Computational Comparison of Acetate and Nitrate Chemical Ionization of Highly Oxidized Cyclohexene Ozonolysis Intermediates and Products

Data-Driven Compound Identification in Atmospheric Mass Spectrometry

Aerosol particles found in the atmosphere affect the climate and worsen air quality. To mitigate these adverse impacts, aerosol particle formation and aerosol chemistry in the atmosphere need to be better mapped out and understood. Currently, mass spectrometry is the single most important analytical technique in atmospheric chemistry and is used to track and identify compounds and processes. Large amounts of data are collected in each measurement of current time-of-flight and orbitrap mass spectrometers using modern rapid data acquisition practices. However, compound identification remains a major bottleneck during data analysis due to lacking reference libraries and analysis tools. Data-driven compound identification approaches could alleviate the problem, yet remain rare to non-existent in atmospheric science. In this perspective, the authors review the current state of data-driven compound identification with mass spectrometry in atmospheric science and discuss current challenges and possible future steps toward a digital era for atmospheric mass spectrometry.

Analytical methodologies for oxidized organic compounds in the atmosphere

Oxidized compounds in the atmosphere can occur as emitted primary compounds or as secondary products when volatile emitted precursors react with various oxidants. Due to the presence of polar functional groups, their vapor pressures decrease, and they condense onto small particles. Thereby, they have an effect on climate change by the formation of clouds and scattering solar radiation. The particles and oxidized compounds themselves can cause serious health problems when inhaled. Therefore, it is of utmost importance to study oxidized compounds in the atmosphere. Much ongoing research is focused on the discovery of new oxidized substances and on the evaluation of their sources and factors influencing their formation. Monitoring biogenic and anthropogenic primary oxidized compounds or secondary oxidized products in chamber experiments or field campaigns is common. New discoveries have been reported, including various oxidized compounds and a new group of compounds called highly oxidized organic molecules (HOMs). Analytics of HOMs are mainly focused on chromatography and high-resolution mass spectrometry employing chemical ionization for identifying and quantifying compounds at low concentrations. Oxidized compounds can also be monitored by spectrophotometric methods in which the determinations of total amounts are based on functional groups. This review highlights recent findings on oxidized organic compounds in the atmosphere and analytical methodologies used for their detection and quantification. The discussion includes gas and liquid chromatographic methods, sampling, extraction, concentration, and derivatization procedures involved, as well as mass spectrometric and spectrophotometric methods.

Unexpected significance of a minor reaction pathway in daytime formation of biogenic highly oxygenated organic compounds

Secondary organic aerosol (SOA), formed by oxidation of volatile organic compounds, substantially influence air quality and climate. Highly oxygenated organic molecules (HOMs), particularly those formed from biogenic monoterpenes, contribute a large fraction of SOA. During daytime, hydroxyl radicals initiate monoterpene oxidation, mainly by hydroxyl addition to monoterpene double bonds. Naturally, related HOM formation mechanisms should be induced by that reaction route, too. However, for α-pinene, the most abundant atmospheric monoterpene, we find a previously unidentified competitive pathway under atmospherically relevant conditions: HOM formation is predominately induced via hydrogen abstraction by hydroxyl radicals, a generally minor reaction pathway. We show by observations and theoretical calculations that hydrogen abstraction followed by formation and rearrangement of alkoxy radicals is a prerequisite for fast daytime HOM formation. Our analysis provides an accurate mechanism and yield, demonstrating that minor reaction pathways can become major, here for SOA formation and growth and related impacts on air quality and climate.

Peroxy Radical and Product Formation in the Gas-Phase Ozonolysis of α-Pinene under Near-Atmospheric Conditions: Occurrence of an Additional Series of Peroxy Radicals O,O-C10H15O(O2)yO2 with y = 1-3

Ozonolysis of α-pinene, C₁₀H₁₆, and other monoterpenes is considered to be one of the important chemical process in the atmosphere leading to condensable vapors, which are relevant to aerosol formation and, finally, for Earth's radiation budget. The formation of peroxy (RO₂) radicals, O,O-C₁₀H₁₅(O₂)_xO₂ with x = 0-3, and closed-shell products has been probed from the ozonolysis of α-pinene for close to atmospheric reaction conditions. (The "O,O" in the chemical formulas indicates the two carbonyl groups formed in the ozonolysis.) An additional series of RO₂ radicals, O,O-C₁₀H₁₅O(O₂)_yO₂ with y = 1-3, emerged in the presence of NO additions of (1.7-50) × 10⁹ molecules cm^-3, whose formation can be explained via different processes starting from alkoxy (RO) radicals, such as the RO-driven autoxidation. The main closed-shell product is a substance with the composition C₁₀H₁₆O₃, probably pinonic acid, obtained with a molar yield (lower limit) of 0.26+0.27-0.14 independent of NO. Total molar product yields accounted for up to 0.71+0.72-0.38 indicating reasonable detection sensitivity of the analytical technique applied. For the isomeric O,O-C₁₀H₁₅O₂ radicals, an average rate coefficient k(RO₂ + NO) = (1.5 ± 0.3) × 10^-11 cm³ molecule^-1 s^-1 at 295 ± 2 K was determined. Product analysis showed a lowering in the formation of highly oxygenated organic molecules (HOMs) by a factor of ∼2.2 when adding 5 × 10¹⁰ molecules cm^-3 of NO. The comparison with former results revealed that total HOM suppression by NO in the α-pinene ozonolysis is slightly stronger than in the OH + α-pinene reaction.

Highly Oxygenated Organic Nitrates Formed from NO3 Radical-Initiated Oxidation of β-Pinene

The reactions of biogenic volatile organic compounds (BVOC) with the nitrate radicals (NO₃) are major night-time sources of organic nitrates and secondary organic aerosols (SOA) in regions influenced by BVOC and anthropogenic emissions. In this study, the formation of gas-phase highly oxygenated organic molecules-organic nitrates (HOM-ON) from NO₃-initiated oxidation of a representative monoterpene, β-pinene, was investigated in the SAPHIR chamber (Simulation of Atmosphere PHotochemistry In a large Reaction chamber). Six monomer (C = 7-10, N = 1-2, O = 6-16) and five accretion product (C = 17-20, N = 2-4, O = 9-22) families were identified and further classified into first- or second-generation products based on their temporal behavior. The time lag observed in the peak concentrations between peroxy radicals containing odd and even number of oxygen atoms, as well as between radicals and their corresponding termination products, provided constraints on the HOM-ON formation mechanism. The HOM-ON formation can be explained by unimolecular or bimolecular reactions of peroxy radicals. A dominant portion of carbonylnitrates in HOM-ON was detected, highlighting the significance of unimolecular termination reactions by intramolecular H-shift for the formation of HOM-ON. A mean molar yield of HOM-ON was estimated to be 4.8% (-2.6%/+5.6%), suggesting significant HOM-ON contributions to the SOA formation.

Gas-to-Particle Partitioning of Cyclohexene- and α-Pinene-Derived Highly Oxygenated Dimers Evaluated Using COSMOtherm

Oxidized organic compounds are expected to contribute to secondary organic aerosol (SOA) if they have sufficiently low volatilities. We estimated saturation vapor pressures and activity coefficients (at infinite dilution in water and a model water-insoluble organic phase) of cyclohexene- and α-pinene-derived accretion products, “dimers”, using the COSMOtherm19 program. We found that these two property estimates correlate with the number of hydrogen bond-donating functional groups and oxygen atoms in the compound. In contrast, when the number of H-bond donors is fixed, no clear differences are seen either between functional group types (e.g., OH or OOH as H-bond donors) or the formation mechanisms (e.g., gas-phase radical recombination vs liquid-phase closed-shell esterification). For the cyclohexene-derived dimers studied here, COSMOtherm19 predicts lower vapor pressures than the SIMPOL.1 group-contribution method in contrast to previous COSMOtherm estimates using older parameterizations and nonsystematic conformer sampling. The studied dimers can be classified as low, extremely low, or ultra-low-volatility organic compounds based on their estimated saturation mass concentrations. In the presence of aqueous and organic aerosol particles, all of the studied dimers are likely to partition into the particle phase and thereby contribute to SOA formation.

Computational Investigation of RO2 + HO2 and RO2 + RO2 Reactions of Monoterpene Derived First-Generation Peroxy Radicals Leading to Radical Recycling

The oxidation of biogenically emitted volatile organic compounds (BVOC) plays an important role in the formation of secondary organic aerosols (SOA) in the atmosphere. Peroxy radicals (RO₂) are central intermediates in the BVOC oxidation process. Under clean (low-NO _x) conditions, the main bimolecular sink reactions for RO₂ are with the hydroperoxy radical (HO₂) and with other RO₂ radicals. Especially for small RO₂, the RO₂ + HO₂ reaction mainly leads to closed-shell hydroperoxide products. However, there exist other known RO₂ + HO₂ and RO₂ + RO₂ reaction channels that can recycle radicals and oxidants in the atmosphere, potentially leading to lower-volatility products and enhancing SOA formation. In this work, we present a thermodynamic overview of two such reactions: (a) RO₂ + HO₂ → RO + OH + O₂ and (b) R'O₂ + RO₂ → R'O + RO + O₂ for selected monoterpene + oxidant derived peroxy radicals. The monoterpenes considered are α-pinene, β-pinene, limonene, trans-β-ocimene, and Δ³-carene. The oxidants considered are the hydroxyl radical (OH), the nitrate radical (NO₃), and ozone (O₃). The reaction Gibbs energies were calculated at the DLPNO-CCSD(T)/def2-QZVPP//ωB97X-D/aug-cc-pVTZ level of theory. All reactions studied here were found to be exergonic in terms of Gibbs energy. On the basis of a comparison with previous mechanistic studies, we predict that reaction a and reaction b are likely to be most important for first-generation peroxy radicals from O₃ oxidation (especially for β-pinene), while being less so for most first-generation peroxy radicals from OH and NO₃ oxidation. This is because both reactions are comparatively more exergonic for the O₃ oxidized systems than their OH and NO₃ oxidized counterparts. Our results indicate that bimolecular reactions of certain complex RO₂ may contribute to an increase in radical and oxidant recycling under high HO₂ conditions in the atmosphere, which can potentially enhance SOA formation.

NO2 Suppression of Autoxidation-Inhibition of Gas-Phase Highly Oxidized Dimer Product Formation

Atmospheric autoxidation of volatile organic compounds (VOC) leads to prompt formation of highly oxidized multifunctional compounds (HOM) that have been found crucial in forming ambient secondary organic aerosol (SOA). As a radical chain reaction mediated by oxidized peroxy (RO2) and alkoxy (RO) radical intermediates, the formation pathways can be intercepted by suitable reaction partners, preventing the production of the highest oxidized reaction products, and thus the formation of the most condensable material. Commonly, NO is expected to have a detrimental effect on RO2 chemistry, and thus on autoxidation, whereas the influence of NO2 is mostly neglected. Here it is shown by dedicated flow tube experiments, how high concentration of NO2 suppresses cyclohexene ozonolysis initiated autoxidation chain reaction. Importantly, the addition of NO2 ceases covalently bound dimer production, indicating their production involving acylperoxy radical (RC(O)OO•) intermediates. In related experiments NO was also shown to strongly suppress the highly oxidized product formation, but due to possibility for chain propagating reactions (as with RO2 and HO2 too), the suppression is not as absolute as with NO2. Furthermore, it is shown how NO x reactions with oxidized peroxy radicals lead into indistinguishable product compositions, complicating mass spectral assignments in any RO2 + NO x system. The present work was conducted with atmospheric pressure chemical ionization mass spectrometry (CIMS) as the detection method for the highly oxidized end-products and peroxy radical intermediates, under ambient conditions and at short few second reaction times. Specifically, the insight was gained by addition of a large amount of NO2 (and NO) to the oxidation system, upon which acylperoxy radicals reacted in RC(O)O2 + NO2 → RC(O)O2NO2 reaction to form peroxyacylnitrates, consequently shutting down the oxidation sequence.

Primary Formation of Highly Oxidized Multifunctional Products in the OH-Initiated Oxidation of Isoprene: A Combined Theoretical and Experimental Study

It is generally assumed that isoprene-derived secondary organic aerosol (SOA) precursors are mainly formed from the secondary reactions of intermediate products with OH radicals in the gas phase and multiphase oxidation in particles. In this paper, we predicted a theoretical mechanism for the primary formation of highly oxygenated molecules (HOM) in the gas phase through successive intramolecular H-shifts and O₂ addition in the specific Z-δ isomer of hydroxyl-peroxy radicals and alkoxy radicals. The position of O₂ addition is different from that in forming hydroperoxy aldehydes. The prediction was further supported experimentally by successfully identifying a few highly oxidized peroxy radicals and closed-shell products such as C₅H₉O_7,9, C₅H₁₀O_6,7,8, and C₄H₈O₅ in a flow reactor by chemical ionization mass spectrometry at air pressure. These HOM products could serve as important precursors to isoprene-derived SOA. Further modeling studies on the effect of NO concentration suggested that HOM formation could account for up to ∼11% of the branching ratio (∼9% from the 4-OH channel and ∼2% from the 1-OH channel) in the reaction of isoprene with OH when the lifetimes of peroxy radicals due to bimolecular reactions are ∼100 s, which is typical in forest regions.

Accretion Product Formation from Ozonolysis and OH Radical Reaction of α-Pinene: Mechanistic Insight and the Influence of Isoprene and Ethylene

α-Pinene (C₁₀H₁₆) represents one of the most important biogenic emissions in the atmosphere. Its oxidation products can significantly contribute to the secondary organic aerosol (SOA) formation. Here, we report on the formation mechanism of C₁₉ and C₂₀ accretion products from α-pinene oxidation, which are believed to be efficient SOA precursors. Measurements have been performed in a free-jet flow system. Detection of RO₂ radicals and accretion products was carried out by recent mass spectrometric techniques using different ionization schemes. Observed C₁₀-RO₂ radicals from α-pinene ozonolysis were O,O-C₁₀H₁₅(O₂) _xO₂ with x = 0, 1, 2, 3 and from the OH radical reaction HO-C₁₀H₁₆(O₂)_αO₂ with α = 0, 1, 2. All detected C₂₀ accretion products can be explained via the accretion reaction RO₂ + R'O₂ → ROOR' + O₂ starting from the measured C₁₀-RO₂ radicals. We speculate that C₁₉ accretion products are formed in an analogous way assuming CH₂O elimination. Addition of isoprene (C₅H₈), producing C₅-RO₂ radicals, leads to C₁₅ accretion products formed via cross-reactions with C₁₀-RO₂ radicals. This process is competing with the formation of C₁₉/C₂₀ products from the pure α-pinene oxidation. A similar behavior has been observed for ethylene additives that form C₁₂ accretion products. In the atmosphere, a complex accretion product spectrum from self- and cross-reactions of available RO₂ radicals can be expected. Modeling atmospheric conditions revealed that C₁₉/C₂₀ product formation is only reduced by a factor of 1.2 or 3.6 in isoprene-dominated environments assuming a 2- or 15-fold isoprene concentration over α-pinene, respectively, as present in different forested areas.

Computational Comparison of Different Reagent Ions in the Chemical Ionization of Oxidized Multifunctional Compounds

High pressure anion chemical ionization is commonly used for the detection of neutral molecules in the gas phase. The detection efficiency in these measurements depends on how strongly the reagent ion binds to the neutral target molecule. We have calculated the binding strength of nitrate (NO₃^-), acetate (CH₃C(O)O^-), lactate (CH₃CH(OH)C(O)O^-), trifluoroacetate (CF₃C(O)O^-), trifluoromethanolate (CF₃O^-), bromide (Br^-), and iodide (I^-) reagent ions to ten different products derived from the OH radical-initiated oxidation of butadiene. We found that the binding of these oxidation products to the reagent ions depends almost linearly on the number of oxygen atoms in the target molecule, with the precise chemical identity of the compound (e.g., the number and relative position of hydroxyl or hydroperoxy groups) playing a more minor role. For acetate, the formation free energy decreases on average by around 4 kcal/mol when the number of oxygen atoms in the sample molecule increases by one. For the other reagent ions the corresponding decrease is around 3 kcal/mol. For all of the molecules studied, acetate forms the most stable clusters and I^- the least stable. We also investigated the effect of humidity on the chemical ionization by calculating how strongly water molecules bind to both the reagent ions and the ion-molecule clusters. Water binds much more strongly to the reagent ion monomers compared to the reagent ion "dimers" (defined here as a cluster of the reagent anion with the corresponding neutral conjugate acid, e.g., HNO₃(NO₃^-)) or the ion-molecule clusters. This likely leads to a stronger humidity dependence when using reagent ions that are not able to form reagent ion dimers (such as CF₃C(O)O^-, CF₃O^-, Br^-, and I^-).

Computational and Experimental Investigation of the Detection of HO2 Radical and the Products of Its Reaction with Cyclohexene Ozonolysis Derived RO2 Radicals by an Iodide-Based Chemical Ionization Mass Spectrometer

The HO₂ radical is an important atmospheric molecule that can potentially influence the termination of autoxidation processes of volatile organic compounds (VOCs) that lead to the formation of highly oxygenated multifunctional compounds (HOMs). In this work, we demonstrate the direct detection of the HO₂ radical using an iodide-based chemical ionization mass spectrometer (iodide-CIMS). Expanding on the previously established correlation between molecule-iodide binding enthalpy and iodide-CIMS instrument sensitivity, the experimental detection of the HO₂ radical was preceded by the quantum chemical calculation of the HO₂*I^- cluster (PBE/aug-cc-pVTZ-PP level), which showed a reasonably strong binding enthalpy of 21.60 kcal/mol. Cyclohexene ozonolysis intermediates and closed-shell products were next detected by the iodide-CIMS. The ozone-initiated cyclohexene oxidation mechanism was perturbed by the introduction of the HO₂ radical, leading to the formation of closed-shell hydroperoxides. The experimental investigation once again followed the initial computational molecule-iodide binding enthalpy calculations. The quantum chemical calculations were performed at the PBE/aug-cc-pVTZ-PP level for radicals and DLPNO-CCSD(T)/def2-QZVPP//PBE/aug-cc-pVTZ-PP level for the closed-shell products. A comparison between the iodide-CIMS and nitrate-CIMS spectra with identical measurement steps revealed that the iodide-CIMS was able to detect the low-oxidized (O/C ratio 0.5 and 0.66) cyclohexene ozonolysis monomer products more efficiently than nitrate-CIMS. Higher-oxidized monomers (O/C ratio 1 to 1.5) were detected equally well by both methods. An investigation of dimers showed that both iodide- and nitrate-CIMS were able to detect the dimer compositions possibly formed from reactions between the peroxy radical monomers considered in this study. Additionally, iodide-CIMS detected organic ions that were formed by a previously suggested mechanism of dehydroxylation of peroxy acids (and deoxygenation of acyl peroxy radicals) by H₂O*I^- clusters. These mechanisms were computationally verified.

Formation of Highly Oxidized Radicals and Multifunctional Products from the Atmospheric Oxidation of Alkylbenzenes

Aromatic hydrocarbons contribute significantly to tropospheric ozone and secondary organic aerosols (SOA). Despite large efforts in elucidating the formation mechanism of aromatic-derived SOA, current models still substantially underestimate the SOA yields when comparing to field measurements. Here we present a new, up to now undiscovered pathway for the formation of highly oxidized products from the OH-initiated oxidation of alkyl benzenes based on theoretical and experimental investigations. We propose that unimolecular H-migration followed by O₂-addition, a so-called autoxidation step, can take place in bicyclic peroxy radicals (BPRs), which are important intermediates of the OH-initiated oxidation of aromatic compounds. These autoxidation steps lead to the formation of highly oxidized multifunctional compounds (HOMs), which are able to form SOA. Our theoretical calculations suggest that the intramolecular H-migration in BPRs of substituted benzenes could be fast enough to compete with bimolecular reactions with HO₂ radicals or NO under atmospheric conditions. The theoretical findings are experimentally supported by flow tube studies using chemical ionization mass spectrometry to detect the highly oxidized peroxy radical intermediates and closed-shell products. This new unimolecular BPR route to form HOMs in the gas phase enhances our understanding of the aromatic oxidation mechanism, and contributes significantly to a better understanding of aromatic-derived SOA in urban areas.