Organic peroxy radicals (often abbreviated RO(2)) play a central role in the chemistry of the Earth's lower atmosphere. Formed in the atmospheric oxidation of essentially every organic species ...emitted, their chemistry is part of the radical cycles that control the oxidative capacity of the atmosphere and lead to the formation of ozone, organic nitrates, organic acids, particulate matter and other so-called secondary pollutants. In this review, laboratory studies of this peroxy radical chemistry are detailed, as they pertain to the chemistry of the atmosphere. First, a brief discussion of methods used to detect the peroxy radicals in the laboratory is presented. Then, the basic reaction pathways - involving RO(2) unimolecular reactions and bimolecular reactions with atmospheric constituents such as NO, NO(2), NO(3), O(3), halogen oxides, HO(2), and other RO(2) species - are discussed. For each of these reaction pathways, basic reaction rates are presented, along with trends in reactivity with radical structure. Focus is placed on recent advances in detection methods and on recent advances in our understanding of radical cycling processes, particularly pertaining to the complex chemistry associated with the atmospheric oxidation of biogenic hydrocarbons.
Multiple trace-gas instruments were deployed during the fourth Fire Lab at Missoula Experiment (FLAME-4), including the first application of proton-transfer-reaction time-of-flight mass spectrometry ...(PTR-TOFMS) and comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC × GC-TOFMS) for laboratory biomass burning (BB) measurements. Open-path Fourier transform infrared spectroscopy (OP-FTIR) was also deployed, as well as whole-air sampling (WAS) with one-dimensional gas chromatography–mass spectrometry (GC-MS) analysis. This combination of instruments provided an unprecedented level of detection and chemical speciation. The chemical composition and emission factors (EFs) determined by these four analytical techniques were compared for four representative fuels. The results demonstrate that the instruments are highly complementary, with each covering some unique and important ranges of compositional space, thus demonstrating the need for multi-instrument approaches to adequately characterize BB smoke emissions. Emission factors for overlapping compounds generally compared within experimental uncertainty, despite some outliers, including monoterpenes. Data from all measurements were synthesized into a single EF database that includes over 500 non-methane organic gases (NMOGs) to provide a comprehensive picture of speciated, gaseous BB emissions. The identified compounds were assessed as a function of volatility; 6–11 % of the total NMOG EF was associated with intermediate-volatility organic compounds (IVOCs). These atmospherically relevant compounds historically have been unresolved in BB smoke measurements and thus are largely missing from emission inventories. Additionally, the identified compounds were screened for published secondary organic aerosol (SOA) yields. Of the total reactive carbon (defined as EF scaled by the OH rate constant and carbon number of each compound) in the BB emissions, 55–77 % was associated with compounds for which SOA yields are unknown or understudied. The best candidates for future smog chamber experiments were identified based on the relative abundance and ubiquity of the understudied compounds, and they included furfural, 2-methyl furan, 2-furan methanol, and 1,3-cyclopentadiene. Laboratory study of these compounds will facilitate future modeling efforts.
The Community Earth System Model version 2 (CESM2) includes a detailed representation of chemistry throughout the atmosphere in the Community Atmosphere Model with chemistry and Whole Atmosphere ...Community Climate Model configurations. These model configurations use the Model for Ozone and Related chemical Tracers (MOZART) family of chemical mechanisms, covering the troposphere, stratosphere, mesosphere, and lower thermosphere. The new MOZART tropospheric chemistry scheme (T1) has a number of updates over the previous version (MOZART‐4) in CESM, including improvements to the oxidation of isoprene and terpenes, organic nitrate speciation, and aromatic speciation and oxidation and thus improved representation of ozone and secondary organic aerosol precursors. An evaluation of the present‐day simulations of CESM2 being provided for Climate Model Intercomparison Project round 6 (CMIP6) is presented. These simulations, using the anthropogenic and biomass burning emissions from the inventories specified for CMIP6, as well as online calculation of emissions of biogenic compounds, lightning NO, dust, and sea salt, indicate an underestimate of anthropogenic emissions of a variety of compounds, including carbon monoxide and hydrocarbons. The simulation of surface ozone in the southeast United States is improved over previous model versions, largely due to the improved representation of reactive nitrogen and organic nitrate compounds resulting in a lower ozone production rate than in CESM1 but still overestimates observations in summer. The simulation of tropospheric ozone agrees well with ozonesonde observations in many parts of the globe. The comparison of NOx and PAN to aircraft observations indicates the model simulates the nitrogen budget well.
Plain Language Summary
The set of chemical reactions for tropospheric chemistry used in the Community Earth System Model version 2 (CESM2) has been updated significantly over CESM1 in the Community Atmosphere Model with chemistry (CAM‐chem) and Whole Atmosphere Community Climate Model (WACCM) configurations. The emissions used for the CESM2 simulations are documented here, with anthropogenic and biomass burning emissions based on the specified inventories for Climate Model Intercomparison Project 6 (CMIP6), and emissions of biogenic compounds, lightning NO, dust, and sea salt are calculated online and dependent on the simulated meteorology. Evaluation of the CAM‐chem and WACCM configurations of CESM2 with observations indicate an underestimate of anthropogenic emissions of a variety of compounds, including carbon monoxide and hydrocarbons. The updated chemistry leads to an improvement in the simulation of tropospheric ozone.
Key Points
This paper fully documents the significant updates to the chemistry mechanisms in version 2 of the Community Earth System Model
The new tropospheric chemistry scheme improves representation of isoprene oxidation as well as other ozone precursors over earlier versions
The simulation of tropospheric ozone is improved in comparison to observations
We present a digital, freely available, searchable, and evaluated compilation of rate coefficients for the gas-phase reactions of organic compounds with OH, Cl, and NO3 radicals and with O3. Although ...other compilations of many of these data exist, many are out of date, most have limited scope, and all are difficult to search and to load completely into a digitized form. This compilation uses results of previous reviews, though many recommendations are updated to incorporate new or omitted data or address errors, and includes recommendations on many reactions that have not been reviewed previously. The database, which incorporates over 50 years of measurements, consists of a total of 2765 recommended bimolecular rate coefficients for the reactions of 1357 organic substances with OH, 709 with Cl, 310 with O3, and 389 with NO3, and is much larger than previous compilations. Many compound types are present in this database, including naturally occurring chemicals formed in or emitted to the atmosphere and anthropogenic compounds such as halocarbons and their degradation products. Recommendations are made for rate coefficients at 298 K and, where possible, the temperature dependences over the entire range of the available data. The primary motivation behind this project has been to provide a large and thoroughly evaluated training dataset for the development of structure–activity relationships (SARs), whose reliability depends fundamentally upon the availability of high-quality experimental data. However, there are other potential applications of this work, such as research related to atmospheric lifetimes and fates of organic compounds, or modelling gas-phase reactions of organics in various environments. This database is freely accessible at https://doi.org/10.25326/36 (McGillen et al., 2019).
Ozone is a greenhouse gas and air pollutant that is harmful to human health and plants. During the summer in the southeastern US, many regional and global models are biased high for surface ozone ...compared to observations. Past studies have suggested different solutions including the need for updates to model representation of clouds, chemistry, ozone deposition, and emissions of nitrogen oxides (NOx) or biogenic hydrocarbons. Here, due to the high biogenic emissions in the southeastern US, more comprehensive and updated isoprene and terpene chemistry is added into CESM/CAM-chem (Community Earth System Model/Community Atmosphere Model with full chemistry) to evaluate the impact of chemistry on simulated ozone. Comparisons of the model results with data collected during the Studies of Emissions Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) field campaign and from the US EPA (Environmental Protection Agency) CASTNET (Clean Air Status and Trends Network) monitoring stations confirm the updated chemistry improves simulated surface ozone, ozone precursors, and NOx reservoir compounds. The isoprene and terpene chemistry updates reduce the bias in the daily maximum 8 h average (MDA8) surface ozone by up to 7 ppb. In the past, terpene oxidation in particular has been ignored or heavily reduced in chemical schemes used in many regional and global models, and this study demonstrates that comprehensive isoprene and terpene chemistry is needed to reduce surface ozone model biases. Sensitivity tests were performed in order to evaluate the impact of lingering uncertainties in isoprene and terpene oxidation on ozone. Results suggest that even though isoprene emissions are higher than terpene emissions in the southeastern US, remaining uncertainties in isoprene and terpene oxidation have similar impacts on ozone due to lower uncertainties in isoprene oxidation. Additionally, this study identifies the need for further constraints on the aerosol uptake of organic nitrates derived from isoprene and terpenes in order to reduce uncertainty in simulated ozone. Although the updates to isoprene and terpene chemistry greatly reduce the ozone bias in CAM-chem, a large bias remains. Evaluation against SEAC4RS field campaign results suggests future improvements to horizontal resolution and cloud parameterizations in CAM-chem may be particularly important for further reducing this bias.
Advances in Atmospheric Chemical and Physical Processes Burkholder, James B.; Orlando, John J.
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
01/2023, Letnik:
127, Številka:
3
Journal Article
Oxidation flow reactors (OFRs) are a promising complement to
environmental chambers for investigating atmospheric oxidation processes and
secondary aerosol formation. However, questions have been ...raised about how
representative the chemistry within OFRs is of that in the troposphere. We
investigate the fates of organic peroxy radicals (RO2), which play
a central role in atmospheric organic chemistry, in OFRs and environmental
chambers by chemical kinetic modeling and compare to a variety of ambient
conditions to help define a range of atmospherically relevant OFR operating
conditions. For most types of RO2, their bimolecular fates in OFRs
are mainly RO2+HO2 and RO2+NO, similar to chambers and
atmospheric studies. For substituted primary RO2 and acyl
RO2, RO2+RO2 can make a significant contribution to
the fate of RO2 in OFRs, chambers and the atmosphere, but
RO2+RO2 in OFRs is in general somewhat less important than in
the atmosphere. At high NO, RO2+NO dominates RO2 fate in
OFRs, as in the atmosphere. At a high UV lamp setting in OFRs,
RO2+OH can be a major RO2 fate and RO2
isomerization can be negligible for common multifunctional RO2,
both of which deviate from common atmospheric conditions. In the OFR254
operation mode (for which OH is generated only from the photolysis of added
O3), we cannot identify any conditions that can simultaneously
avoid significant organic photolysis at 254 nm and lead to RO2
lifetimes long enough (∼ 10 s) to allow atmospherically relevant
RO2 isomerization. In the OFR185 mode (for which OH is generated
from reactions initiated by 185 nm photons), high relative humidity, low UV
intensity and low precursor concentrations are recommended for the
atmospherically relevant gas-phase chemistry of both stable species and
RO2. These conditions ensure minor or negligible RO2+OH
and a relative importance of RO2 isomerization in RO2
fate in OFRs within ∼×2 of that in the atmosphere. Under these
conditions, the photochemical age within OFR185 systems can reach a few
equivalent days at most, encompassing the typical ages for maximum secondary
organic aerosol (SOA) production. A small increase in OFR temperature may
allow the relative importance of RO2 isomerization to approach the
ambient values. To study the heterogeneous oxidation of SOA formed under
atmospherically relevant OFR conditions, a different UV source with higher
intensity is needed after the SOA formation stage, which can be done with
another reactor in series. Finally, we recommend evaluating the atmospheric
relevance of RO2 chemistry by always reporting measured and/or
estimated OH, HO2, NO, NO2 and OH reactivity (or at least
precursor composition and concentration) in all chamber and flow reactor
experiments. An easy-to-use RO2 fate estimator program is included
with this paper to facilitate the investigation of this topic in future
studies.
OH reactivity (OHR) is an important control on the oxidative capacity in the atmosphere but remains poorly constrained in many environments, such as
remote, rural, and urban atmospheres, as well as ...laboratory experiment setups under low-NO conditions. For an improved understanding of OHR, its
evolution during oxidation of volatile organic compounds (VOCs) is a major aspect requiring better quantification. We use the fully explicit
Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) model to study the OHR evolution in the NO-free photooxidation
of several VOCs, including decane (an alkane), m-xylene (an aromatic), and isoprene (an alkene). Oxidation progressively produces more saturated and functionalized species. Total organic OHR (including precursor and products, OHRVOC) first increases for decane (as functionalization increases OH rate coefficients) and m-xylene (as much more reactive oxygenated alkenes are formed). For isoprene, C=C bond consumption leads to a rapid drop in OHRVOC before significant production of the first main saturated multifunctional product, i.e., isoprene epoxydiol. The saturated multifunctional species in the oxidation of different precursors have similar average OHRVOC per C atom. The latter oxidation follows a similar course for different precursors, involving fragmentation of multifunctional species to eventual oxidation of C1 and C2 fragments to CO2, leading to a similar evolution of OHRVOC per C atom. An upper limit of the total OH consumption during complete oxidation to CO2 is roughly three per C atom. We also explore the trends in radical recycling ratios. We show that differences in the evolution of OHRVOC between the atmosphere and an environmental chamber, and between the atmosphere and an oxidation flow reactor (OFR), can be substantial, with the former being even larger, but these differences are often smaller than between precursors. The Teflon wall losses of oxygenated VOCs in chambers result in large deviations of OHRVOC from atmospheric conditions, especially for the oxidation of larger precursors, where multifunctional species may suffer substantial wall losses, resulting in significant underestimation of OHRVOC. For OFR, the deviations of OHRVOC evolution from the atmospheric case are mainly due to significant OHR contribution from RO2 and lack of efficient organic photolysis. The former can be avoided by lowering the UV lamp setting in OFR, while the latter is shown to be very difficult to avoid. However, the former may significantly offset the slowdown in fragmentation of multifunctional species due to lack of efficient organic photolysis.
The methods that have been used to study alkoxy radical chemistry are summarized, and the current state of knowledge regarding the rates and mechanisms of the various reactions pathways are ...presented. Some of the remaining uncertainties in the atmospheric chemistry of the alkoxy radicals are described.
The XPA protein functions together with the single-stranded DNA (ssDNA) binding protein RPA as the central scaffold to ensure proper positioning of repair factors in multi-protein nucleotide excision ...repair (NER) machinery. We previously determined the structure of a short motif in the disordered XPA N-terminus bound to the RPA32C domain. However, a second contact between the XPA DNA-binding domain (XPA DBD) and the RPA70AB tandem ssDNA-binding domains, which is likely to influence the orientation of XPA and RPA on the damaged DNA substrate, remains poorly characterized. NMR was used to map the binding interfaces of XPA DBD and RPA70AB. Combining NMR and X-ray scattering data with comprehensive docking and refinement revealed how XPA DBD and RPA70AB orient on model NER DNA substrates. The structural model enabled design of XPA mutations that inhibit the interaction with RPA70AB. These mutations decreased activity in cell-based NER assays, demonstrating the functional importance of XPA DBD-RPA70AB interaction. Our results inform ongoing controversy about where XPA is bound within the NER bubble, provide structural insights into the molecular basis for malfunction of disease-associated XPA missense mutations, and contribute to understanding of the structure and mechanical action of the NER machinery.
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