SUMMARY

This paper describes the 3D-atmospheric model MESSy for a comprehensive evaluation of the impact of aqueous-phase chemistry on SOA in a CAABA/MECCA box model platform.  The authors need to clarify the fundamental assumption and the limitation of the model. This manuscript may be suitable to be published in ACP after major revision by considering the comments as listed below.

Comments:

1. The authors should clarify the criteria of the SOA model. It is unclear that the SOA model of this paper is subjective to aqueous droplet or any aerosol including SOA aerosol without aqueous phase.  For the organic and inorganic mix, it is possible for the aerosol to be phase separable into organic phase and inorganic phase or form homogeneous phase. Without the assumption and the suitable criteria of the model to a specific aerosol conditions, it is difficult to understand the usage of model.
2. There is no demonstration of model against laboratory data or simulation in regional scale. It is hard to know whether the simulation of the SOA model is suitable to apply to ambient air.  
3. In addition to IEPOX, there are other chemical species that can form oligomers via acid-catalyzed reactions. The authors needs to clarify limitation in the model.
4. Line 9 (Abstract) : Only up to C8 but it is characterized as “long-chain alkanes”. Probably not appropriate to say C8 and below are long-chain alkanes considering they do not form any SOA.
5. Line 12 (Abstract): “aqueous phase” has no hyphen here but is hyphenated in the previous sentence (Line 11)
6. Line 14 (Abstract): “LVOC is…” should be replaced with “LVOC are…”
7. Line 33. Please provide a more detailed explanation on the impact of aqueous-phase oxidation products on the vertical distribution of SOA in the atmosphere would enhance the understanding. 
8. Line 90: “…small oxidized compounds like ” Should be “…small, oxidized compounds like glyoxal.”
9. Figure 1: Unclear what happens in the abstraction of the red H step. It seems like some compound must be being released from the mechanism other than the ones shown. I can see maybe H2O from the OH and one O atom from the radical but how is the red H involved?
10. Henry’s solubility. In aqueous aerosol, there will be electrolytic inorganic species which can influence the solubility of organic species. The salt composition and humidity can influence organics’ Henry’s constants.  The authors need to clarify the impact of salts on gas-particle partitioning of organic species.
11. Section 2.3.1: Phase partitioning is simulated through Henry’s law constants. Can this model handle dry conditions without an aqueous phase? It seems like this would be necessary in a global SOA model.
12. 5. Please check the legend in Fig. 5. Legend for aldehydes is missing.
13. Line 215. Please check figure number. It should be Fig. S17, not Fig. S11.
14. Line 216 - 218. Is this because the concentration of the BASE run is high regardless of temperature conditions (Fig. 6)? While you have provided a reference, further explanation about why the increase in the SOA precursor from isoprene is expected in the global model would be needed.
15. Line 224. The previous sentence stated that the oxidation by ozone and NO3 is dominant before sunrise. What is the effect of the limonene NO3 mechanism? Table 1 mentioned that the main reactant of d-limonene is ozone. Please briefly describe the effect of NO3 on d-limonene.
16. Line 254. What are the factors that the box model neglects and what are the potential effects?
17. Line 256. Please provide the detail conditions of SOAS campaign applied in this study (e.g., temperature, humidity, and pollutant concentrations).
18. Line 265 – 266. Please check figure number.
19. Line 271 – 272. I wonder if the model setup was based on the average value of the entire SOAS campaign or a specific case of SOAS campaign. If there are special cases showing high/low NOx or high/low isoprene conditions during the campaign, box model can be performed for those cases. If the results show a good agreement with measurements in those cases, it will show the good quality of the box model under various conditions. If the final goal of this box model is to improve prediction of SOA concentration by applying it to the global model, it is necessary to show that the box model can produce reasonable results under more various conditions than the paper presents.
20. Line 297 - 298. The model was performed under various conditions and the results were presented. It would be beneficial to emphasize the significance of the results for each specific condition. If this box model is applied to the global model to predict the SOA concentration in global scale, please suggest expected outcomes and their potential role considering the variations in NOx and temperature conditions.

The manuscript by Wieser et al. presents an updated multiphase chemical mechanism in the CAABA/MECCA model, designed to improve predictions of secondary organic aerosol (SOA), particularly via aqueous oxidation pathways. The manuscript was submitted as a development and technical paper, which describe technical updates leading to model improvements, including new parameterizations. Such papers are expected to include a significant amount of evaluation. The manuscript largely fits this description and is appropriate for GMD. However, the manuscript is lacking clarity and specificity in several key areas, which are noted below. It is recommended that these areas be addressed before the manuscript is further considered for publication in GMD.

Major scientific comments:

1. Processes and phases included in the base version of CAABA/MECCA. The language regarding SOA formation is sometimes unclear in the context of whether this model only includes SOA formation via aqueous uptake (aqSOA) or whether gas-particle partitioning to a mostly organic phase is also included. This needs to be better clarified and considered in the discussion of the model updates and results. It is particularly confusing in 3.2, where it is unclear what is being evaluated. The authors state that analysis of the LVOCs is useful as an assessment on potential SOA formation, but then also go on to say they analyzed the total gas, aqueous, and aerosol mixing ratios. The results in 3.2 and 3.3 seem to focus only on LVOC production, to understand how much aqSOA forms, the authors also need to couple that with aqueous solubility and reactive uptake. Additionally, if the compounds are of sufficiently low volatility, there will be competition for partitioning to a mostly organic phase if present. On pp. 15-16, it is not clear what O/C ratios are being compared. Literature reported O/C ratios for SOA are typically based on bulk composition of the condensed phase (organic and/or aqueous depending on analytical technique). It seems that those values are being compared with the O/C ratio for all LVOCs, independent of phase. These are not the same thing.
2. Activity coefficients. The manuscript has no discussion of activity coefficients, or effective Henry’s law constants (i.e., salting in or salting out). This is a major omission. The effective Henry’s law constants of organic compounds in the aqueous particles will be composition dependent and may deviate significantly from the Henry’s law constant for a pure water. It is particularly important for the compounds with moderate solubility. This has been widely discussed in the literature from both experimental and theoretical perspectives.
3. Mechanism details. While the mechanism details can be obtained from the code and other external documents, it is suggested that the SI be expanded to more clearly define the differences between the original and updated mechanism and any changes that were made to published data (e.g., reaction rate constants, branching ratios, etc.) as implemented in the new mechanism. The text is very minimal and non-specific on these aspects, which reduces the clarity and reproducibility of this work. To provide some examples: 1) On p. 3 line 76, the authors discuss redistributing the product yields for isoprene + NO3. How are these redistributed? Does the affect any prior performance evaluations? 2) The authors describe that the new chemical mechanism for limonene was based on MCM, and on p. 4 line 83 state “low-yield reaction pathways are excluded”. What was the cutoff yield value? How was this determined? 3) Similarly, the authors describe implementation of the new n-alkane mechanism based on Atkinson et al. (2008), and on line 96 state that the “mechanism is simplified” to only cover oxidation at specific sites and only one H-abstraction process. Which sites? How was this determined? Does this affect prior performance evaluation? What is the implication of these choices in the context of this model application? Line 115-What is considered fast? What is the rate (s-1) cutoff value? These are only some examples, but such detail is important for all new mechanisms and updates presented in this manuscript, especially if modified from published literature.
4. The evaluation should focus on how the mechanism updates affect the performance of CAABA/MECCA as has been previously evaluated, and using experimental data where available. There is too much general comparison with one-off published literature results, which are inconclusive in the context of model performance, and too much speculation of how the mechanism will improve global model performance. Evaluation is also needed for the new Henry’s law constants and their dependence on temperature, as compared with the base model.

Minor scientific comments:

1. The authors note that limonene was added to simulate a wide range of monoterpenes. It would be useful to know what other monoterpenes are included. Limonene is known as having one of the highest SOA yields under most (if not all) reaction conditions. Thus including limonene to expand the range makes sense only if monoterpenes with low yields are well represented. Related to comment #2 above, what small adjustments based on Vereecken and Peeters were introduced for beta-pinene? The authors note lack of a compelling chemical mechanism for monoterpenes including camphene. Several camphene mechanism papers have been published recently including: Li et al., 2022 ACP; Subramani et al., 2021 Chemosphere; Afreh et al., 2021 ACP, and Mehra et al., 2020 ACP.
2. Line 100: The statement about significant amounts of SOA precursors is unexpected in the methods and also unsupported.
3. Line 163: What is the rationale for choosing GROHME over HenryWIN? This is not made clear in the discussion.
4. Line 200: Does this mean that the model does not include new particle formation? Or does it mean that gas-particle partitioning to an organic phase is not considered (see also major scientific comments #1)?
5. Line 217-218: The suggestion of increased isoprene SOA precursors is unclear and unsupported. Increase because of what? In a global model you also have the temperature dependence of emissions and possibly deposition, so I’m not sure how the box model sensitivities are being translated to expectations for a global model. Similar comment on lines 226-227: There is not strong support for the logic connecting the box model observations (particularly when many monoterpene mechanisms are not included) to expected global model results.

Editorial comments:

-It is not clear to me why the supplemental figures were not ordered so they could be called consecutively in the text.

-line 90, typo in glyoxal