the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 26 Oct 2023
Incorporating Oxygen Isotopes of Oxidized Reactive Nitrogen in the Regional Atmospheric Chemistry Mechanism, Version 2 (ICOIN-RACM2)
Abstract. The oxygen-stable isotope mass-independent composition (Δ(17O) = δ(17O) – 0.52×δ(18O)) has proven to be a robust tool for probing photochemical cycling and atmospheric formation pathways of oxidized reactive nitrogen (NOy). Several studies have developed modeling techniques to implicitly model Δ(17O) based on numerous assumptions that may not always be valid. Thus, these models may be oversimplified and limit our ability to compare model Δ(17O) values of NOy with observations. In this work, we introduce a novel method for explicit tracking of O3 transfer and propagation into NOy and odd oxygen (Ox), integrated into the Regional Atmospheric Chemistry Mechanism, version 2 (RACM2). Termed ICOIN-RACM2 (InCorporating Oxygen Isotopes of NOy in RACM2), this new model includes the addition of 55 new species and 727 replicate reactions to represent the oxygen isotopologues of NOy and Ox. Employing this mechanism within a box model, we simulate Δ(17O) for various NOy and Ox molecules for chamber experiments with varying initial nitrogen oxides (NOx = NO + NO2) and α-pinene conditions, revealing response shifts in Δ(17O) linked to distinct oxidant conditions. Furthermore, diel cycles are simulated under two summertime scenarios, representative of an urban and rural site, revealing pronounced Δ(17O) diurnal patterns for several NOy components and substantial Δ(17O) differences associated with pollution levels (urban vs. rural). Overall, the proposed mechanism offers the potential to assess NOy oxidation chemistry in chamber studies and air quality campaigns through Δ(17O) model comparisons against observations. The integration of this mechanism into a 3-D atmospheric chemistry transport model is expected to notably enhance our capacity to model and anticipate Δ(17O) across landscapes, consequently refining model representations of atmospheric chemistry and tropospheric oxidation capacity.
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CEC1: 'Comment on egusphere-2023-2293', Juan Antonio Añel, 20 Dec 2023
Dear authors,
A short comment to highlight that the "Code and Data Availability" statement in your submitted manuscript must be changed in potential future versions. Currently, it says that the code is available in GitHub, which is incorrect and moreover, would not comply with our code and data policy. Actually, the repository, linked in the references is in Zenodo. Therefore, please, fix this in future versions, and include the link and DOI to the Zenodo repository in the "Code and Data Availability" section, not as a reference.
Regards
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2023-2293-CEC1 -
RC1: 'Comment on egusphere-2023-2293', Anonymous Referee #1, 02 Feb 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2293/egusphere-2023-2293-RC1-supplement.pdf
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RC2: 'Comment on egusphere-2023-2293', Anonymous Referee #2, 08 Mar 2024
Overall, I found the paper to be very well written and found that the novel isotopic tagging chemical mechanism developed in this study could serve as a very useful tool in the future to evaluate and understand NOy chemistry and is of great interest for the readership of GMD. However, I did have several major concerns that should be addressed before final publication:
(1) I could not find the mechanism files on GitHub and at minimum a link of where to find these files should be included in the text. They should be indexed with a DOI for permanence /reference and should be accessible for reviewers to see before publication. Currently, the unavailability of these files means the work is not reproduceable and is not in compliance with GMD's data policy.
(2) The mechanism developed adds 55 new species and 727 replicate reactions to RACM2. In order for these improvements to more easily be incorporated into other box model mechanisms available in F0AM (that may treat BVOC reactions with NOy differently than RACM2), or for these improvements to more easily make their way into CTMs as the authors suggest, I firmly believe the authors need to include as a supplement a table with a complete listing of the 55 species added including their SMILES or InChI codes like is done in the Bates et al., 2022 ACPD supplement (https://doi.org/10.5194/acp-22-1467-2022-supplement). Including this information will allow anyone wanting to take these reactions w/ new species and map them to chemical mechanisms other than RACM2 to their mechanism in an automated way that may lump compounds in different ways (e.g. using python's RDKit library). Pye et al., 2023 (https://acp.copernicus.org/articles/23/5043/2023/) makes an incredibly strong case that when SMILES or InChI codes available with new chemical mechanisms, end users who may want to take what's developed and incorporate it into other mechanisms is much easier to do in an automated way using RDKit. This is *especially* true for large mechanisms where doing this by hand is extraordinarily tedious. I specifically recommend the authors include the InChI codes rather than SMILES codes because they are better at taking into account isomerization and isotopes in a way that SMILES codes do not. Using RD-Kit, end users can transform the new species into molecules when InChI codes or SMILES codes are provided, thus enabling automated comparisons to other mechanisms (e.g. like MCM, which also provides these codes), CMAQ (Pye et al., 2023), and GEOS-Chem, which is moving to also incorporate these codes currently in their mechanism metadata. Thus, for the more widespread adoption of this tool, and for it to truly have the impact the authors are hoping, I really think its extremely critical for the authors to provide these with the paper in a supplement. I know this may seem tedious especially for small inorganic molecules, but the value add for future users by providing this is quite critical for mechanisms of this size.
(3) The other reviewer raises a really critical point that the average tropospheric d17O(O3) is 26%, but the authors currently don't take into account known variations from this average. To address this point, I think there should at least be some discussion of the known variations away from this in the main text. I agree this assumption certainly limits the extension of the mechanism for 3D-CTMS and suggest that if that it would be very valuable for future users of the mechanism if there was some built in way to account for this variation within the mechanism (perhaps by including other +/-% values with suggestions of when to use as a comment in the mechanism for the relevant rxns?). At minimum some discussion is needed about this in the main text.
For the Editors/Authors: I didn't find the lack of comparison to observational data as problematic as the other reviewer. I don't think the purpose of this paper was to actually interpret observations, but merely provide a tool for people to do so in the future. To that end, I think the choice of submitting to GMD was entirely appropriate and that it is not necessary for its publication to include that analysis here. I believe that is an entirely different paper for an entirely different journal, but that this work simply provides the tools necessary to enable others to do that sort of work.
Citation: https://doi.org/10.5194/egusphere-2023-2293-RC2 -
AC1: 'Comment on egusphere-2023-2293', Wendell Walters, 11 Apr 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2293/egusphere-2023-2293-AC1-supplement.pdf
Status: closed
-
CEC1: 'Comment on egusphere-2023-2293', Juan Antonio Añel, 20 Dec 2023
Dear authors,
A short comment to highlight that the "Code and Data Availability" statement in your submitted manuscript must be changed in potential future versions. Currently, it says that the code is available in GitHub, which is incorrect and moreover, would not comply with our code and data policy. Actually, the repository, linked in the references is in Zenodo. Therefore, please, fix this in future versions, and include the link and DOI to the Zenodo repository in the "Code and Data Availability" section, not as a reference.
Regards
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2023-2293-CEC1 -
RC1: 'Comment on egusphere-2023-2293', Anonymous Referee #1, 02 Feb 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2293/egusphere-2023-2293-RC1-supplement.pdf
-
RC2: 'Comment on egusphere-2023-2293', Anonymous Referee #2, 08 Mar 2024
Overall, I found the paper to be very well written and found that the novel isotopic tagging chemical mechanism developed in this study could serve as a very useful tool in the future to evaluate and understand NOy chemistry and is of great interest for the readership of GMD. However, I did have several major concerns that should be addressed before final publication:
(1) I could not find the mechanism files on GitHub and at minimum a link of where to find these files should be included in the text. They should be indexed with a DOI for permanence /reference and should be accessible for reviewers to see before publication. Currently, the unavailability of these files means the work is not reproduceable and is not in compliance with GMD's data policy.
(2) The mechanism developed adds 55 new species and 727 replicate reactions to RACM2. In order for these improvements to more easily be incorporated into other box model mechanisms available in F0AM (that may treat BVOC reactions with NOy differently than RACM2), or for these improvements to more easily make their way into CTMs as the authors suggest, I firmly believe the authors need to include as a supplement a table with a complete listing of the 55 species added including their SMILES or InChI codes like is done in the Bates et al., 2022 ACPD supplement (https://doi.org/10.5194/acp-22-1467-2022-supplement). Including this information will allow anyone wanting to take these reactions w/ new species and map them to chemical mechanisms other than RACM2 to their mechanism in an automated way that may lump compounds in different ways (e.g. using python's RDKit library). Pye et al., 2023 (https://acp.copernicus.org/articles/23/5043/2023/) makes an incredibly strong case that when SMILES or InChI codes available with new chemical mechanisms, end users who may want to take what's developed and incorporate it into other mechanisms is much easier to do in an automated way using RDKit. This is *especially* true for large mechanisms where doing this by hand is extraordinarily tedious. I specifically recommend the authors include the InChI codes rather than SMILES codes because they are better at taking into account isomerization and isotopes in a way that SMILES codes do not. Using RD-Kit, end users can transform the new species into molecules when InChI codes or SMILES codes are provided, thus enabling automated comparisons to other mechanisms (e.g. like MCM, which also provides these codes), CMAQ (Pye et al., 2023), and GEOS-Chem, which is moving to also incorporate these codes currently in their mechanism metadata. Thus, for the more widespread adoption of this tool, and for it to truly have the impact the authors are hoping, I really think its extremely critical for the authors to provide these with the paper in a supplement. I know this may seem tedious especially for small inorganic molecules, but the value add for future users by providing this is quite critical for mechanisms of this size.
(3) The other reviewer raises a really critical point that the average tropospheric d17O(O3) is 26%, but the authors currently don't take into account known variations from this average. To address this point, I think there should at least be some discussion of the known variations away from this in the main text. I agree this assumption certainly limits the extension of the mechanism for 3D-CTMS and suggest that if that it would be very valuable for future users of the mechanism if there was some built in way to account for this variation within the mechanism (perhaps by including other +/-% values with suggestions of when to use as a comment in the mechanism for the relevant rxns?). At minimum some discussion is needed about this in the main text.
For the Editors/Authors: I didn't find the lack of comparison to observational data as problematic as the other reviewer. I don't think the purpose of this paper was to actually interpret observations, but merely provide a tool for people to do so in the future. To that end, I think the choice of submitting to GMD was entirely appropriate and that it is not necessary for its publication to include that analysis here. I believe that is an entirely different paper for an entirely different journal, but that this work simply provides the tools necessary to enable others to do that sort of work.
Citation: https://doi.org/10.5194/egusphere-2023-2293-RC2 -
AC1: 'Comment on egusphere-2023-2293', Wendell Walters, 11 Apr 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2293/egusphere-2023-2293-AC1-supplement.pdf
Model code and software
ICOIN_RACM2 Wendell Walters https://doi.org/10.5281/zenodo.8418755
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