An innovative method to identify structural change through ion-molecule collision, making use of Time-Of-Flight measurements and SIMION simulations.

Structural change of ions induced by collision with a neutral has been studied in a guided ion beam tandem mass spectrometer, using Time-Of-Flight measurements and SIMION simulation. The exothermic catalytic isomerization of HOC+ to HCO+ is used to explore the new methodology. Isomerization is catalyzed via a proton transport mechanism through the interplay of a neutral molecule, the catalyst. Four different potential catalysts, Ne, D2, CH4, and C18O, were studied at different collision energies. SIMION simulation of the ion path and collision in the instrument leads to the highlight of a specific signature related to the catalytic isomerization in the time-of-flight spectra. This signature is used to identify the experimental conditions where isomerization takes place. Only C18O, at low collision energies, gives a clear signature of catalytic isomerization, and a quantitative estimate of the catalyzed isomerization cross-section and rate constant is derived. This new methodology is sensitive to clear presence of catalyzed isomerization and can be used in instruments designed for cross-section measurements, provided low collision energy is used and ion bunching is available.

Ionic Route to Atmospheric Relevant HO2 and Protonated Formaldehyde from Methanol Cation and O2.

Gas-phase ion chemistry influences atmospheric processes, particularly in the formation of cloud condensation nuclei by producing ionic and neutral species in the upper troposphere-stratosphere region impacted by cosmic rays. This work investigates an exothermic ionic route to the formation of hydroperoxyl radical (HO2) and protonated formaldehyde from methanol radical cation and molecular oxygen. Methanol, a key atmospheric component, contributes to global emissions and participates in various chemical reactions affecting atmospheric composition. The two reactant species are of fundamental interest due to their role in atmospheric photochemical reactions, and HO2 is also notable for its production during lightning events. Our experimental investigations using synchrotron radiation reveal a fast hydrogen transfer from the methyl group of methanol to oxygen, leading to the formation of CH2OH+ and HO2. Computational analysis corroborates the experimental findings, elucidating the reaction dynamics and hydrogen transfer pathway. The rate coefficients are obtained from experimental data and shows that this reaction is fast and governed by capture theory. Our study contributes to a deeper understanding of atmospheric processes and highlights the role of ion-driven reactions in atmospheric chemistry.

Structural Elucidation of C6 H4 +. Using Chemical Reaction Monitoring: Charge Transfer Versus Bond Forming Reactions.

Mass spectrometry is a powerful tool but when used on its own, without specific activation of ions, the ion mass is the single observable and the structural information is absent. One way of retrieving this information is by using ion-molecule reactions. We propose a general method to disentangle isomeric structures by combining mass spectrometry, tunable synchrotron light source, and quantum-chemistry calculations. We use reactive chemical monitoring technique, which consists in tracking reactivity changes as a function of photoionization energy i. e. the ionic structure. We illustrate the power of this technique with charge transfer reactions of C6 H4 +. isomers with allene and propyne and discuss its universal applicability. Furthermore, we emphasize the special reactivity characteristics of distonic ions, where strong charge transfer reactivity but very limited reactivity involving bond formation and following cleavages were observed and attributed to the unconventional ortho-benzyne distonic cation.

Singlet Oxygen Oxidation of the Radical Cations of 8-Oxo-2'-deoxyguanosine and Its 9-Methyl Analogue: Dynamics, Potential Energy Surface, and Products Mediated by C5-O2 -Addition.

8-Oxo-2'-deoxyguanosine (OG) is the most common DNA lesion. Notably, OG becomes more susceptible to oxidative damage than the undamaged nucleoside, forming mutagenic products in vivo. Herein the reactions of singlet O2 with the radical cations of 8-oxo-2'-deoxyguanosine (OG.+ ) and 9-methyl-8-oxoguanine (9MOG.+ ) were investigated using ion-molecule scattering mass spectrometry, from which barrierless, exothermic O2 -addition products were detected for both reaction systems. Corroborated by static reaction potential energy surface constructed using multi-reference CASPT2 theory and molecular dynamics simulated in the presence of the reactants' kinetic and internal energies, the C5-terminal O2 -addition was pinpointed as the most probable reaction pathway. By elucidating the reaction mechanism, kinetics and dynamics, and reaction products and energetics, this work constitutes the first report unraveling the synergetic damage of OG by ionizing radiation and singlet O2 .

Discriminant Profiles of Volatile Compounds in the Alveolar Air of Patients with Squamous Cell Lung Cancer, Lung Adenocarcinoma or Colon Cancer.

The objective of the present work was to analyze volatile compounds in alveolar air in patients with squamous cell lung cancer, lung adenocarcinoma or colon cancer, to prepare algorithms able to discriminate such specific pathological conditions. The concentration of 95 volatile com-pounds was measured in the alveolar air of 45 control subjects, 36 patients with lung adenocarci-noma, 25 patients with squamous cell lung cancer and 52 patients with colon cancer. Volatile compounds were measured with ion molecule reaction mass spectrometry (IMR-MS). An iterat-ed least absolute shrinkage and selection operator multivariate logistic regression model was used to generate specific algorithms and discriminate control subjects from patients with differ-ent kinds of cancer. The final predictive models reached the following performance: by using 11 compounds, patients with lung adenocarcinoma were identified with a sensitivity of 86% and specificity of 84%; nine compounds allowed us to identify patients with lung squamous cell car-cinoma with a sensitivity of 88% and specificity of 84%; patients with colon adenocarcinoma could be identified with a sensitivity of 96% and a specificity of 73% using a model comprising 13 volatile compounds. The different alveolar profiles of volatile compounds, obtained from pa-tients with three different kinds of cancer, suggest dissimilar biological-biochemistry condi-tions; each kind of cancer has probably got a specific alveolar profile.

Structural rearrangement of the acrylonitrile (AN) cluster in the gas phase under VUV one-photon radiation explored by mass-selected infrared spectroscopy.

Acrylonitrile (AN), one of the most abundant nitriles in space, is considered to closely relate to the formation of interstellar prebiotic nitrogen-containing aromatics. Herein, we measured the vibrational spectra of acrylonitrile cluster cations (AN)2,3+ in a supersonic jet using infrared (IR) dissociation with vacuum-ultraviolet (VUV) photoionization and time-of-flight mass spectroscopy. Interestingly, the observed IR spectra demonstrate that a new molecular ion [Formula: see text] , is generated from the dimer and trimer of AN upon VUV single-photo ionization. Calculation results reveal that the new molecular cations can be generated through a relative low energy barrier after ionization of the neutral (AN)2. However, the reaction pathways are barrierless for the trimer, in which the third solvent AN acts as a catalyst. The mechanisms of those reactions also have been discussed in detail. This study contributes to a deeper understanding of ion-molecule reaction in gas-phase and the quest for the formation of prebiotic N -containing molecules in the outer space.

State-Selected Reactivity of Carbon Dioxide Cations ( CO 2 + ) With Methane.

The reactivity of CO 2 + with CD4 has been experimentally investigated for its relevance in the chemistry of plasmas used for the conversion of CO2 in carbon-neutral fuels. Non-equilibrium plasmas are currently explored for their capability to activate very stable molecules (such as methane and carbon dioxide) and initiate a series of reactions involving highly reactive species (e.g., radicals and ions) eventually leading to the desired products. Energy, in the form of kinetic or internal excitation of reagents, influences chemical reactions. However, putting the same amount of energy in a different form may affect the reactivity differently. In this paper, we investigate the reaction of CO 2 + with methane by changing either the kinetic energy of CO 2 + or its vibrational excitation. The experiments were performed by a guided ion beam apparatus coupled to synchrotron radiation in the VUV energy range to produce vibrationally excited ions. We find that the reactivity depends on the reagent collision energy, but not so much on the vibrational excitation of CO 2 + . Concerning the product branching ratios ( CD 4 + / CD 3 + /DOCO+) there is substantial disagreement among the values reported in the literature. We find that the dominant channel is the production of CD 4 + , followed by DOCO+ and CD 3 + , as a minor endothermic channel.

Gas-Phase Synthesis and Reactivity of Ligated Group 10 Ions in the Formal +1 Oxidation State.

Electrospray ionization of the group 10 complexes [(phen)M(O2CCH3)2] (phen=1,10-phenanthroline, M = Ni, Pd, Pt) generates the cations [(phen)M(O2CCH3)]+, whose gas-phase chemistry was studied using multistage mass spectrometry experiments in an ion trap mass spectrometer with the combination of collision-induced dissociation (CID) and ion-molecule reactions (IMR). Decarboxylation of [(phen)M(O2CCH3)]+ under CID conditions generates the organometallic cations [(phen)M(CH3)]+, which undergo bond homolysis upon a further stage of CID to generate the cations [(phen)M]+· in which the metal center is formally in the +1 oxidation state. In the case of [(phen)Pt(CH3)]+, the major product ion [(phen)H]+ was formed via loss of the metal carbene Pt=CH2. DFT calculated energetics for the competition between bond homolysis and M=CH2 loss are consistent with their experimentally observed branching ratios of 2% and 98% respectively. The IMR of [(phen)M]+· with O2, N2, H2O, acetone, and allyl iodide were examined. Adduct formation occurs for O2, N2, H2O, and acetone. Upon CID, all adducts fragment to regenerate [(phen)M]+·, except for [(phen)Pt(OC(CH3)2)]+·, which loses a methyl radical to form [(phen)Pt(OCCH3)]+ which upon a further stage of CID regenerates [(phen)Pt(CH3)]+ via CO loss. This closes a formal catalytic cycle for the decomposition of acetone into CO and two methyl radicals with [(phen)Pt]+· as catalyst. In the IMR of [(phen)M]+· with allyl iodide, formation of [(phen)M(CH2CHCH2)]+ was observed for all three metals, whereas for M = Pt also [(phen)Pt(I)]+ and [(phen)Pt(I)2(CH2CHCH2)]+ were observed. Finally, DFT calculated reaction energetics for all IMR reaction channels are consistent with the experimental observations.

Selective Gas-Phase Mass Tagging via Ion/Molecule Reactions Combined with Single Analyzer Neutral Loss Scans to Probe Pharmaceutical Mixtures.

We have demonstrated the use of a simple single ion trap mass spectrometer to identify classes of compounds as well as individual components in complex mixtures. First, a neutral reagent was used to mass tag oxygen-containing analytes using a gas-phase ion/molecule reaction. Then, a neutral loss scan was used to indicate the carboxylic acids. The lack of unit mass selectivity in the neutral loss scan required subsequent product ion scans to confirm the presence and identity of the individual carboxylic acids. The neutral loss scan technique reduced the number of data-dependent MS/MS scans required to confirm identification of signals as protonated carboxylic acids. The method was demonstrated on neat mixtures of standard carboxylic acids as well as on solutions of relevant pharmaceutical tablets and may be generalizable to other ion/molecule reactions.

Ab Initio Molecular Dynamics Simulation Study on the Stereo Reactions between Atomic Oxygen Anion and Methane.

Ion⁻molecule reaction between atomic oxygen anion (O-) and methane (CH4) has been systematically investigated employing the on-the-fly ab initio molecular dynamics simulations. Besides the major H-abstraction process as the exothermic reaction studied widely, an endothermic pathway to produce OCH3- and H is also observed in this study. Three typical O- attack modes with reference to the pyramid structure of CH4 fixed in space have been considered. It was found that the internal motions of the radical products are significantly dependent on the O- attack modes. As for the reaction between O- and the thermally vibrating CH4, the major pathway to produce OH- and CH3 is preferred by the direct H-abstraction and the minor pathway to produce H and OCH3- is the roaming reaction via the transient negative ion [HO-CH3]-.

Intermediate detection in real time using reactive surface desorption dielectric-barrier discharge ionization mass spectrometry.

Reactive intermediates play key roles for reaction mechanism elucidation. A suitable tool for identifying the key intermediates is crucial and highly desirable. In this study, surface desorption dielectric-barrier discharge ionization (reactive SDDBDI) was developed for characterization of the reactive intermediates. In reactive SDDBDI, the plasma is doped with a reagent before the plasma ions are directed at a cover slip surface bearing another analyte. Different from SDDBDI, reactive SDDBDI can be used both as an ambient ionization source and as a means to produce reagent ions for ambient ion/molecule reactions. The online derivation of 4-aminophenol with trifluoroacetic anhydride demonstrated that reactive SDDBDI can be used for chemical analysis where improved specificity or sensitivity is required. The utility of this approach for real-time detection of reactive intermediate was demonstrated by the Schiff-base and Eberlin reactions. The formed intermediates and products could be readily detected and identified by tandem mass spectrometry. These results indicate that reactive SDDBDI can be used to generate reagent ions that undergo ion/molecule reactions in the open air with an analyte at condensed phase on a surface. Reactive SDDBDI has high-efficiency ion transmission and high MS sensitivity. It is thus a potential tool to perform ambient ion/molecule reactions and detect reactive intermediates.

Probing the rate-determining region of the potential energy surface for a prototypical ion-molecule reaction.

We report a joint experimental-theoretical study of the F- + HCl → HF + Cl- reaction kinetics. The experimental measurement of the rate coefficient at several temperatures was made using the selected ion flow tube method. Theoretical rate coefficients are calculated using the quasi-classical trajectory method on a newly developed global potential energy surface, obtained by fitting a large number of high-level ab initio points with augmentation of long-range electrostatic terms. In addition to good agreement between experiment and theory, analyses suggest that the ion-molecule reaction rate is significantly affected by shorter-range interactions, in addition to the traditionally recognized ion-dipole and ion-induced dipole terms. Furthermore, the statistical nature of the reaction is assessed by comparing the measured and calculated HF product vibrational state distributions to that predicted by the phase space theory.This article is part of the theme issue 'Modern theoretical chemistry'.

Oxygen anion (O- ) and hydroxide anion (HO- ) reactivity with a series of old and new refrigerants.

The reactivity of a series of commonly used halogenated compounds (trihalomethanes, chlorofluorocarbon, hydrochlorofluorocarbon, fluorocarbons, and hydrofluoroolefin) with hydroxide and oxygen anion is studied in a compact Fourier transform ion cyclotron resonance. O- is formed by dissociative electron attachment to N2 O and HO- by a further ion-molecule reaction with ammonia. Kinetic experiments are performed by increasing duration of introduction of the studied molecule at a constant pressure. Hydroxide anion reactions mainly proceed by proton transfer for all the acidic compounds. However, nucleophilic substitution is observed for chlorinated and brominated compounds. For fluorinated compounds, a specific elimination of a neutral fluorinated alkene is observed in our results in parallel with the proton transfer reaction. Oxygen anion reacts rapidly and extensively with all compounds. Main reaction channels result from nucleophilic substitution, proton transfer, and formal H2+ transfer. We highlight the importance of transfer processes (atom or ion) in the intermediate ion-neutral complex, explaining part of the observed reactivity and formed ions. In this paper, we present the first reactivity study of anions with HFO 1234yf. Finally, the potential of O- and HO- as chemical ionization reagents for trace analysis is discussed.

Degradation of the Neonicotinoid Pesticides in the Atmospheric Pressure Ionization Source.

During the analysis of neonicotinoid pesticide standards (thiamethoxam, clothianidin, imidacloprid, acetamiprid, and thiacloprid) by mass spectrometry, the degradation of these pesticides (M-C=N-R is degraded into M-C=O, M is the skeleton moiety, and R is NO2 or CN) was observed in the atmospheric pressure ionization interfaces (ESI and APCI). In APCI, the degradation of all the five neonicotinoid pesticides studied took place, and the primary mechanism was in-source ion/molecule reaction, in which a molecule of water (confirmed by use of H218O) attacked the carbon of the imine group accompanying with loss of NH2R (R=NO2, CN). For the nitroguanidine neonicotinoid pesticides (R=NO2, including thiamethoxam, clothianidin, and imidacloprid), higher auxiliary gas heater temperature also contributed to their degradation in APCI due to in-source pyrolysis. The degradation of the five neonicotinoid pesticides studied in ESI was not significant. In ESI, only the nitroguanidine neonicotinoid pesticides could generate the degradation products through in-source fragmentation mechanism. The degradation of cyanoamidine neonicotinoid pesticides (R=CN, including acetamiprid and thiacloprid) in ESI was not observed. The degradation of neonicotinoid pesticides in the ion source of mass spectrometer renders some adverse consequences, such as difficulty interpreting the full-scan mass spectrum, reducing the sensitivity and accuracy of quantitative analysis, and misleading whether these pesticides have degraded in the real samples. Therefore, a clear understanding of these unusual degradation reactions should facilitate the analysis of neonicotinoid pesticides by atmospheric pressure ionization mass spectrometry. Graphical Abstract.

Identifying the D-Pentoses Using Water Adduction to Lithium Cationized Molecule.

A method has been developed that is capable of distinguishing an exhaustive list of underivatized D-pentoses with only a mass spectrometer. Electrospray ionization (ESI) of a solution containing a pentose and a lithium salt yields [Pentose + Li]+. These lithiated pentoses adduct water in a quadrupole ion trap. The reaction rate of water adduction is unique for several of the pentose isomers. Additionally, there are multiple potential gas-phase lithiation sites to form [Pentose + Li]+. A mixture of ions with at least one reactive (water adducting) and at least one unreactive (non-adducting) lithiation site is formed for each pentose. The water adduction reaction rate along with the unreactive fraction of lithiated pentose can be used to completely discriminate all D-pentoses. Graphical Abstract ᅟ.

Quantification of propionaldehyde in breath of patients after lung transplantation.

Oxygen-derived free radicals (ROS) have been identified to contribute significantly to ischemia-reperfusion (I/R) injury by initiating chain reactions with polyunsaturated membrane lipids (lipid peroxidation, LPO) resulting in the generation of several aldehydes and ketones. Due to their volatile nature these LPO products can be measured noninvasively in breath. We hypothesized that one of these markers, namely propionaldehyde, will be increased in lung and heart-lung transplant patients where severe oxidative stress due to I/R injury with early graft dysfunction represents one of the major postoperative complications resulting in prolonged ventilation and increased in-hospital morbidity and mortality. Expiratory air measurements for acetone, isoprene, and propionaldehyde were performed in seven patients after lung (n = 5) or heart-lung (n = 2) transplantation, ventilated patients (n = 12), and healthy volunteers (n = 17) using online ion-molecule reaction mass spectrometry. Increased concentrations of acetone (transplanted: 3812 [2347-12498]; ventilated: 1255 [276-1959]; healthy: 631 [520-784] ppbv; P < .001) and propionaldehyde (transplanted: 270 [70-424]; ventilated: 82 [41.8-142]; healthy: 1.7 [0.1-11.8] ppbv; P < .001) were found in expiratory air of transplanted and ventilated patients. Propionaldehyde resulting from spontaneous fragmentation of peroxides due to free radical-induced LPO after I/R injury in patients after lung or heart-lung transplantation can be quantified in expired breath.

Negative charge induced dissociation: fragmentation of deprotonated N-benzylidene-2-hydroxylanilines in electrospray ionization mass spectrometry.

Unimolecular reactivities of different N-benzylidene-2-hydroxylaniline anions were investigated in gas phase by electrospray ionization tandem mass spectrometry. All the collision-induced dissociation spectra of N-benzylidene-2-hydroxylaniline anions show similar ions at phenyl anions, neutral loss of benzonitrile and benzoxazole anions, respectively. The possible fragmentation pathway was probed through deuterium labeling and various group substituents experiments. Computational results were applied to shed light on the mechanism of fragmentation patterns. The proton in the CH=N is reactive in the formation of the concerned ions. Its direct transfer to the oxygen results in 2-hydroxyphenyl anion. Proton abstraction between benzoxazole and phenyl anion leads to the formation of benzene and benzoxazole anion.

Selectivity of gas-phase ion/molecule reaction of carbon dioxide with phenide ions.

On contrary to the widely accepted conviction that the m/z 93 ion derived from phenol does not react with CO2, we demonstrate that it makes an adduct with CO2 to a small but demonstrable extent. For example, the product-ion mass spectrum recorded for the m/z 98 ion derived from [(2)H6]phenol showed a small peak at m/z 142 when CO2 was used as the collision gas. The formation of an m/z 137 adduct ion from the m/z 93 ion (generated either directly from phenol, or indirectly from salicylic acid by in-source decarboxylation) was demonstrated also by multiple-reaction-monitoring tandem mass spectrometric experiments. According to literature, the m/z 93 ion derived from salicylic acid does not undergo CO2 addition because it is deemed to exist only in the phenoxide form. This reaction has been previously proposed as a method for differentiating phenoxide ion from its isomeric hydroxyphenide ions. We propose that the m/z 93 ion, albeit small, exists also as the phenide form together with the predominant phenoxide ion.

Acetone cation chemistry under varying electron density conditions: from unimolecular decomposition to dissociative recombination processes.

The chemistry of ionized acetone:Ar mixtures under varied ionizing electron density conditions has been studied using matrix-isolation techniques. Gaseous acetone diluted in excess argon gas was subjected to electron bombardment with 300 eV electrons at currents between 20 and 200 µA. Linear wire 'pin' and metal 'plate' electron collector geometries were employed, allowing a wide range of electron density conditions to be explored. The products of subsequent reaction processes were matrix isolated and analyzed by Fourier transform infrared absorption spectroscopy. Products included methane, ketene, 1-propen-2-ol (the enol isomer of acetone), CO, HCO, ethane, ethane, acetylene and CCCO. Product absolute and relative yields varied with acetone number density, the choice of anode geometry and the rate of electron bombardment. The overall chemistry observed is rationalized in terms of mechanistic steps involving unimolecular cation decomposition, ion-molecule reactions, radical-radical reactions and dissociative recombination processes.

Photochemistry of Methane in the Photoionization Region.

Methane was irradiated with microwave operated helium (21.2 eV) and neon (16.7-16.8 eV) resonance lamps which were separated from the reaction vessel by an aluminum window. The quantum yields of the stable end products have been determined at methane pressures ranging from 1 to 20 torr. Over this pressure range the abundances of the primary ions, determined through various diagnostic experiments, are within experimental error the same at 21.2 eV as at 16.7-16.8 eV ( CH 4 + ≃ CH 3 + ≃ 0.5 , CH 2 + ⩽ 0.02 ), and are in good agreement with the primary mass spectra obtained in a photoionization mass spectrometer under collision free conditions (P < 10-5 torr). The C 2 H 5 + which is formed by the reaction: CH 3 + + CH 4 → C 2 H 5 + + H 2 loses a proton by an undetermined mechanism to give C2H4 as a product. There is no evidence for the formation of neutral fragments such as H2, C, CH or CH2 at 16.7-16.8 eV. The fact that the ionization quantum is equal to unity in this energy range accounts for the absence of these intermediates. At 21.2 eV where (Φionization = 0.95) there is concrete evidence for the formation of carbon atoms (Φ(C) ⩾ 0.002). In an attempt to demonstrate the usefulness of enclosed neon and helium resonance light sources in the ion-molecule kinetic studies, the relative probabilities of transfer of H- over D- from various partially deuterium labeled hydrocarbons to C 2 H 5 + (or C 2 D 5 + ) has been determined. The results presented in this article resolve the existing disagreements between previous helium resonance photolysis studies on CH4.