the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 12 May 2025
A Modeling Study of Global Distribution and Formation Pathways of Highly Oxygenated Organic Molecules (HOMs) from Monoterpenes
Abstract. Highly oxygenated organic molecules (HOMs) derived from monoterpenes are key precursors of secondary organic aerosols (SOA), yet their global-scale formation pathways and climate impacts remain poorly quantified due to uncertainties in autoxidation kinetics and branching ratios of peroxy radicals. Here, we integrate a comprehensive HOMs chemical mechanism into a global climate model, enabling a systematic evaluation of HOMs-derived SOA (HOMs-SOA) contributions and their sensitivity to key chemical parameters. The improved model shows reasonable agreement in the diurnal cycle and average HOM concentrations (normalized mean biases of 69 % and 121 % at the two sites). Sensitivity experiments identify the branching ratio of autoxidation-capable peroxy radicals (MT-bRO2) as the dominant uncertainty source. While the MT-bRO2 branching ratio has limited impact on C10-HOMs concentrations (~60 % formed via NO-terminated autoxidation), it strongly regulates C15/C20-HOM concentrations produced through cross-reactions of biogenic peroxy radicals. The contribution of HOMs-SOA to total monoterpene-derived SOA ranges from 19 % to 41 %, depending on the MT-bRO2 branching ratio used in chamber experiments. C15 and C20 accretion products dominate in pristine regions (e.g., the Amazon, contributing ~50 % of HOMs-SOA), whereas anthropogenic-influenced areas (e.g., southeastern China and India) exhibit higher contributions from NO-mediated formation of C10-ON (nitrate HOMs). Our findings advance the representation of organic aerosols in climate models and provide critical insights to bridge gaps between chamber experiments and global-scale simulations.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Atmospheric Chemistry and Physics.
Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.-
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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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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
-
RC1: 'Comment on egusphere-2025-1526', Anonymous Referee #1, 04 Jun 2025
- AC1: 'Reply on RC1', Xinyue Shao, 04 Sep 2025
-
RC2: 'Comment on egusphere-2025-1526', Anonymous Referee #2, 17 Jul 2025
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1526/egusphere-2025-1526-RC2-supplement.pdf
- AC2: 'Reply on RC2', Xinyue Shao, 04 Sep 2025
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2025-1526', Anonymous Referee #1, 04 Jun 2025
Review of ACP submission “A Modeling Study of Global Distribution and Formation Pathways of Highly Oxygenated Organic Molecules (HOMs) from Monoterpenes” by X. Shao et al.
Significance
HOMS are key players in atmospheric new particle formation and subsequent growth of secondary organic aerosol (SOA). They are formed through complex oxidation reaction networks and the process is called autoxidation. Due to the inherent complexity in gas-phase organic oxidation reactions combined with the multitude of uncertain and unknown branching pathways with minimal information of their number, efficency and extent, describing HOM formation in atmospheric models is a formidable task. Hence, notwithstanding the importance of atmospheric autoxidation and direct aerosol precursor formation, describing it especially at the atmospheric scale remains an important barrier to overcome. Thus the work is novel, timely and aims to alleviate a persistent pain on the shoulders of the community. As such, it is certainly within scope of ACP and should be of interest to its readers. However, the inadequacies in reporting the work together with badly justified choice of parameters make the work untractable and not representative, and thus I can’t propose publishing the work in ACP. I’ll detail my concerns in the comments below.
Major comments
The two major issues with the current work are i) the apparent deliberate choice of parameters and ii) the insufficient documentation of the work. These are detailed separately below.
About the choice of parameters:
*It seems the authors have chosen to use very high values for the crucial autoxidation parameters in several parts of the work, and thus it is not possible to assess the results at more realistic settings representing more atmospherically relevant conditions. The current study is probably closer to the maximum impact of monoterpenes on ambient HOM loads, though with the necessarily very reduced description of the oxidation chemistry in global models, no one could know today.
*Importantly, the current work appears to almost completely hinge on the previous work of Xu et al., and uses its parameterizations without explaining the choices or what has actually been done. Whereas in Xu et al., there is a good discussion on the choice of parameters, here it is absent and the reader is left with very little informatio to understand the basis of the choices. It is also important to realize that the lower limit rate coefficients for autoxidation used here (i.e., around 0.1 s^-1 if I read it correctly) are already termed rapid rates in Xu et al., as they should be, as at around this rate the autoxidation is competitive in most atmospheric environments. In order to understand such a complex modelling work, it would be crucial to carefully detail the choice of parameters.
*Related: H ow do you justify so high branching ratios to autoxidation, and why are they not described in the main text? Generally HOM yields have been found to lie between 0.1 and 7% of the VOC turnover.
*” The reaction rate constants used are the same as those in the default monoterpene + OH/O3 reactions.”
So, what are they exactly and how reasonable is their use here? How does the lumping affect the diurnal cycles for example, as the actual rates depend on individual RO2 concentrations.
*I don’t understand how the autoxidation rate can
“critically regulate the formation pathways of accretion product generation by directly affecting the concentration of MT-HOM-RO2”
Autoxidation only converts R’O2 to R’’O2, so how would it affect total RO2 abundance? Are you modelling the RO2 + RO2 with increasing k as a function of the oxygen content?
*Similarly this is a somewhat confusing statement
”In addition, the reaction rates of autoxidation reactions remain highly uncertain, with different measurements in different chamber experiments ranging from 0.6 to 21 /s, differing by 1 to 2 orders of magnitude (Lee et al., 2023; Berndt et al., 2016; Moller et al., 2020).”
From this it appears that you are using too high autoxidation rates. Are the actual used rates described anywhere in the paper? 21 s^-1 is an exceptionally fast isomerization that outcompetes almost any RO2 loss process in almost any atmospheric environment. It is not representative number for general autoxidation in the atmosphere. It’s also stated that autoxidation rates vary by 2 orders of magnitude, which is wrong. The meaningful variation is around 5 to 6 orders of magnitude (i.e., from around 10-4 to 100 s-1), but obviously the values can vary more than this.
*Moreover you say
“The yields and reaction rates of the accretion products also vary by one to two orders of magnitude in different experimental measurements (Berndt et al., 2018; Zhao et al., 2018).”
Commonly RO2 + RO2 rates have been found to vary by over 6 orders of magnitude, which should be relevant for the RO2 +RO2 here as well. It appears that here all the RO2 + RO2 in the work have been given very high rate coefficients. Also the chosen CH3O2 rate coefficients seem strangely high (see e.g., https://doi.org/10.1016/j.atmosenv.2004.09.072)
**Related, you mention you have modelled self and cross reactions of the accretion products, but I suppose this is not what you meant.
*“while two experiments (Fast and Slow) explore autoxidation rate extremes (~10 and ~0.1 of the Control rate).”
What is the actual Control Rate?
“Building on this, we use sensitivity experiments (Table 2) to inform the uncertainties associated with the contribution of HOMs-SOA to MTSOA and total SOA.”
The Table 2 is hard to follow and thus it is not very clear what has been accomplished.
About the documentation:
*The minimum requirement of reporting a research work is that the work needs to be repeatable with the information given. Evenmore, the work has to be repeatable with the information given in the main text, and the supportting material is there to avoid unnecessary repetition and too big tables, etc. One should not need to look at the supporting material to comprehend what is presented in the main text. With the current level of documentation, I don’t know how I could repeat the work.
*You talk about “comprehensive HOMs chemical mechanism”, but you are only showing a crude and rather ambiguous schematic of a handful of reaction steps that you apply for the whole pool of monoterpenes. This is really not a mechanism, which has a very specific meaning in the chemical literature. If there is no real base mechanism, then the involvement of NOx is even harder to understand. The NOx involvement seems to be particularly important for the current work, yet only the final results in the form of formed products seem to be represented and the mechanistic steps are not discussed. I would have really liked to see more discussion around the chemistry, which should be at the heart and sould of this work based on the title. Figure 1 actually proposes a rather complex reaction chemistry but the text says you use 5 gaseous and 5 particle phase HOM in total. Where is this mismatch coming from?
*Please use actual molecular compositions and not symbolic language. “TERP1OOH” is hardly a chemical name.
*The photolysis assumptions. You say that photolysis of accretion products is not considered, but based on first principles they should be even more photosensitive as they contain the parent compound cromophores together with the added peroxide bond. Right? Or do you expect the HOM photochemistry to change considerably by addition of the peroxide bond? Also, shouldn’t the photolysis frequency go down with the secondary particle size (i.e., shielding) or not? It is also unclear to me that where do you base the particle phase photolysis frequancy that is as high as 1/60 of the jNO2?
*Unclear how the species would react together in Figure 1. Also, in each and every Figure you should explain all the names and symbols used. As an example, the Figure 2 is terribly hard to understood with the details given and one is left pondering about the numbers in them.
Explain all the terms and symbols in Table and Figure captions. For example, can’t understand Table 2.
Less Major Comments
“In the LowNOx sensitivity experiment, total C10 concentrations decreased from 736 to 339 ng/m3 at the Centreville site (anthropogenically influenced) due to reduced NOx emissions, with C10-ON showing a more pronounced reduction (117 to 30 ng/m3) than C10-NON (619 to 310 ng/m3), consistent with the NO-dependent formation of C10-ON (Figs. 2 and 3).” There seems to be a bad disconnect here as the C10 How does the C10 concentrations decrease with reducing NOx? Is the NO involvement through RO formation taken into consideration.
“The MT-RO2 formed by the oxidation of monoterpenes by NO₃ radicals are not considered in this study, as some studies report the branching ratio to be insignificant“
This seems strange as several recent studies are finding NO3 oxidation far more important than has been previously thought. Perhaps you’re confusing with the work of Kurtén et al., who explained that the one monoterpene that most people seem to concentrate do not have facile paths to HOM upon NO3 initiated oxidation (https://pubs.acs.org/doi/10.1021/acs.jpclett.7b01038), but it is unlikely that this result transfers to other monoterpene systems.
About the modelled data and the assumptions on volatility
*It is unclear how you are using the field data here. Do you estimate the individual C10 species concentrations from the experimental data? Did you obtain the raw data from the authors, or how did you come up with the signals? What sort of calibration factors were used?
*Related, I would like the authors to comment on the assumed volatility classes. How sure it is that the compounds assumed ELVOC, are actully ELVOC? This seems critical for understanding the work.
*Finally, If you want to claim “Addressing these gaps requires coordinated laboratory measurements and targeted ambient observations to disentangle competing chemical processes.” Then could you please specifically explain what type of ambient measurement would help in this task. How do you envision one could speciate the corresponding chemicals from the ambient gas-phase.
Picked up
*There’s an error: “As the number of oxygen atoms in the functional group increases, the volatility of the organics gradually decreases.”
*Please reword (page 3): “but the models still lack fully understand the uncertainties.”
*“nitrogen dioxide (NOx)” – nitrogen oxides
*NOx is not either of the NO and NO2, it is both. Please clarify the staments claiming NOx can help autoxidation.
Citation: https://doi.org/10.5194/egusphere-2025-1526-RC1 - AC1: 'Reply on RC1', Xinyue Shao, 04 Sep 2025
-
RC2: 'Comment on egusphere-2025-1526', Anonymous Referee #2, 17 Jul 2025
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1526/egusphere-2025-1526-RC2-supplement.pdf
- AC2: 'Reply on RC2', Xinyue Shao, 04 Sep 2025
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Xinyue Shao
Yaman Liu
Ruochong Xu
Joel A. Thornton
Duseong S. Jo
Wenxiang Shen
Manish Shrivastava
Stephen R. Arnold
Ken S. Carslaw
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(6982 KB) - Metadata XML
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Supplement
(1604 KB) - BibTeX
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- Final revised paper
Review of ACP submission “A Modeling Study of Global Distribution and Formation Pathways of Highly Oxygenated Organic Molecules (HOMs) from Monoterpenes” by X. Shao et al.
Significance
HOMS are key players in atmospheric new particle formation and subsequent growth of secondary organic aerosol (SOA). They are formed through complex oxidation reaction networks and the process is called autoxidation. Due to the inherent complexity in gas-phase organic oxidation reactions combined with the multitude of uncertain and unknown branching pathways with minimal information of their number, efficency and extent, describing HOM formation in atmospheric models is a formidable task. Hence, notwithstanding the importance of atmospheric autoxidation and direct aerosol precursor formation, describing it especially at the atmospheric scale remains an important barrier to overcome. Thus the work is novel, timely and aims to alleviate a persistent pain on the shoulders of the community. As such, it is certainly within scope of ACP and should be of interest to its readers. However, the inadequacies in reporting the work together with badly justified choice of parameters make the work untractable and not representative, and thus I can’t propose publishing the work in ACP. I’ll detail my concerns in the comments below.
Major comments
The two major issues with the current work are i) the apparent deliberate choice of parameters and ii) the insufficient documentation of the work. These are detailed separately below.
About the choice of parameters:
*It seems the authors have chosen to use very high values for the crucial autoxidation parameters in several parts of the work, and thus it is not possible to assess the results at more realistic settings representing more atmospherically relevant conditions. The current study is probably closer to the maximum impact of monoterpenes on ambient HOM loads, though with the necessarily very reduced description of the oxidation chemistry in global models, no one could know today.
*Importantly, the current work appears to almost completely hinge on the previous work of Xu et al., and uses its parameterizations without explaining the choices or what has actually been done. Whereas in Xu et al., there is a good discussion on the choice of parameters, here it is absent and the reader is left with very little informatio to understand the basis of the choices. It is also important to realize that the lower limit rate coefficients for autoxidation used here (i.e., around 0.1 s^-1 if I read it correctly) are already termed rapid rates in Xu et al., as they should be, as at around this rate the autoxidation is competitive in most atmospheric environments. In order to understand such a complex modelling work, it would be crucial to carefully detail the choice of parameters.
*Related: H ow do you justify so high branching ratios to autoxidation, and why are they not described in the main text? Generally HOM yields have been found to lie between 0.1 and 7% of the VOC turnover.
*” The reaction rate constants used are the same as those in the default monoterpene + OH/O3 reactions.”
So, what are they exactly and how reasonable is their use here? How does the lumping affect the diurnal cycles for example, as the actual rates depend on individual RO2 concentrations.
*I don’t understand how the autoxidation rate can
“critically regulate the formation pathways of accretion product generation by directly affecting the concentration of MT-HOM-RO2”
Autoxidation only converts R’O2 to R’’O2, so how would it affect total RO2 abundance? Are you modelling the RO2 + RO2 with increasing k as a function of the oxygen content?
*Similarly this is a somewhat confusing statement
”In addition, the reaction rates of autoxidation reactions remain highly uncertain, with different measurements in different chamber experiments ranging from 0.6 to 21 /s, differing by 1 to 2 orders of magnitude (Lee et al., 2023; Berndt et al., 2016; Moller et al., 2020).”
From this it appears that you are using too high autoxidation rates. Are the actual used rates described anywhere in the paper? 21 s^-1 is an exceptionally fast isomerization that outcompetes almost any RO2 loss process in almost any atmospheric environment. It is not representative number for general autoxidation in the atmosphere. It’s also stated that autoxidation rates vary by 2 orders of magnitude, which is wrong. The meaningful variation is around 5 to 6 orders of magnitude (i.e., from around 10-4 to 100 s-1), but obviously the values can vary more than this.
*Moreover you say
“The yields and reaction rates of the accretion products also vary by one to two orders of magnitude in different experimental measurements (Berndt et al., 2018; Zhao et al., 2018).”
Commonly RO2 + RO2 rates have been found to vary by over 6 orders of magnitude, which should be relevant for the RO2 +RO2 here as well. It appears that here all the RO2 + RO2 in the work have been given very high rate coefficients. Also the chosen CH3O2 rate coefficients seem strangely high (see e.g., https://doi.org/10.1016/j.atmosenv.2004.09.072)
**Related, you mention you have modelled self and cross reactions of the accretion products, but I suppose this is not what you meant.
*“while two experiments (Fast and Slow) explore autoxidation rate extremes (~10 and ~0.1 of the Control rate).”
What is the actual Control Rate?
“Building on this, we use sensitivity experiments (Table 2) to inform the uncertainties associated with the contribution of HOMs-SOA to MTSOA and total SOA.”
The Table 2 is hard to follow and thus it is not very clear what has been accomplished.
About the documentation:
*The minimum requirement of reporting a research work is that the work needs to be repeatable with the information given. Evenmore, the work has to be repeatable with the information given in the main text, and the supportting material is there to avoid unnecessary repetition and too big tables, etc. One should not need to look at the supporting material to comprehend what is presented in the main text. With the current level of documentation, I don’t know how I could repeat the work.
*You talk about “comprehensive HOMs chemical mechanism”, but you are only showing a crude and rather ambiguous schematic of a handful of reaction steps that you apply for the whole pool of monoterpenes. This is really not a mechanism, which has a very specific meaning in the chemical literature. If there is no real base mechanism, then the involvement of NOx is even harder to understand. The NOx involvement seems to be particularly important for the current work, yet only the final results in the form of formed products seem to be represented and the mechanistic steps are not discussed. I would have really liked to see more discussion around the chemistry, which should be at the heart and sould of this work based on the title. Figure 1 actually proposes a rather complex reaction chemistry but the text says you use 5 gaseous and 5 particle phase HOM in total. Where is this mismatch coming from?
*Please use actual molecular compositions and not symbolic language. “TERP1OOH” is hardly a chemical name.
*The photolysis assumptions. You say that photolysis of accretion products is not considered, but based on first principles they should be even more photosensitive as they contain the parent compound cromophores together with the added peroxide bond. Right? Or do you expect the HOM photochemistry to change considerably by addition of the peroxide bond? Also, shouldn’t the photolysis frequency go down with the secondary particle size (i.e., shielding) or not? It is also unclear to me that where do you base the particle phase photolysis frequancy that is as high as 1/60 of the jNO2?
*Unclear how the species would react together in Figure 1. Also, in each and every Figure you should explain all the names and symbols used. As an example, the Figure 2 is terribly hard to understood with the details given and one is left pondering about the numbers in them.
Explain all the terms and symbols in Table and Figure captions. For example, can’t understand Table 2.
Less Major Comments
“In the LowNOx sensitivity experiment, total C10 concentrations decreased from 736 to 339 ng/m3 at the Centreville site (anthropogenically influenced) due to reduced NOx emissions, with C10-ON showing a more pronounced reduction (117 to 30 ng/m3) than C10-NON (619 to 310 ng/m3), consistent with the NO-dependent formation of C10-ON (Figs. 2 and 3).” There seems to be a bad disconnect here as the C10 How does the C10 concentrations decrease with reducing NOx? Is the NO involvement through RO formation taken into consideration.
“The MT-RO2 formed by the oxidation of monoterpenes by NO₃ radicals are not considered in this study, as some studies report the branching ratio to be insignificant“
This seems strange as several recent studies are finding NO3 oxidation far more important than has been previously thought. Perhaps you’re confusing with the work of Kurtén et al., who explained that the one monoterpene that most people seem to concentrate do not have facile paths to HOM upon NO3 initiated oxidation (https://pubs.acs.org/doi/10.1021/acs.jpclett.7b01038), but it is unlikely that this result transfers to other monoterpene systems.
About the modelled data and the assumptions on volatility
*It is unclear how you are using the field data here. Do you estimate the individual C10 species concentrations from the experimental data? Did you obtain the raw data from the authors, or how did you come up with the signals? What sort of calibration factors were used?
*Related, I would like the authors to comment on the assumed volatility classes. How sure it is that the compounds assumed ELVOC, are actully ELVOC? This seems critical for understanding the work.
*Finally, If you want to claim “Addressing these gaps requires coordinated laboratory measurements and targeted ambient observations to disentangle competing chemical processes.” Then could you please specifically explain what type of ambient measurement would help in this task. How do you envision one could speciate the corresponding chemicals from the ambient gas-phase.
Picked up
*There’s an error: “As the number of oxygen atoms in the functional group increases, the volatility of the organics gradually decreases.”
*Please reword (page 3): “but the models still lack fully understand the uncertainties.”
*“nitrogen dioxide (NOx)” – nitrogen oxides
*NOx is not either of the NO and NO2, it is both. Please clarify the staments claiming NOx can help autoxidation.