ionization and excitation have been extensively studied. Beside primary collision mechanisms, the relaxation processes of the collision partners after the collision have been another specific source of interest. Progresses on other fundamental processes such as Young type interferences induced by ion-molecule collisions or shake off ionization resulting from nuclear beta decay are also presented.

Setup for measuring angular anisotropies in slow ion-molecule collisions

A recoil ion momentum spectrometer has been fabricated for studying angular anisotropies in ion-induced molecular dissociation. The spectrometer is characterized for its time and momentum resolution by studying test cases of ion-atom and ion-molecule collisions. The typical time resolution is measured to be 2.9×10−3(Δt/t) and typical momentum resolution is of the order of 32 atomic units. Some preliminary results on the measurements of angular anisotropies in ion molecule collisions are presented.

Influence of atomic physics on EDGE2D-EIRENE simulations of JET divertor detachment with carbon and beryllium/tungsten plasma-facing components

The EDGE2D-EIRENE code is applied for simulation of divertor detachment during matched density ramp experiments in high triangularity, L-mode plasmas in both JET-Carbon (JET-C) and JET-ITER-Like Wall (JET-ILW). The code runs without drifts and includes either C or Be as impurity, but not W, assuming that the W targets have been coated with Be via main chamber migration. The simulations reproduce reasonably well the observed particle flux detachment as density is raised in both JET-C and JET-ILW experiments and can better match the experimental in-out divertor target power asymmetry if the heat flux entering the outer divertor is artificially set at around 2–3 times that entering the inner divertor. A careful comparison between different sets of atomic physics processes used in EIRENE shows that the detachment modelled by EDGE2D-EIRENE relies only on an increase of the particle sinks and not on a decrease of the ionization source. For the rollover and the beginning of the partially detached phase, the particle losses by perpendicular transport and the molecular activated recombination processes are mainly involved. For a deeper detachment with significant target ion flux reduction, volume recombination appears to be the main contributor. The elastic molecule-ion collisions are also important to provide good neutral confinement in the divertor and thus stabilize the simulations at low electron temperature (Te), when the sink terms are strong. Comparison between EDGE2D-EIRENE and SOLPS4.3 simulations of the density ramp in C shows similar detachment trends, but the importance of the elastic ion-molecule collisions is reduced in SOLPS4.3. Both codes suggest that any process capable of increasing the neutral confinement in the divertor should help to improve the modelling of the detachment. A further outcome of this work has been to demonstrate that key JET divertor diagnostic signals—Langmuir probe Te and bolometric tomographic reconstructions—are running beyond the limit of validity in high recycling and detached conditions and cannot be reliably used for code validation. The simulations do, however, reproduce the trend of the evolution of the line integrated bolometer chord measurements. The comparison between the code results and high-n Balmer line radiation intensity profiles confirms that a strong volume recombination is present during the experimental detachment and may play a role in this process, as suggested by the code.

Production of cold beams of ND3 with variable rotational state distributions by electrostatic extraction of He and Ne buffer-gas-cooled beams.

The measurement of the rotational state distribution of a velocity-selected, buffer-gas-cooled beam of ND3 is described. In an apparatus recently constructed to study cold ion-molecule collisions, the ND3 beam is extracted from a cryogenically cooled buffer-gas cell using a 2.15 m long electrostatic quadrupole guide with three 90° bends. (2+1) resonance enhanced multiphoton ionization spectra of molecules exiting the guide show that beams of ND3 can be produced with rotational state populations corresponding to approximately T(rot) = 9-18 K, achieved through manipulation of the temperature of the buffer-gas cell (operated at 6 K or 17 K), the identity of the buffer gas (He or Ne), or the relative densities of the buffer gas and ND3. The translational temperature of the guided ND3 is found to be similar in a 6 K helium and 17 K neon buffer-gas cell (peak kinetic energies of 6.92(0.13) K and 5.90(0.01) K, respectively). The characterization of this cold-molecule source provides an opportunity for the first experimental investigations into the rotational dependence of reaction cross sections in low temperature collisions.

Multielectronic close-coupling treatment of atomic and molecular collisions: applications to H+-Li collisions in the keV energy range

We present a new approach to describe electronic processes occurring in ion-atom and ion-molecule collisions at impact energies ranging from 50 eV.u−1 to 1 MeV.u−1. The treatment is based on the semiclassical approximation in which the time-dependent Schrödinger equation is solved non perturbatively, taking into account all the electrons of the collision system. This allows to describe exactly multielectronic processes and also, at the same footing, processes involving valence and inner shell electrons. We apply this model to describe electron transfer in a genuine three-electron system, H+-Li.

Basis generator method study of electron removal from water molecules by multiply-charged ion impact

We apply the basis generator method for ion-molecule collisions to study He2+ and C6+ impact on H2O in the energy range of 20-5000 keV/amu. Results are compared with experimental data and previous calculations where available.

Thermodynamics and Mechanism of Protonated Cysteine Decomposition: A Guided Ion Beam and Computational Study

A quantitative molecular description of the decomposition of protonated cysteine, H(+)Cys, is provided by studying the kinetic energy dependence of threshold collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Primary dissociation channels are deamidation (yielding both NH3 loss and NH4(+) formation) and (H2O + CO) loss reactions, followed by an additional six subsequent decompositions. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for six different reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels. To identify the mechanisms associated with these reactions, quantum chemical calculations performed at the B3LYP/6-311 + G(d,p) level were used to locate the transition states (TSs) and intermediates for these processes. Single point energies of the reactants, products, and key optimized TSs and intermediates are calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311 + G(2d,2p) basis set. The computational characterization of the elementary steps of these reactions, including the structures of the final products, is validated by quantitative agreement with the experimental energetics. In agreement with previous work, deamidation is facilitated by anchimeric assistance of the thio group, which also leads to an interesting rearrangement of the intact amino acid identified computationally.

Status of the Bio-Nano electron cyclotron resonance ion source at Toyo University

In the paper, the material science experiments, carried out recently using the Bio-Nano electron cyclotron resonance ion source (ECRIS) at Toyo University, are reported. We have investigated several methods to synthesize endohedral C60 using ion-ion and ion-molecule collision reaction in the ECRIS. Because of the simplicity of the configuration, we can install a large choice of additional equipment in the ECRIS. The Bio-Nano ECRIS is suitable not only to test the materials production but also to test technical developments to improve or understand the performance of an ECRIS.