the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 24 Aug 2023
Impacts of updated reaction kinetics on the global GEOS-Chem simulation of atmospheric chemistry
Abstract. We updated the chemical mechanism of the GEOS-Chem global 3-D model of atmospheric chemistry to include new recommendations from the JPL chemical kinetics Data Evaluation 19-5 and from IUPAC, and to balance carbon and nitrogen. We examined the impact of these updates on the GEOS-Chem version 14.0.1 simulation. Notable changes include: eleven updates to reactions of reactive nitrogen species, resulting in a 7 % net increase in the stratospheric NOx (NO + NO2) burden; an updated CO + OH rate formula leading to a 2.7 % reduction in total tropospheric CO; adjustments to the rate coefficient and branching ratios of propane + OH, leading to reduced tropospheric propane (-17 %) and increased acetone (+3.5 %) burdens; a 41 % increase in the tropospheric burden of peroxyacetic acid due to a decrease in the rate coefficient for its reaction with OH, further contributing to reductions in peroxyacetyl nitrate (PAN; -3.8 %) and acetic acid (-3.4 %); and a number of minor adjustments to halogen radical cycling. Changes to the global tropospheric burdens of other species include -0.7 % for ozone, +0.3 % for OH (-0.4 % for methane lifetime against oxidation by tropospheric OH), +0.8 % for formaldehyde, and -1.7 % for NOx. The updated mechanism reflects the current state of the science including complex chemical dependencies of key atmospheric species on temperature, pressure, and concentrations of other compounds. The improved conservation of carbon and nitrogen will facilitate future studies of their overall atmospheric budgets.
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Journal article(s) based on this preprint
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2023-1374', Anonymous Referee #1, 06 Oct 2023
In this manuscript the authors present the results of their efforts to update the chemical mechanism of the GEOS-Chem chemical transport model, bringing its simulated chemistry more inline with recent recommendations from JPL and IUPAC sources. These updates represent mostly incremental progress towards mechanism improvements, including updated rate constants, temperature dependence, and branching ratios, as well as steps towards the conservation of modeled carbon and nitrogen. Impacts on annual budgets of key trace gas species appear to be mostly subtle, but certainly non-negligible, and likely have even more pronounced impacts at finer spatiotemporal scales. This effort represents an important step towards ongoing model maintenance and improvement, and will benefit the current and future modeling studies whose findings rely on accurate representation of the species included in these updates.On the whole I find this paper to be straightforward, well-written, and ready for publication. Manuscript text is clear and concise, figures are effective and well-designed, and I have no concerns regarding the the authors' methods or decisions.Citation: https://doi.org/
10.5194/egusphere-2023-1374-RC1 -
RC2: 'Comment on egusphere-2023-1374', Anonymous Referee #2, 15 Nov 2023
Summary
This manuscript describes recent updates to the gas-phase thermal reaction rate coefficients in the commonly used GEOS-Chem chemical transport model to match those of the most recent NASA JPL and IUPAC recommendations. Of particular value, the authors also report improvements in the stoichiometric closure of carbon and nitrogen in the non-elementary organic oxidation reactions. While acknowledging there is still work to be done in this regard, it is a significant and important update for helping to achieve mass conservation and interpret chemical budgets in the model. The manuscript describes changes in the key gaseous chemical species in the model for the troposphere and stratosphere. It reports non-zero but generally small changes in abundance, although there are some interesting outliers (e.g., an ~20% decrease in tropospheric propane). The manuscript is well-written and clear, and I recommend publishing it, pending some minor suggestions below.
General Comments(1) I wish the paper had some discussion of the differences with respect to atmospheric observations. For example, do the objective improvements in the rate constants move the spatial and temporal correlation of ozone in the model away from or closer to the TOAR climatological products (doi:10.1594/PANGAEA.876108)? However, I realize it is within the scope of GMD to allow the publication of development and technical papers without evaluation.
(2) I was curious when reading the manuscript if the authors ever found discrepancies between the JPL and IUPAC recommendations, and if so, how did they prioritize one over the other? It would be helpful to add a sentence to that effect.
(3) The simulations used were initialized for one year, and then one year was used for analysis in both the troposphere and stratosphere. It would be important to explicitly mention in the vicinity of Section 3 Paragraph 2 that these simulations only reflect changes from the rate constants on such time scales, and the stratospheric results should be taken through such a lens. In reality, the changes in the stratospheric (and even tropospheric) abundances of many of these species would be different than reported here if both simulations were allowed to achieve equilibrium with respect to stratospheric-tropospheric exchange, i.e., they were initialized for 10-15 years.
Minor/Technical Comments
L30 - corrupted BibTeX reference
S2 - It would be useful for readers, especially new GEOS-Chem users, if the authors could include a brief summary of the key historical papers/updates to the GEOS-Chem chemical mechanism up until this work.
L51 - Please define the NOz family
L56 - Erroneous extra “of”
L57 - Typo in “resulting an increases”
L143 - van der Werf et al. 2017 is a more direct reference for GFED4
S3 Model Description - should probably include the natural NOx sources and marine organic sources for completeness
L160 - HNOz should have a subscript
L183 - typo in “Indo-Gangentic”
Citation: https://doi.org/10.5194/egusphere-2023-1374-RC2 -
RC3: 'Comment on egusphere-2023-1374', Anonymous Referee #3, 17 Nov 2023
The manuscript by Bates et al. describes a series of updates to reaction rate coefficients and products in the GEOS-Chem model to reflect the most recent recommendations in a pair of widely used evaluations of chemical kinetics, the JPL and IUPAC reports. Additional modifications to improve the conservation of carbon and nitrogen in the chemical reactions are also described. The effects of the modifications on the distributions of a number of key chemical species in GEOS-Chem are then analysed using output from a one-year run.
The GEOS-Chem model is very, very widely used in the community and the description and analysis of the modifications to the gas-phase chemical scheme will be received with interest. The manuscript is very well written and the changes are clearly described, including a very extensive set of tables and graphs showing the temperature and pressure dependence of the original and updated reaction rates in the supplementary information. I have no significant concerns with the manuscript in its present form. Although I do have a few questions about how changes in the model distribution of a couple of species are attributed that I would like to see clarified or expanded on - these are listed with other minor comments below. These questions are specific to a couple of species and do not detract from the overall strong presentation of the updates and the analysis of the effects.Minor comments:
Lines 29 - 30: There is a question mark in the list of references '(Hu et al., 2018; ?; Fritz et al., 2022).'
Line 38: The wording of 'The mechanism goes beyond these recommendations.' is a bit open to interpretation. I understand the authors mean to say the reactions included in the mechanism for isoprene, monoterpenes, etc. are not all covered in the JPL and IUPAC recommendations and, if this is what is meant, it could be more clearly stated.
Line 65: The change to the rate of NO2 + NO3 is described as resulting in a strong temperature dependence ['stronger temperature dependencies for NO2 + NO3 (-33% - -25%)'] but the range is given as -33% to -25%, so it seems like the more significant change is a reduction in the rate - at least at atmospheric relevant temperatures?
Line 111: The reaction of the CH2OO criegee intermediate with water vapour is mentioned as being updated, having been included in the latest JPL recommendations. Does GEOS-CHEM account for the reaction with the H2O dimer, which seems to account for a significant amount of the reaction with water vapour? I will note that the reaction rate constant given in Table 1 is for the reaction with the monomer.
Lines 149 - 150: Because of the extension into the stratosphere and the long timescales for transport in that region, are the initial conditions provided at January 1, 2017 'spun up' to have a fairly realistic distribution through the stratosphere?
Lines 164 - 165: Could the authors expand on the explanation for the decreases in upper tropospheric ozone that are attributed to 'higher NOx-driven losses brought about by changes to the HNOz + OH (z=2-4) reactions'? The heart of the problem is that I am not sure what exactly is meant by 'NOx-driven losses' and it is not readily apparent to me how, for example, the much faster rate for OH + HNO2 -> NO2 + H2O should result in decreased ozone through 'NOx-driven losses'. There is a decrease in NOx in the upper troposphere shown in Figure 2a, but I would have thought ozone production would be NOx limited in this region so the decreased ozone would be due to a decrease in ozone production?
Lines 184 - 187: These are significant changes in stratospheric NOx and I fully agree with your explanation. Very interesting.
Lines 188 - 190: Can the 0.4% increase in NO3 in the stratosphere be separated from the general 7 - 8% increase in NOx? In fact, given the increase in NOx and the increase in the rate of O + NO2 -> NO3, I would have thought the change in NO3 would have been more similar in magnitude, or larger, than the change in NOx?Citation: https://doi.org/10.5194/egusphere-2023-1374-RC3 -
AC1: 'Authors' response to reviewer comments', K.H. Bates, 24 Dec 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-1374/egusphere-2023-1374-AC1-supplement.pdf
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2023-1374', Anonymous Referee #1, 06 Oct 2023
In this manuscript the authors present the results of their efforts to update the chemical mechanism of the GEOS-Chem chemical transport model, bringing its simulated chemistry more inline with recent recommendations from JPL and IUPAC sources. These updates represent mostly incremental progress towards mechanism improvements, including updated rate constants, temperature dependence, and branching ratios, as well as steps towards the conservation of modeled carbon and nitrogen. Impacts on annual budgets of key trace gas species appear to be mostly subtle, but certainly non-negligible, and likely have even more pronounced impacts at finer spatiotemporal scales. This effort represents an important step towards ongoing model maintenance and improvement, and will benefit the current and future modeling studies whose findings rely on accurate representation of the species included in these updates.On the whole I find this paper to be straightforward, well-written, and ready for publication. Manuscript text is clear and concise, figures are effective and well-designed, and I have no concerns regarding the the authors' methods or decisions.Citation: https://doi.org/
10.5194/egusphere-2023-1374-RC1 -
RC2: 'Comment on egusphere-2023-1374', Anonymous Referee #2, 15 Nov 2023
Summary
This manuscript describes recent updates to the gas-phase thermal reaction rate coefficients in the commonly used GEOS-Chem chemical transport model to match those of the most recent NASA JPL and IUPAC recommendations. Of particular value, the authors also report improvements in the stoichiometric closure of carbon and nitrogen in the non-elementary organic oxidation reactions. While acknowledging there is still work to be done in this regard, it is a significant and important update for helping to achieve mass conservation and interpret chemical budgets in the model. The manuscript describes changes in the key gaseous chemical species in the model for the troposphere and stratosphere. It reports non-zero but generally small changes in abundance, although there are some interesting outliers (e.g., an ~20% decrease in tropospheric propane). The manuscript is well-written and clear, and I recommend publishing it, pending some minor suggestions below.
General Comments(1) I wish the paper had some discussion of the differences with respect to atmospheric observations. For example, do the objective improvements in the rate constants move the spatial and temporal correlation of ozone in the model away from or closer to the TOAR climatological products (doi:10.1594/PANGAEA.876108)? However, I realize it is within the scope of GMD to allow the publication of development and technical papers without evaluation.
(2) I was curious when reading the manuscript if the authors ever found discrepancies between the JPL and IUPAC recommendations, and if so, how did they prioritize one over the other? It would be helpful to add a sentence to that effect.
(3) The simulations used were initialized for one year, and then one year was used for analysis in both the troposphere and stratosphere. It would be important to explicitly mention in the vicinity of Section 3 Paragraph 2 that these simulations only reflect changes from the rate constants on such time scales, and the stratospheric results should be taken through such a lens. In reality, the changes in the stratospheric (and even tropospheric) abundances of many of these species would be different than reported here if both simulations were allowed to achieve equilibrium with respect to stratospheric-tropospheric exchange, i.e., they were initialized for 10-15 years.
Minor/Technical Comments
L30 - corrupted BibTeX reference
S2 - It would be useful for readers, especially new GEOS-Chem users, if the authors could include a brief summary of the key historical papers/updates to the GEOS-Chem chemical mechanism up until this work.
L51 - Please define the NOz family
L56 - Erroneous extra “of”
L57 - Typo in “resulting an increases”
L143 - van der Werf et al. 2017 is a more direct reference for GFED4
S3 Model Description - should probably include the natural NOx sources and marine organic sources for completeness
L160 - HNOz should have a subscript
L183 - typo in “Indo-Gangentic”
Citation: https://doi.org/10.5194/egusphere-2023-1374-RC2 -
RC3: 'Comment on egusphere-2023-1374', Anonymous Referee #3, 17 Nov 2023
The manuscript by Bates et al. describes a series of updates to reaction rate coefficients and products in the GEOS-Chem model to reflect the most recent recommendations in a pair of widely used evaluations of chemical kinetics, the JPL and IUPAC reports. Additional modifications to improve the conservation of carbon and nitrogen in the chemical reactions are also described. The effects of the modifications on the distributions of a number of key chemical species in GEOS-Chem are then analysed using output from a one-year run.
The GEOS-Chem model is very, very widely used in the community and the description and analysis of the modifications to the gas-phase chemical scheme will be received with interest. The manuscript is very well written and the changes are clearly described, including a very extensive set of tables and graphs showing the temperature and pressure dependence of the original and updated reaction rates in the supplementary information. I have no significant concerns with the manuscript in its present form. Although I do have a few questions about how changes in the model distribution of a couple of species are attributed that I would like to see clarified or expanded on - these are listed with other minor comments below. These questions are specific to a couple of species and do not detract from the overall strong presentation of the updates and the analysis of the effects.Minor comments:
Lines 29 - 30: There is a question mark in the list of references '(Hu et al., 2018; ?; Fritz et al., 2022).'
Line 38: The wording of 'The mechanism goes beyond these recommendations.' is a bit open to interpretation. I understand the authors mean to say the reactions included in the mechanism for isoprene, monoterpenes, etc. are not all covered in the JPL and IUPAC recommendations and, if this is what is meant, it could be more clearly stated.
Line 65: The change to the rate of NO2 + NO3 is described as resulting in a strong temperature dependence ['stronger temperature dependencies for NO2 + NO3 (-33% - -25%)'] but the range is given as -33% to -25%, so it seems like the more significant change is a reduction in the rate - at least at atmospheric relevant temperatures?
Line 111: The reaction of the CH2OO criegee intermediate with water vapour is mentioned as being updated, having been included in the latest JPL recommendations. Does GEOS-CHEM account for the reaction with the H2O dimer, which seems to account for a significant amount of the reaction with water vapour? I will note that the reaction rate constant given in Table 1 is for the reaction with the monomer.
Lines 149 - 150: Because of the extension into the stratosphere and the long timescales for transport in that region, are the initial conditions provided at January 1, 2017 'spun up' to have a fairly realistic distribution through the stratosphere?
Lines 164 - 165: Could the authors expand on the explanation for the decreases in upper tropospheric ozone that are attributed to 'higher NOx-driven losses brought about by changes to the HNOz + OH (z=2-4) reactions'? The heart of the problem is that I am not sure what exactly is meant by 'NOx-driven losses' and it is not readily apparent to me how, for example, the much faster rate for OH + HNO2 -> NO2 + H2O should result in decreased ozone through 'NOx-driven losses'. There is a decrease in NOx in the upper troposphere shown in Figure 2a, but I would have thought ozone production would be NOx limited in this region so the decreased ozone would be due to a decrease in ozone production?
Lines 184 - 187: These are significant changes in stratospheric NOx and I fully agree with your explanation. Very interesting.
Lines 188 - 190: Can the 0.4% increase in NO3 in the stratosphere be separated from the general 7 - 8% increase in NOx? In fact, given the increase in NOx and the increase in the rate of O + NO2 -> NO3, I would have thought the change in NO3 would have been more similar in magnitude, or larger, than the change in NOx?Citation: https://doi.org/10.5194/egusphere-2023-1374-RC3 -
AC1: 'Authors' response to reviewer comments', K.H. Bates, 24 Dec 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-1374/egusphere-2023-1374-AC1-supplement.pdf
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Cited
Mathew Evans
Barron Henderson
Daniel Jacob
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(8258 KB) - Metadata XML
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Supplement
(14720 KB) - BibTeX
- EndNote
- Final revised paper