the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 26 Jul 2023
Towards a mechanistic description of autoxidation chemistry: from precursors to atmospheric implications
Abstract. In the last decades, atmospheric formation of secondary organic aerosol (SOA) gained increasing attention due to its impact on air quality and climate. However, methods to predict its abundance are mainly empirical and may fail at real atmospheric conditions. In this work, a close-to mechanistic approach allowing SOA quantification is presented, with focus on a chain-like chemical reaction called “autoxidation”. A novel framework is employed to a) describe the gas-phase chemistry, b) predict the products’ molecular structures and c) explore the contribution of autoxidation chemistry on SOA formation under various conditions. As a proof of concept, the method is applied to benzene, an important anthropogenic SOA precursor.
Our results suggest autoxidation to explain up to 100 % of the benzene-SOA formed under low-NOx laboratory conditions. While under atmospheric-like day-time conditions, the calculated aerosol mass continuously increases, as expected based on prior work. Additionally, a prompt increase, driven by the NO3 radical, is predicted at dawn. This increase has not yet been observed experimentally and questions the applicability of the widely accepted concept of OH-based SOA mass yield in the atmosphere.
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RC1: 'Comment on egusphere-2023-1415', Anonymous Referee #1, 24 Aug 2023
A method is presented for including autoxidation chemistry in detailed explicit chemical mechanisms. Using the oxidation of benzene, as represented in the Master Chemical Mechanism (MCM), as a starting point, autoxidation chemistry involving H atom shift isomerization reactions and association reactions for peroxy radicals is included, along with competing reactions. The mechanism is guided and constrained using distributions of product species masses obtained in laboratory studies, using CIMS, with the OH-initiated oxidation of benzene used as a “proof-of-concept” example. Vapor pressures are estimated for the closed-shell product species, to allow gas-particle partitioning to be represented, and the resultant simulations of SOA formation provide a good description of the laboratory results. The mechanism is also applied in a trajectory model to simulate the chemistry development and SOA formation on trajectories arriving in southern Sweden in April 2021, with the results confirming an important contribution from benzene-derived species formed from the autoxidation chemistry.
This paper considers an important topic, and provides an interesting discussion and illustration of the complexity of autoxidation chemistry and its role in SOA formation. However, I do have some concerns about the details of the generated mechanism and the identities of the species it contains, and the practicalities of applying the methods more widely to the range of precursor VOCs that contribute to SOA formation. These are outlined in the following comments.
1) Is the aim to create a genuine “mechanistic understanding” of autoxidation or a practical tool? At present the method seems to fall somewhere in between and do neither properly. Outside its ability to describe a particular experiment it is optimized and constrained to, it does not really move mechanistic understanding forward in that some of the core reactions seem to be mechanistically impossible, and the (optimized) parameters assigned to the isomerization reactions cannot therefore be rationalized in terms of what is predicted for actual species (e.g., by methods such as Vereecken and Noziere, 2020), or compared to those predictions.
Consider the initial set of autoxidation initiation reactions:
{1} BZBIPERO2 -> BZo_RO2_O7
{2} BZBIPERO -> BZeo_RO2_O6
{3} BZBIPERO2 -> C5_RO2_O6 + CO
{4} BZEMUCO2 -> BZeo_RO2_O8
{5} BZEMUCO2 -> C5_RO2_O7 + CO
{6} PHENO2 -> BZeo_RO2_O8
{7} PHENO2 -> C5_RO2_O7 + CO
The species BZBIPERO2 is the main peroxy radical formed from OH + benzene, which has been observed (e.g., Elrod, 2011). However, the products of reactions {1} and {3} cannot be formed from it (and they do not contain the expected -OOH group).
As a result, the subsequent sequences of reactions, following isomerization of this main peroxy radical, generate an incorrect set of closed-shell product species, for which the vapor pressures are then rigorously estimated to allow SOA simulations. This cannot be regarded as predictive. In passing, it is noted that peroxy radical isomerizations can also proceed by ring-closure (addition to a double bond), and might this more likely be the case for species like BZBIPERO2?
Some of the same is also true for the other starting peroxy radicals, BZEMUCO2 and PHENO2, which each isomerize to the same pair of peroxy radicals (BZeo_RO2_O8 and C5_RO2_O7), despite these not being products that cannot obviously be formed from either BZEMUCO2 or PHENO2 (although these do contain -OOH groups).
There is a limited series of subsequent isomerization reactions forming progressively more oxidized peroxy radicals. However, most peroxy radicals in the mechanism react by the set of conventional reactions (e.g., with NO, HO2, RO2), with RO2+R’O2 association reactions also added. However, it is not clear what criteria are applied to decide which isomerize and which do not. As indicated above, it does not seem to be related to peroxy radical structure and the isomerization reactions that are predicted/expected to be available.
Regarding its practicality as a tool, inclusion of autoxidation chemistry inevitably increases the complexity of the mechanism substantially. In MCM, complete benzene degradation (i.e., notionally to CO2 and H2O) is treated by 406 reactions of 149 species, which is regarded as far too complex for most practical atmospheric models. The ADPRAM module adds 934 reactions and over 800 species. In practice, some of these species are closed shell products that are sufficiently volatile to react (e.g., with OH) in the gas phase, and these reactions are ideally required for a complete description – so it is not even a full description. The point here is that the added autoxidation chemistry inevitably causes an explosion of complexity, so that the mechanism is even more remote from being able to be used in most practical atmospheric models – and it only considers one of many precursor VOCs.
2) The trajectory model simulations highlight an important contribution resulting from the NO3-initiated oxidation of the nitro-catechol product in MCM, specifically resulting from association reactions of the product peroxy radical, NNCATECO2. Although this is an interesting observation, it should be noted it is not clear if this species is actually formed from the NO3 + nitro-catechol reaction. The preceding MCM chemistry systematically oxidizes phenol to aromatic products containing increasing numbers of polar substituents, with an arbitrary limit of three substituents (-OH or -NO2). For practical reasons, the subsequent chemistry then aims to produce ring-opened species that promote break down to smaller species. NNCATECO2 is therefore produced as the first step in this break down process, assuming the chemistry proceeds analogously to the main OH + benzene oxidation sequence. Some caveats should probably therefore be included for this result.
Other comments
Line 47: For clarity, “particular” could be replaced by “particulate” – in particular because “particular”, in its more general meaning, is used in the preceding sentence (and at other points in the manuscript).
Line 183: Many (probably most) acyl radicals add O2 to form the corresponding acyl peroxy radical rather than decomposing by loss of CO.
Line 198: The primary beta-hydroxy and primary alkyl plots in Fig. S10 do not seem to tally with those presented in Fig. 3 of Jenkin et al. (2019). The former seems to be elevated by an order of magnitude. The latter seems to be presenting that for secondary alkyl.
Supplement, page 4: The information on the benzene scheme states that the rate coefficient units are “cm3 molecules-1 s-1 if not stated differently”. As far as I can see, there are no examples of “stated differently” even though many of the early reactions should presumably have units s-1.
References
Elrod, M. J.: Kinetics study of the aromatic bicyclic peroxy radical + NO reaction: overall rate constant and nitrate product yield measurements, J. Phys. Chem. A, 115, 8125–8130, 2011.
Jenkin, M. E., Valorso, R., Aumont, B., and Rickard, A. R.: Estimation of rate coefficients and branching ratios for reactions of organic peroxy radicals for use in automated mechanism construction, Atmos. Chem. Phys., 19, 7691–7717, https://doi.org/10.5194/acp-19-7691-2019, 2019.
Vereecken, L., and Nozière, B.: H migration in peroxy radicals under atmospheric conditions, Atmos. Chem. Phys., 20, 7429-7458,
10.5194/acp-20-7429-2020, 2020.Citation: https://doi.org/10.5194/egusphere-2023-1415-RC1 -
RC2: 'Comment on egusphere-2023-1415', Anonymous Referee #2, 01 Oct 2023
This manuscript described a framework to model gas-phase autoxidation chemistry and to predict the secondary organic aerosol (SOA) formation. This framework was tested on benzene oxidation under both laboratory conditions and ambient conditions. This study addressed an important topic, autoxidation, and aimed to link gas phase chemistry to aerosol formation. However, the major finding in the manuscript, which is that autoxidation explains nearly all benzene SOA under low-NOx conditions, contradicts previous experimental findings in the literature. This issue must be addressed before I can recommend it for publication.
Major Comments.
- Previous chamber experiments have demonstrated that phenolic pathway contributes to aromatic SOA formation1-3. The experimental benzene SOA yield is about 20% under high NOx conditions where RO2 autoxidation is suppressed2, which is a manifestation of the phenolic contribution of SOA. And previous studies have estimated that phenolic pathway contributes to 20-40% of benzene SOA under low-NOx conditions. Thus, the discrepancy between this study and previous findings needs to be addressed/discussed. It is highly possible that the SOA yield from the phenolic pathway is underestimated in the model, given the modeled SOA yield under higher NOx condition is only 1% (Line 466), much smaller than the 20% yield in the literature. In addition to adjusting the reaction rate coefficients based on NO3- CIMS measurements, the measurements of phenol, catechol, etc. also provide critical constraints on model performance.
- The manuscript describes the adjustment/tuning of reaction rate coefficients in detail. Is such adjustment required for each VOC system? If so, the deployment of the proposed framework could be quite cumbersome. The adjustment is based on comparing the simulated mass spectra to measured mass spectra by NO3- CIMS in flow tube experiments. If the HOMs contribute significantly to SOA, several questions arise. First, how much SOA is produced from the flow tube experiments? Second, given the NO3- CIMS only measured the gas-phase HOMs, does the simulated mass spectra consider the gas/particle partition?
- Please compare the tuned reaction rates to literature values or estimates from SAR.
Minor Comments
- Line 32-33. This sentence is confusing. If the modeled increase has not yet been observed experimentally, one would naturally imagine the model results may not be accurate. I assume what the authors tried to argue is that “the modeled increase in SOA formation from NO3 chemistry of benzene oxidation products has been not explored in laboratory experiments.”
- Line 356. The model evaluation figures under elevated NOx conditions should also be included in the main text, not hidden in the SI.
- Line 538. Yields up to 1000% or 100%? Also, please specify that this is “observed in models”, not experimentally in the atmosphere.
Reference
Nakao, S.; Clark, C.; Tang, P.; Sato, K.; Cocker Iii, D., Secondary organic aerosol formation from phenolic compounds in the absence of NO<sub>x</sub>. Atmos. Chem. Phys. 2011, 11 (20), 10649-10660.
Ng, N. L.; Kroll, J. H.; Chan, A. W. H.; Chhabra, P. S.; Flagan, R. C.; Seinfeld, J. H., Secondary organic aerosol formation from m-xylene, toluene, and benzene. Atmos. Chem. Phys. 2007, 7 (14), 3909-3922.
Schwantes, R. H.; Schilling, K. A.; McVay, R. C.; Lignell, H.; Coggon, M. M.; Zhang, X.; Wennberg, P. O.; Seinfeld, J. H., Formation of highly oxygenated low-volatility products from cresol oxidation. Atmos. Chem. Phys. 2017, 17 (5), 3453-3474.
Citation: https://doi.org/10.5194/egusphere-2023-1415-RC2 - AC1: 'Comment on egusphere-2023-1415', Lukas Pichelstorfer, 10 Nov 2023
Status: closed
-
RC1: 'Comment on egusphere-2023-1415', Anonymous Referee #1, 24 Aug 2023
A method is presented for including autoxidation chemistry in detailed explicit chemical mechanisms. Using the oxidation of benzene, as represented in the Master Chemical Mechanism (MCM), as a starting point, autoxidation chemistry involving H atom shift isomerization reactions and association reactions for peroxy radicals is included, along with competing reactions. The mechanism is guided and constrained using distributions of product species masses obtained in laboratory studies, using CIMS, with the OH-initiated oxidation of benzene used as a “proof-of-concept” example. Vapor pressures are estimated for the closed-shell product species, to allow gas-particle partitioning to be represented, and the resultant simulations of SOA formation provide a good description of the laboratory results. The mechanism is also applied in a trajectory model to simulate the chemistry development and SOA formation on trajectories arriving in southern Sweden in April 2021, with the results confirming an important contribution from benzene-derived species formed from the autoxidation chemistry.
This paper considers an important topic, and provides an interesting discussion and illustration of the complexity of autoxidation chemistry and its role in SOA formation. However, I do have some concerns about the details of the generated mechanism and the identities of the species it contains, and the practicalities of applying the methods more widely to the range of precursor VOCs that contribute to SOA formation. These are outlined in the following comments.
1) Is the aim to create a genuine “mechanistic understanding” of autoxidation or a practical tool? At present the method seems to fall somewhere in between and do neither properly. Outside its ability to describe a particular experiment it is optimized and constrained to, it does not really move mechanistic understanding forward in that some of the core reactions seem to be mechanistically impossible, and the (optimized) parameters assigned to the isomerization reactions cannot therefore be rationalized in terms of what is predicted for actual species (e.g., by methods such as Vereecken and Noziere, 2020), or compared to those predictions.
Consider the initial set of autoxidation initiation reactions:
{1} BZBIPERO2 -> BZo_RO2_O7
{2} BZBIPERO -> BZeo_RO2_O6
{3} BZBIPERO2 -> C5_RO2_O6 + CO
{4} BZEMUCO2 -> BZeo_RO2_O8
{5} BZEMUCO2 -> C5_RO2_O7 + CO
{6} PHENO2 -> BZeo_RO2_O8
{7} PHENO2 -> C5_RO2_O7 + CO
The species BZBIPERO2 is the main peroxy radical formed from OH + benzene, which has been observed (e.g., Elrod, 2011). However, the products of reactions {1} and {3} cannot be formed from it (and they do not contain the expected -OOH group).
As a result, the subsequent sequences of reactions, following isomerization of this main peroxy radical, generate an incorrect set of closed-shell product species, for which the vapor pressures are then rigorously estimated to allow SOA simulations. This cannot be regarded as predictive. In passing, it is noted that peroxy radical isomerizations can also proceed by ring-closure (addition to a double bond), and might this more likely be the case for species like BZBIPERO2?
Some of the same is also true for the other starting peroxy radicals, BZEMUCO2 and PHENO2, which each isomerize to the same pair of peroxy radicals (BZeo_RO2_O8 and C5_RO2_O7), despite these not being products that cannot obviously be formed from either BZEMUCO2 or PHENO2 (although these do contain -OOH groups).
There is a limited series of subsequent isomerization reactions forming progressively more oxidized peroxy radicals. However, most peroxy radicals in the mechanism react by the set of conventional reactions (e.g., with NO, HO2, RO2), with RO2+R’O2 association reactions also added. However, it is not clear what criteria are applied to decide which isomerize and which do not. As indicated above, it does not seem to be related to peroxy radical structure and the isomerization reactions that are predicted/expected to be available.
Regarding its practicality as a tool, inclusion of autoxidation chemistry inevitably increases the complexity of the mechanism substantially. In MCM, complete benzene degradation (i.e., notionally to CO2 and H2O) is treated by 406 reactions of 149 species, which is regarded as far too complex for most practical atmospheric models. The ADPRAM module adds 934 reactions and over 800 species. In practice, some of these species are closed shell products that are sufficiently volatile to react (e.g., with OH) in the gas phase, and these reactions are ideally required for a complete description – so it is not even a full description. The point here is that the added autoxidation chemistry inevitably causes an explosion of complexity, so that the mechanism is even more remote from being able to be used in most practical atmospheric models – and it only considers one of many precursor VOCs.
2) The trajectory model simulations highlight an important contribution resulting from the NO3-initiated oxidation of the nitro-catechol product in MCM, specifically resulting from association reactions of the product peroxy radical, NNCATECO2. Although this is an interesting observation, it should be noted it is not clear if this species is actually formed from the NO3 + nitro-catechol reaction. The preceding MCM chemistry systematically oxidizes phenol to aromatic products containing increasing numbers of polar substituents, with an arbitrary limit of three substituents (-OH or -NO2). For practical reasons, the subsequent chemistry then aims to produce ring-opened species that promote break down to smaller species. NNCATECO2 is therefore produced as the first step in this break down process, assuming the chemistry proceeds analogously to the main OH + benzene oxidation sequence. Some caveats should probably therefore be included for this result.
Other comments
Line 47: For clarity, “particular” could be replaced by “particulate” – in particular because “particular”, in its more general meaning, is used in the preceding sentence (and at other points in the manuscript).
Line 183: Many (probably most) acyl radicals add O2 to form the corresponding acyl peroxy radical rather than decomposing by loss of CO.
Line 198: The primary beta-hydroxy and primary alkyl plots in Fig. S10 do not seem to tally with those presented in Fig. 3 of Jenkin et al. (2019). The former seems to be elevated by an order of magnitude. The latter seems to be presenting that for secondary alkyl.
Supplement, page 4: The information on the benzene scheme states that the rate coefficient units are “cm3 molecules-1 s-1 if not stated differently”. As far as I can see, there are no examples of “stated differently” even though many of the early reactions should presumably have units s-1.
References
Elrod, M. J.: Kinetics study of the aromatic bicyclic peroxy radical + NO reaction: overall rate constant and nitrate product yield measurements, J. Phys. Chem. A, 115, 8125–8130, 2011.
Jenkin, M. E., Valorso, R., Aumont, B., and Rickard, A. R.: Estimation of rate coefficients and branching ratios for reactions of organic peroxy radicals for use in automated mechanism construction, Atmos. Chem. Phys., 19, 7691–7717, https://doi.org/10.5194/acp-19-7691-2019, 2019.
Vereecken, L., and Nozière, B.: H migration in peroxy radicals under atmospheric conditions, Atmos. Chem. Phys., 20, 7429-7458,
10.5194/acp-20-7429-2020, 2020.Citation: https://doi.org/10.5194/egusphere-2023-1415-RC1 -
RC2: 'Comment on egusphere-2023-1415', Anonymous Referee #2, 01 Oct 2023
This manuscript described a framework to model gas-phase autoxidation chemistry and to predict the secondary organic aerosol (SOA) formation. This framework was tested on benzene oxidation under both laboratory conditions and ambient conditions. This study addressed an important topic, autoxidation, and aimed to link gas phase chemistry to aerosol formation. However, the major finding in the manuscript, which is that autoxidation explains nearly all benzene SOA under low-NOx conditions, contradicts previous experimental findings in the literature. This issue must be addressed before I can recommend it for publication.
Major Comments.
- Previous chamber experiments have demonstrated that phenolic pathway contributes to aromatic SOA formation1-3. The experimental benzene SOA yield is about 20% under high NOx conditions where RO2 autoxidation is suppressed2, which is a manifestation of the phenolic contribution of SOA. And previous studies have estimated that phenolic pathway contributes to 20-40% of benzene SOA under low-NOx conditions. Thus, the discrepancy between this study and previous findings needs to be addressed/discussed. It is highly possible that the SOA yield from the phenolic pathway is underestimated in the model, given the modeled SOA yield under higher NOx condition is only 1% (Line 466), much smaller than the 20% yield in the literature. In addition to adjusting the reaction rate coefficients based on NO3- CIMS measurements, the measurements of phenol, catechol, etc. also provide critical constraints on model performance.
- The manuscript describes the adjustment/tuning of reaction rate coefficients in detail. Is such adjustment required for each VOC system? If so, the deployment of the proposed framework could be quite cumbersome. The adjustment is based on comparing the simulated mass spectra to measured mass spectra by NO3- CIMS in flow tube experiments. If the HOMs contribute significantly to SOA, several questions arise. First, how much SOA is produced from the flow tube experiments? Second, given the NO3- CIMS only measured the gas-phase HOMs, does the simulated mass spectra consider the gas/particle partition?
- Please compare the tuned reaction rates to literature values or estimates from SAR.
Minor Comments
- Line 32-33. This sentence is confusing. If the modeled increase has not yet been observed experimentally, one would naturally imagine the model results may not be accurate. I assume what the authors tried to argue is that “the modeled increase in SOA formation from NO3 chemistry of benzene oxidation products has been not explored in laboratory experiments.”
- Line 356. The model evaluation figures under elevated NOx conditions should also be included in the main text, not hidden in the SI.
- Line 538. Yields up to 1000% or 100%? Also, please specify that this is “observed in models”, not experimentally in the atmosphere.
Reference
Nakao, S.; Clark, C.; Tang, P.; Sato, K.; Cocker Iii, D., Secondary organic aerosol formation from phenolic compounds in the absence of NO<sub>x</sub>. Atmos. Chem. Phys. 2011, 11 (20), 10649-10660.
Ng, N. L.; Kroll, J. H.; Chan, A. W. H.; Chhabra, P. S.; Flagan, R. C.; Seinfeld, J. H., Secondary organic aerosol formation from m-xylene, toluene, and benzene. Atmos. Chem. Phys. 2007, 7 (14), 3909-3922.
Schwantes, R. H.; Schilling, K. A.; McVay, R. C.; Lignell, H.; Coggon, M. M.; Zhang, X.; Wennberg, P. O.; Seinfeld, J. H., Formation of highly oxygenated low-volatility products from cresol oxidation. Atmos. Chem. Phys. 2017, 17 (5), 3453-3474.
Citation: https://doi.org/10.5194/egusphere-2023-1415-RC2 - AC1: 'Comment on egusphere-2023-1415', Lukas Pichelstorfer, 10 Nov 2023
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