Thermalized Epoxide Formation in the Atmosphere

Epoxide formation was established a decade ago as a possible reaction pathway for beta-hydroperoxy alkyl radicals in the atmosphere. This epoxide-forming pathway required excess energy to compete with O-2 addition, as the thermal reaction rate coefficient is many orders of magnitude too slow. However, recently, a thermal epoxide forming reaction was discovered in the ISOPOOH + OH oxidation pathway. Here, we computationally investigate the effect of substituents on the epoxide formation rate coefficient of a series of substituted beta-hydroperoxy alkyl radicals. We find that the thermal reaction is likely to be competitive with O-2 addition when the alkyl radical carbon has a OH group, which is able to form a hydrogen bond to a substituent on the other carbon atom in the epoxide ring being formed. Reactants fulfilling these requirements can be formed in the OH-initiated oxidation of many biogenic hydrocarbons. Further, we find that beta-OOR alkyl radicals react similarly to beta-OOH alkyl radicals, making epoxide formation a possible decomposition pathway in the oxidation of ROOR peroxides. GEOS-Chem modeling shows that the total annual production of isoprene dihydroxy hydroperoxy epoxide is 23 Tg, making it by far the most abundant C-5-tetrafunctional species from isoprene oxidation.Peer reviewe

Formation of Highly Oxidized Molecules from NO3 Radical Initiated Oxidation of Delta-3-Carene : A Mechanistic Study

NO3 radical oxidation of most monoterpenes is a significant source of secondary organic aerosol (SOA) in many regions influenced by both biogenic and anthropogenic emissions, but there are very few published mechanistic studies of NO3 chemistry beyond simple first generation products. Here, we present a computationally derived mechanism detailing the unimolecular pathways available to the second generation of peroxy radicals following NO3 oxidation of Delta-3-carene, defining generations based on the sequence of peroxy radicals formed rather than number of oxidant attacks. We assess five different types of unimolecular reactions, including peroxy and alkoxy radical (RO2 and RO) hydrogen shifts, RO2 and RO ring closing (e.g., endoperoxide formation), and RO decomposition. Rate constants calculated using quantum chemical methods indicate that this chemical system has significant contribution from both bimolecular and unimolecular pathways. The dominant unimolecular reactions are endoperoxide formation, RO H-shifts, and RO decomposition. However, the complexity of the overall reaction is tempered as only 1 or 2 radical propagation pathways dominate the fate of each radical intermediate. Chemical ionization mass spectrometry (CIMS) measurements using the NO3- reagent ion during Delta-3-carene + NO3 chamber experiments show products consistent with each of the three types of unimolecular reactions predicted to be important from the computational mechanism. Moreover, the SIMPOL group contribution method for predicting vapor pressures suggests that a majority of the closed-shell products inferred from these unimolecular reactions are likely to have low enough vapor pressure to be able to contribute to SOA formation.Peer reviewe

Nitrogen fixation and denitrification activity differ between coral- and algae-dominated Red Sea reefs

Coral reefs experience phase shifts from coral- to algae-dominated benthic communities, which could affect the interplay between processes introducing and removing bioavailable nitrogen. However, the magnitude of such processes, i.e., dinitrogen (N-2) fixation and denitrification levels, and their responses to phase shifts remain unknown in coral reefs. We assessed both processes for the dominant species of six benthic categories (hard corals, soft corals, turf algae, coral rubble, biogenic rock, and reef sands) accounting for>98% of the benthic cover of a central Red Sea coral reef. Rates were extrapolated to the relative benthic cover of the studied organisms in co-occurring coral- and algae-dominated areas of the same reef. In general, benthic categories with high N-2 fixation exhibited low denitrification activity. Extrapolated to the respective reef area, turf algae and coral rubble accounted for>90% of overall N-2 fixation, whereas corals contributed to more than half of reef denitrification. Total N-2 fixation was twice as high in algae- compared to coral-dominated areas, whereas denitrification levels were similar. We conclude that algae-dominated reefs promote new nitrogen input through enhanced N-2 fixation and comparatively low denitrification. The subsequent increased nitrogen availability could support net productivity, resulting in a positive feedback loop that increases the competitive advantage of algae over corals in reefs that experienced a phase shift.Peer reviewe

High rates of carbon and dinitrogen fixation suggest a critical role of benthic pioneer communities in the energy and nutrient dynamics of coral reefs

Following coral mortality in tropical reefs, pioneer communities dominated by filamentous and crustose algae efficiently colonize substrates previously occupied by coral tissue. This phenomenon is particularly common after mass coral mortality following prolonged bleaching events associated with marine heatwaves. Pioneer communities play an important role for the biological succession and reorganization of reefs after disturbance. However, their significance for critical ecosystem functions previously mediated by corals, such as the efficient cycling of carbon (C) and nitrogen (N) within the reef, remains uncertain. We used 96 carbonate tiles to simulate the occurrence of bare substrates after disturbance in a coral reef of the central Red Sea. We measured rates of C and dinitrogen (N-2) fixation of pioneer communities on these tiles monthly over an entire year. Coupled with elemental and stable isotope analyses, these measurements provide insights into macronutrient acquisition, export and the influence of seasonality. Pioneer communities exhibited high rates of C and N(2)fixation within 4-8 weeks after the introduction of experimental bare substrates. Ranging from 13 to 25 mu mol C cm(-2) day(-1)and 8 to 54 nmol N cm(-2) day(-1), respectively, C and N(2)fixation rates were comparable to reported values for established Red Sea coral reefs. This similarity indicates that pioneer communities may quickly compensate for the loss of benthic productivity by corals. Notably, between 40% and 85% of fixed organic C was exported into the environment, constituting a vital source of energy for the coral reef food web. Our findings suggest that benthic pioneer communities may play a crucial, yet overlooked role in the C and N dynamics of oligotrophic coral reefs by contributing to the input of new C and N after coral mortality. While not substituting other critical ecosystem functions provided by corals (e.g. structural habitat complexity and coastal protection), pioneer communities likely contribute to maintaining coral reef nutrient cycling through the accumulation of biomass and import of macronutrients following coral loss. A freePlain Language Summarycan be found within the Supporting Information of this article.Peer reviewe

The charging of neutral dimethylamine and dimethylamine-sulfuric acid clusters using protonated acetone

Sulfuric acid is generally considered one of the most important substances taking part in atmospheric particle formation. However, in typical atmospheric conditions in the lower troposphere, sulfuric acid and water alone are unable to form particles. It has been suggested that strong bases may stabilize sulfuric acid clusters so that particle formation may occur. More to the point, amines - strong organic bases - have become the subject of interest as possible cause for such stabilization. To probe whether amines play a role in atmospheric nucleation, we need to be able to measure accurately the gas-phase amine vapour concentration. Such measurements often include charging the neutral molecules and molecular clusters in the sample. Since amines are bases, the charging process should introduce a positive charge. This can be achieved by, for example, using chemical ionization with a positively charged reagent with a suitable proton affinity. In our study, we have used quantum chemical methods combined with a cluster dynamics code to study the use of acetone as a reagent ion in chemical ionization and compared the results with measurements performed with a chemical ionization atmospheric pressure interface time-of-flight mass spectrometer (CI-APi-TOF). The computational results indicate that protonated acetone is an effective reagent in chemical ionization. However, in the experiments the reagent ions were not depleted at the predicted dimethylamine concentrations, indicating that either the modelling scheme or the experimental results - or both - contain unidentified sources of error.Peer reviewe

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-NOx) 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 + O-2 and (b) R'O-2 + RO2 -> R'O + RO + O-2 for selected monoterpene + oxidant derived peroxy radicals. The monoterpenes considered are alpha-pinene, beta-pinene, limonene, trans-beta-ocimene, and Delta(3)-carene. The oxidants considered are the hydroxyl radical (OH), the nitrate radical (NO3), and ozone (O-3). The reaction Gibbs energies were calculated at the DLPNO-CCSD(T)/def2-QZVPP//omega B97X-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 O-3 oxidation (especially for beta-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 O-3 oxidized systems than their OH and NO3 oxidized counterparts. Our results indicate that bimolecular reactions of certain complex RO, may contribute to an increase in radical and oxidant recycling under high HO2 conditions in the atmosphere, which can potentially enhance SOA formation.Peer reviewe

Pathways to Highly Oxidized Products in the Delta 3-Carene + OH System

Oxidation of the monoterpene Delta 3-carene (C10H16) is a potentially important and understudied source of atmospheric secondary organic aerosol (SOA). We present chamber-based measurements of speciated gas and particle phases during photochemical oxidation of Delta 3-carene. We find evidence of highly oxidized organic molecules (HOMs) in the gas phase and relatively low-volatility SOA dominated by C-7-C-10 species. We then use computational methods to develop the first stages of a Delta 3-carene photochemical oxidation mechanism and explain some of our measured compositions. We find that alkoxy bond scission of the cyclohexyl ring likely leads to efficient HOM formation, in line with previous studies. We also find a surprising role for the abstraction of primary hydrogens from methyl groups, which has been calculated to be rapid in the alpha-pinene system, and suggest more research is required to determine if this is more general to other systems and a feature of autoxidation. This work develops a more comprehensive view of Delta 3-carene photochemical oxidation products via measurements and lays out a suggested mechanism of oxidation via computationally derived rate coefficients.Peer reviewe

Constraining the sensitivity of iodide adduct chemical ionization mass spectrometry to multifunctional organic molecules using the collision limit and thermodynamic stability of iodide ion adducts

The sensitivity of a chemical ionization mass spectrometer (ions formed per number density of analytes) is fundamentally limited by the collision frequency between reagent ions and analytes, known as the collision limit, the ion-molecule reaction time, and the transmission efficiency of product ions to the detector. We use the response of a time-of-flight chemical ionization mass spectrometer (ToF-CIMS) to N2O5, known to react with iodide at the collision limit, to constrain the combined effects of ion-molecule reaction time, which is strongly influenced by mixing and ion losses in the ion-molecule reaction drift tube. A mass spectrometric voltage scanning procedure elucidates the relative binding energies of the ion adducts, which influence the transmission efficiency of molecular ions through the electric fields within the vacuum chamber. Together, this information provides a critical constraint on the sensitivity of a ToF-CIMS towards a wide suite of routinely detected multifunctional organic molecules for which no calibration standards exist. We describe the scanning procedure and collision limit determination, and we show results from the application of these constraints to the measurement of organic aerosol composition at two different field locations.Peer reviewe