the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 02 Dec 2024
Opinion: Challenges and needs of tropospheric chemical mechanism development
Bernard Aumont
William P. L. Carter
Max McGillen
Abdelwahid Mellouki
John Orlando
Bénédicte Picquet-Varrault
Paul Seakins
William R. Stockwell
Luc Vereecken
Timothy J. Wallington
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- Final revised paper (published on 02 Dec 2024)
- Preprint (discussion started on 14 May 2024)
Interactive discussion
Status: closed
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CC1: 'Comment on egusphere-2024-1316', Mike Jenkin, 09 Jul 2024
A chemical mechanism is one of a number of a key components of science and policy models applied to air quality and climate issues - and it is an insurmountable task for an individual modeller to be able to appraise the vast wealth of published information to assemble that mechanism. It is therefore essential that sustainable methods and activities are in place to allow mechanisms to be constructed and freely available to the atmospheric chemistry community, and that such activities are well supported. This opinion paper provides a detailed and comprehensive overview and discussion of the many challenges and requirements for sustainable development of tropospheric chemical mechanisms, authored by a set of experts with considerable expertise and experience in a number of fields relevant to this topic. It thus provides an important benchmark reference and summary document of those methods and activities, which can help to guide and inform future mechanism development strategies.
My previous work in this field largely focused on gas phase mechanism development for organic compounds, mainly through contributions to the Master Chemical Mechanism (MCM). Since that mechanism was first constructed (manually) in the mid 1990s, there have been progressive and considerable developments in understanding of VOC degradation that have required increasing detail to be evaluated and represented in tropospheric chemical mechanisms. I therefore fully concur with the requirements for reliable (and ideally more extensive) evaluated data (sections 3.1 and 4.1); the development of SARs (section 3.2) and generation protocols (section 3.3); and the need to apply automated methods (section 3.4) to allow that detail to be included easily, for mechanisms to be updated regularly and efficiently, and to allow sensitivity tests to be carried out.
The developments in understanding have also highlighted the important requirement for systematic and justifiable methods of mechanism reduction, which are now more important than ever. Accordingly, this is covered in section 3.5, and I agree that this is one of the major challenges for the construction of practical mechanisms that are fully traceable to the fundamental detail derived from laboratory, chamber and theoretical studies. Some particular developments in understanding that have caused a potential explosion of detail in explicit mechanisms, and therefore an increased need for mechanism reduction strategies, are:
- "Autoxidation" mechanisms leading to rapid formation of highly-oxidised organic molecules (HOMs). These mechanisms can involve any number of (1,n) H-shift or ring-closure RO2 isomerisation reactions (sometimes reversible), the rate coefficients for which depend on the precise structure of the species and cannot be represented generically - and which can lead to orders of magnitude increases in mechanism size.
- The formation of large, involatile ROOR' (or other accretion) products from RO2 + R'O2 (permutation) reactions. These cannot be represented easily with the pseudo-unimolecular "peroxy radical pool" parameterisation which is so essential to restrict mechanism size in some mechanisms, including GECKO-A and the MCM.
- New information on the formation and reactions of Criegee intermediates (CIs) formed from O3 + alkene reactions. For example, this includes the very rapid reactions of all stabilised CIs with all organic acids in the mechanism, and the degradation of the hydroperoxyester products (i.e. essentially another class of permutation reaction with large association products).
These mechanistic features are all highlighted in this paper. In view of this, the particular impact of these (and other) features on mechanism size could possibly be given a little more emphasis, along with the resultant related challenges for mechanism reduction.
Minor comments
Page 3, line 73: For consistency with elsewhere, “geckoa” should read “GECKO-A”.
Page 7, Figure 3: For consistency with the section title, “Protocols of mechanism generation” should read “Protocols for mechanism generation”. There is also an “off” that should be an “of” in the auto generation box.
Page 19, lines 525-527: I do not fully understand how elevated O3 and suppressed NOx in megacities might invalidate prevailing understanding of RO2 chemistry. Perhaps this could be explained (note also that the reader is referred to “section 5.2” here, which is the same section). However, I do agree with the general point that changes in the ranges of ambient conditions need to be borne in mind.
Citation: https://doi.org/10.5194/egusphere-2024-1316-CC1 -
RC1: 'Comment on egusphere-2024-1316', John Wenger, 12 Aug 2024
This opinion paper provides an excellent overview of the challenges and needs for the continued development of tropospheric chemical mechanisms to support research and policy on air quality and climate. Following a summary of the strategies and procedures currently employed in chemical mechanism development, the authors cover key advances in the experimental and theoretical research activities that are used as the basis for developing and improving the mechanisms. The current and future challenges for chemical mechanism development are well considered and in general, clearly presented. The authors finish up with some strong conclusions on research needs for the future.
The article is written by key experts currently working in chemical mechanism development and associated research fields and, as such, provides valuable and insightful commentary on the state-of-the-art, challenges and future needs in chemical mechanism development. In general, the article is well-constructed, has good information flow and the errors/typos are at a minimum. I am in favour of publication following appropriate responses to the minor comments below.
Page 2, lines 17-21: The phrasing in these two sentences could be improved. Change “photochemical degradation” to “atmospheric degradation” as not all oxidation processes are photochemical.
Page 2, line 29: Oxidants such as…….
Page 3, line 54: Complementarity instead of complementary
Page 3, lines 55-59: It appears that section 3 and section 4 have been mixed up here
Page 3, line 62, title: Strategies for chemical mechanism development
Figure 1: In the green box, replace “constants” with “coefficients”
Figure 2: I really like this figure!
Page 5, line 98: …continued funding or continuing to fund…
Page 5, line 104: environmental chamber or atmospheric simulation chamber?
Page 7, line 138, title: Steps involved in chemical mechanism development or General procedure for chemical mechanism development
Figure 3, caption: Principal steps involved in (or General procedure for) chemical mechanism development
Page 7, line 155: the sentence “They emphasized….” Should be rephrased and possibly moved to somewhere else in the paragraph. Also, here the authors might want to strengthen the last sentence to give it more impact.
Page 8, line 170: …that rely largely on chemical intuition,
Page 10, line 240: “The concept of protocol….” sounds a bit odd. Consider re-phrasing.
Page 10, line 255, title: Replace “Auto” with automated or automatic, whichever is more appropriate
Page 10, line 260: Is “automating” correct here?
Page 11, 268-269: suggest…emulate the process of mechanism development carried out by chemists
Page 11, line 276: might want to add the huge number of chemical reactions for emphasis
Page 11, line 282: might want to specify model results or model simulation results to avoid any potential confusion with simulation chamber experiments
Page 12, line 300: might want to specify model results or model simulation results
Page 12, line 304: Current phrasing implies that organic multiphase processes are not represented at all. Is this true? If not, then the phrase “may lead to more accurate representation of the complexity” more appropriate here.
Page 12, line 322: suggest…elucidation of chemical mechanisms for the formation of processing of aerosol particles…
Figure 4 caption: impacts instead of implications?
Page 15, lines 400-409: The authors correctly identify the detection of HO2 and RO2 in chambers as being a valuable addition to the atmospheric chemist’s toolbox. However, some more context is probably needed here, because the required instrumentation is complex and expensive, with the result that HO2/RO2 measurements are far from commonplace. In fact, only a handful of facilities can measure HO2/RO2, and while NO3 detection techniques are slightly more prevalent in chambers, instrumentation for measuring absolute concentrations of OH is extremely rare. The development of more sensitive and accessible methods for measuring all types of radicals would be of huge benefit to the field of tropospheric chemical mechanism development.
Page 16, line 431: Not sure what is meant by sensor networks here. I presume it is referring to a global network of observation sites with advanced instrumentation rather than low-cost sensor networks? Please clarify and rephrase as required.
Page 17, line 450: underlying appears twice in this sentence
Page 18, line 491: Suggest ending the paragraph here and starting a new one for the discussion on the Criegee chemistry.
Page 18, line 511: Phrasing seems a bit awkward here…how about “Over the last decades, atmospheric chemists have increasingly recognised the need to investigate chemical regimes with more extreme conditions……”
Page 19, line 527: Refers to the current section in error?
Page 19, line 528: …warmer, dryer climate in some regions of the planet…
Page 20, line 549: Since this paragraph follows on from anthropogenic VCPs, it is probably better to write “….development also arises from…”
Page 21, line 588: It is more accurate to state that “The mass concentration of PM2.5 is the most commonly used metric to correlate aerosol particles and health effects.” In the lines that follow, I think that the role of chemical pathways in affecting the aerosol composition and subsequent health impacts could be made more explicitly.
Page 22, line 630: Delete “brief”
Page 23, line 655: typo…thoroughly
Page 23, line 676: missing bracket
Citation: https://doi.org/10.5194/egusphere-2024-1316-RC1 -
RC2: 'Comment on egusphere-2024-1316', Anonymous Referee #2, 23 Aug 2024
MS No.: egusphere-2024-1316
The authors provide a nice overview regarding tropospheric chemical mechanisms, their current status and different strategies for mechanism development.
The subject of this opinion paper is highly topical because of the better and better understanding of individual processes based on much better experimental approaches and detection systems over the last while allowing us to run the investigations under close to atmospheric reaction conditions etc. So, e.g., we got a deeper insight into the gas-phase chemistry of RO2 radicals, realized the importance of RO2 isomerization even for the atmospheric temperature range and its potential importance for generation of SOA precursors, or the importance of RO2 accretion product formation. This changed our view regarding tropospheric degradation processes dramatically in some cases, e.g., for the DMS oxidation characterizing HPMTF as a new main intermediate.
This paper is well structured and easy to read. The authors considered all the different parts needed for successful mechanism development. I think any basic changes are not needed. And it is an “opinion” paper and all authors are well-known experts in their field. Some minor comments for potential improvement of the quality of the paper are already given by other reviewers.
Citation: https://doi.org/10.5194/egusphere-2024-1316-RC2 -
RC3: 'Comment on egusphere-2024-1316', Anonymous Referee #3, 29 Aug 2024
Opinion: Challenges and needs of tropospheric chemical mechanism development
This is a very nicely written Opinion paper that provides a good overview of the state of the field. The title states an aim to describe the current challenges and the resulting needs in the field of tropospheric mechanism development. The paper is structured into six sections, two sections on mechanism development (Strategies and Steps), that function more as a review, a section on recent underpinning research activities, a discussion of Challenges, before concluding and discussing Needs. The challenges are treated in more depth, and the needs are discussed more briefly. I would be happy to see if published as an ACP Opinion, but would suggest that the authors expand the MS somewhat. Firstly to offer more examples of how their community can continue to develop connections with the wider atmospheric community. How can the mechanism community connect better with the needs of field, lab and wider community of composition modellers ? Secondly, to give more input on the outcome of recent work as it relates to best practices for the field, and finally to give more indication of potential for ML/AI techniques in the field.
Section 3 (Steps) provides a good summary of state of field of the chemical mechanism development, and the description of the key area of Structure Activity Relationships is a highlight. The focus of this section (and most of the MS) is on tropospheric gas-phase VOC chemistry, with a less extensive discussion of aerosol chemistry, beyond the liquid phase CAPRAM mechanism for clouds/aerosols. Most the discussion of aerosol chemistry is through its connection to SOA, and this slightly skews discussion away from the implementation of heterogeneous chemistry in CTM/GCM systems where it is necessarily more heavily parameterised, and which should be discussed. I'd also suggest some extra text added to Section 3.5 and Section 3.6 on mechanism reduction/evaluation for heterogeneous chemistry, and also for aerosol nucleation, as these are key areas where gas phase chemistry connects to aerosol formation and radiative forcing and of intense current interest.
In fact, a wider discussion on model metrics and model intercomparison would be helpful - metrics are briefly alluded to in section 2 but not returned to. Some idea of the useful metrics for quantifying mechanism's variation between mechanisms in e.g. OPE or across models would be welcome, both between different master mechanisms and the variation between master mechanisms and its reduced forms. This would add value in describing best practice to others in the field, particularly those involved in mechanism reduction for larger scale models. It would be good to hear what the authors consider are the key metrics for such mechanistic activities. It's also important to discuss best practices for identification of critical processes, model sensitivities, and how we might better use the underpinning physicochemical data.
Section 4 on activities related to mechanism development gives recent examples of underpinning activities, and Section 5 is on the Challenges: new insights, new regimes, new compounds, multiphase and FAIR methods. These sections provide a good summary of the limits of the field.
The MS could be improved with a better description of how the authors feel the community should address the Challenges. I think the manuscript would certainly be improved by more discussion within the text as to how the authors feel the mechanism development community should engage with the wider community, building stronger connections, identifying research questions and exploiting existing work. I suggest that the MS really needs to go further in identifying some specific critical gaps and to make recommendations - how to better exploit work from field, chambers and laboratory studies, how the mechanism development community can add value to these activities. Similarly, as they draw on theoretical chemistry work, how can these efforts be made more useful: what level of theory is sufficient for SARs, how to use these studies to reduce explicit mechanisms for CTM/GCM approaches?
ML forms a part of the backdrop but I would say too much is deferred to future machine learning efforts, and the MS feels rather empty of examples. The MS could discuss what are the factors that make ML/AI approaches suitable. I'd like to see more discussion of work that exemplifies the success of machine learning/AI techniques and I'd reduce the emphasis on the idea that future ML/AI will somehow fix things, as I think the MS would be improved by giving examples of useful datasets, approaches, and tractable problems. In short, where could the available effort most usefully go?
Citation: https://doi.org/10.5194/egusphere-2024-1316-RC3 -
AC1: 'Author response to all referee and community comments', Barbara Ervens, 02 Oct 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1316/egusphere-2024-1316-AC1-supplement.pdf
Peer review completion
