Estimation of rate coefficients and branching ratios for gas-phase reactions of OH with aliphatic organic compounds for use in automated mechanism construction

Reaction with the hydroxyl (OH) radical is the dominant removal process for volatile organic compounds (VOCs) in the atmosphere. Rate coefficients for reactions of OH with VOCs are therefore essential parameters for chemical mechanisms used in chemistry transport models, and are required more generally for impact assessments involving the estimation of atmospheric lifetimes or oxidation rates for VOCs. Updated and extended structure–activity relationship (SAR) methods are presented for the reactions of OH with aliphatic organic compounds, with the reactions of aromatic organic compounds considered in a companion paper. The methods are optimized using a preferred set of data including reactions of OH with 489 aliphatic hydrocarbons and oxygenated organic compounds. In each case, the rate coefficient is defined in terms of a summation of partial rate coefficients for H abstraction or OH addition at each relevant site in the given organic compound, so that the attack distribution is defined. The information can therefore guide the representation of the OH reactions in the next generation of explicit detailed chemical mechanisms. Rules governing the representation of the subsequent reactions of the product radicals under tropospheric conditions are also summarized, specifically their reactions with O2 and competing processes

Trends in stabilisation of Criegee intermediates from alkene ozonolysis

Criegee Intermediates (CI), formed in the ozonolysis of alkenes, play a central role in tropospheric chemistry as an important source of radicals, with stabilised CI (SCI) able to participate in bimolecular reactions, affecting climate through the formation of inorganic and organic aerosol. However, total SCI yields have only been determined for a few alkene systems, while speciated SCI yields from asymmetrical alkenes are almost entirely unknown. Here we report for the first time a systematic experimental exploration of the stabilisation of CH2OO and (CH3)2COO CI, formed from ten alkene–ozone systems with a range of different sizes and structures, under atmospherically relevant conditions in the EUPHORE chamber. Experiments in the presence of excess SO2 (an SCI scavenger) determined total SCI yields from each alkene–ozone system. Comparison of primary carbonyl yields in the presence/absence of SO2 determined the stabilisation fraction of a given CI. The results show that the stabilisation of a given CI increases as the size of the carbonyl co-product increases. This is interpreted in terms of the nascent population of CI formed following decomposition of the primary ozonide (POZ) having a lower mean energy distribution when formed with a larger carbonyl co-product, as more of the energy from the POZ is taken by the carbonyl. These findings have significant implications for atmospheric modelling of alkene ozonolysis. Higher stabilisation of small CI formed from large alkenes is expected to lead to lower radical yields from CI decomposition, and higher SCI concentrations, increasing the importance of SCI bimolecular reactions

Photochemistry of 2-butenedial and 4-oxo-2-pentenal under atmospheric boundary layer conditions

Unsaturated 1,4-dicarbonyl compounds, such as 2-butenedial and 4-oxo-2-pentenal are produced in the atmospheric boundary layer from the oxidation of aromatic compounds and furans. These species are expected to undergo rapid photochemical processing, affecting atmospheric composition. In this study, the photochemistry of (E)-2-butenedial and both E and Z isomers of 4-oxo-2- pentenal was investigated under natural sunlight conditions at the large outdoor atmospheric simulation chamber EUPHORE. Photochemical loss rates, relative to j(NO2), are determined to be j((E)-2-butenedial)/j(NO2) = 0.14 (0.02), j((E)-4-oxo-2-pentenal)/j(NO2) = 0.18 (0.01), and j((Z)-4-oxo-2-pentenal)/j(NO2) = 0.20 (0.03). The major products detected for both species are a furanone (30 – 42%) and, for (E)-2-butenedial, maleic anhydride (2,5-furandione) (12 – 14%). The mechanism appears to proceed predominantly via photoisomerization to a ketene- enol species following -H abstraction. The lifetimes of the ketene-enol species in the dark from 2-butenedial and 4-oxo-2-pentenal are determined to be 465 s and 235 s, respectively. The ketene-enol can undergo ring closure to yield the corresponding furanone, or further unimolecular rearrangement which can subsequently form maleic anhydride. A minor channel (10 – 15%) also appears to form CO directly. This is presumed to be via a molecular elimination route of an initial biradical intermediate formed in photolysis, with an unsaturated carbonyl (detected here but not quantified) as co-product. -dicarbonyl and radical yields are very low, which has implications for ozone production from the photo-oxidation of unsaturated 1,4-dicarbonyls in the boundary layer. Photochemical removal is determined to be the major loss process for these species in the boundary layer with lifetimes of the order of 10 – 15 minutes, compared to > 3 hours for reaction with OH

Estimation of rate coefficients and branching ratios for reactions of organic peroxy radicals for use in automated mechanism construction

Organic peroxy radicals (RO2), formed from the degradation of hydrocarbons and other volatile organic compounds (VOCs), play a key role in tropospheric oxidation mechanisms. Several competing reactions may be available for a given RO2 radical, the relative rates of which depend on both the structure of RO2 and the ambient conditions. Published kinetics and branching ratio data are reviewed for the bimolecular reactions of RO2 with NO, NO2, NO3, OH and HO2; and for their self-reactions and cross-reactions with other RO2 radicals. This information is used to define generic rate coefficients and structure–activity relationship (SAR) methods that can be applied to the bimolecular reactions of a series of important classes of hydrocarbon and oxygenated RO2 radicals. Information for selected unimolecular isomerization reactions (i.e. H-atom shift and ring-closure reactions) is also summarized and discussed. The methods presented here are intended to guide the representation of RO2 radical chemistry in the next generation of explicit detailed chemical mechanisms

The CRI v2.2 reduced degradation scheme for isoprene

The reduced representation of isoprene degradation in the Common Representative Intermediates (CRI) mechanism has been systematically updated, using the Master Chemical Mechanism (MCM v3.3.1) as a reference benchmark, with the updated mechanism being released as CRI v2.2. The complete isoprene degradation mechanism in CRI v2.2 consists of 186 reactions of 56 closed shell and free radical species, this being an order of magnitude reduction in size compared with MCM v3.3.1. The chemistry initiated by reaction with OH radicals, NO3 radicals and ozone (O3) is treated. An overview of the updates is provided, within the context of reported kinetic and mechanistic information. The revisions mainly relate to the OH-initiated chemistry, which tends to dominate under atmospheric conditions, although these include updates to the chemistry of products that are also generated from the O3- and NO3-initiated oxidation. The revisions have impacts in a number of key areas, including recycling of HOx and NOx. The performance of the CRI v2.2 isoprene mechanism has been compared with those of the preceding version (CRI v2.1) and the reference MCM v3.3.1 over a range of relevant conditions, using a box model of the tropical forested boundary layer. In addition, tests are carried out to ensure that the performance of MCM v3.3.1 remains robust to more recently reported information. CRI v2.2 has also been implemented into the STOCHEM chemistry-transport model, with a customized close-variant of CRI v2.2 implemented into the EMEP MSC-W chemistry-transport model. The results of these studies are presented and used to illustrate the global-scale impacts of the mechanistic updates on HOx radical concentrations

AtChem (version 1), an open-source box model for the Master Chemical Mechanism

AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License

A self-consistent, multi-variate method for the determination of gas phase rate coefficients, applied to reactions of atmospheric VOCs and the hydroxyl radical

Gas-phase rate coefficients are fundamental to understanding atmospheric chemistry, yet experimental data are not available for the oxidation reactions of many of the thousands of volatile organic compounds (VOCs) observed in the troposphere. Here a new experimental method is reported for the simultaneous study of reactions between multiple different VOCs and OH, the most important daytime atmospheric radical oxidant. This technique is based upon established relative rate concepts but has the advantage of a much higher throughput of target VOCs. By evaluating multiple VOCs in each experiment, and through measurement of the depletion in each VOC after reaction with OH, the OH + VOC reaction rate coefficients can be derived. Results from experiments conducted under controlled laboratory conditions were in good agreement with the available literature for the reaction of nineteen VOCs, prepared in synthetic gas mixtures, with OH. This approach was used to determine a rate coefficient for the reaction of OH with 2,3-dimethylpent-1-ene for the first time; k = 5.7 (±0.3) × 10–11–cm3 molecule−1 s−1. In addition, a further seven VOCs had only two, or fewer, individual OH rate coefficient measurements available in the literature. The results from this work were in good agreement with those measurements. A similar dataset, at an elevated temperature of 323 (±10) K, was used to determine new OH rate coefficients for twelve aromatic, five alkane, five alkene and three monoterpene VOC + OH reactions. In OH relative reactivity experiments that used ambient air at the University of York, a large number of different VOCs were observed, of which 23 were positively identified. 19 OH rate coefficients were derived from these ambient air samples, including ten reactions for which data was previously unavailable at the elevated reaction temperature of T = 323 (±10) K

Seasonality of isoprene emissions and oxidation products above the remote Amazon

The Amazon rainforest is the largest source of isoprene emissions to the atmosphere globally. Under low nitric oxide (NO) conditions (i.e. at NO mixing ratios less than about 40 pptv), isoprene reacts rapidly with hydroxyl (OH) to form isoprene-derived peroxy radicals (ISOPOO), which subsequently react with the hydroperoxyl radical (HO2) to form isoprene epoxydiols (IEPOX). IEPOX compounds are efficient precursors to the formation of secondary organic aerosols (SOA). Natural isoprene emissions, therefore, have the potential to influence cloudiness, rainfall, radiation balance and climate. Here, we present the first seasonal analysis of isoprene emissions and concentrations above the Amazon based on eddy covariance flux measurements made at a remote forest location. We reveal the forest to maintain a constant emission potential of isoprene throughout the year (6.9 mg m-2 h-1). The emission potential of isoprene is calculated by normalising the measured fluxes to a set of standard conditions (303 K and 1500 mmol m-2 s-1). During the wet season a factor of two reduction in absolute emissions was observed but this is explained entirely on the basis of meteorology and leaf area index, not by a change in isoprene emissions potential. Using an innovative analysis of the isoprene fluxes, in combination with measurements of its oxidation products and detailed chemical box-modelling, we explore whether concentrations of IEPOX follow the same seasonal cycle as the isoprene precursor. Our analysis implies that during the dry season (Sep–Jan) air pollution from regional biomass burning provides a modest increase in NO concentrations (indirectly inferred from a combination of other anthropogenic tracer measurements and box-modelling) which creates a competing oxidation pathway for ISOPOO; rather than forming IEPOX, alternative products are formed with less propensity to produce aerosol. This competition decreases IEPOX formation rates by a factor of two in the dry season compared with a scenario with no anthropogenic NO pollution, and by 30% throughout the year. The abundance of biogenic SOA precursors in the Amazon appears not to be dictated by the seasonality of natural isoprene emissions as previously thought, but is instead driven by regional anthropogenic pollution which modifies the atmospheric chemistry of isoprene

Low-NO atmospheric oxidation pathways in a polluted megacity

The impact of emissions of volatile organic compounds (VOCs) to the atmosphere on the production of secondary pollutants, such as ozone and secondary organic aerosol (SOA), is mediated by the concentration of nitric oxide (NO). Polluted urban atmospheres are typically considered to be “high-NO” environments, while remote regions such as rainforests, with minimal anthropogenic influences, are considered to be “low NO”. However, our observations from central Beijing show that this simplistic separation of regimes is flawed. Despite being in one of the largest megacities in the world, we observe formation of gas- and aerosol-phase oxidation products usually associated with low-NO “rainforest-like” atmospheric oxidation pathways during the afternoon, caused by extreme suppression of NO concentrations at this time. Box model calculations suggest that during the morning high-NO chemistry predominates (95 %) but in the afternoon low-NO chemistry plays a greater role (30 %). Current emissions inventories are applied in the GEOS-Chem model which shows that such models, when run at the regional scale, fail to accurately predict such an extreme diurnal cycle in the NO concentration. With increasing global emphasis on reducing air pollution, it is crucial for the modelling tools used to develop urban air quality policy to be able to accurately represent such extreme diurnal variations in NO to accurately predict the formation of pollutants such as SOA and ozone