This paper demonstrates the incorporation of phase-separation and phase state within CMAQ and shows this incorporation leads to a decrease in overall simulated IEPOX-SOA formation. Three models were used to predict phase state, which each used a different combination of parameters, which led to large discrepancies in Tg predictions between models for some compounds contributing to differences in phase state predictions between models. The addition of phase separation and phase state predictions leads to better predictions of  2-MT, but an underprediction of MTS and overall IEPOX-SOA formation. Overall, I believe this will be suitable for publication in ACP after the authors address the following comments.

General comments:

Please ensure that all of your figures are consistent and easy to follow (i.e., be consistent with latitude and longitude lines, label model used, be clear when observational data is from LRK or CTR on the figure, increase font size when possible). Also, ensure to resolve the problem with readability that is on several figures.

I would recommend either using different species abbreviations for the most common IEPOX-SOA compounds (2-MT for 2-methyltetrols, OS for organosulfates, MTS for methyltetrolsulfates, etc.) or being explicit that these are the species names given in CMAQ as this could be confusing for readers who do not use CMAQ.

Make sure you are consistent with units used.

Specific comments:

Line 40: “2-methyltetrol performance improved” Please be more specific.

Line 52: “Gas-phase SOA precursor species can also dissolve into existing aqueous aerosols and cloud droplets and undergo aqueous-phase oxidation leading to lower volatility species - known as multiphase and/or heterogeneous chemistry” While heterogeneous chemistry can lead to lower volatility species, there are also heterogeneous reactions that can lead to more volatile products.

Line 56: “The isoprene epoxydiol (IEPOX) is…” Referring to IEPOX in the singular and as a definite subject here is slightly confusing since IEPOX has multiple isomers, I would recommend removing “the” from the beginning of the sentence.

Line 59: “In atmospheres that have higher hydrogen oxides (HOx = OH + HO2) than nitric oxide (NO) concentrations,” Implies that you are discussing at a planetary level, alter wording to clarify.

Line 65: “Field campaigns and chamber studies have also found that IEPOX-SOA species with higher volatilities (2- methyltetrols and C5-alkene triols) can have some fraction remaining in the particle phase…” Wording is confusing here, what is higher volatility in reference to in this case, these species should be much lower in volatility than IEPOX. According to your source for the following sentence, based on the C*s alone the alkane triols should be mostly in the gas phase but 2-MT should only be 43% in the gas phase.

Figure 1 is very hard to read, please increase the font and line size where possible and ensure that there are no compression issues during export.

Line 168: “Given the numerical precision of CMAQ and the likelihood of very small 𝑤𝑠 values-characteristic of dry OAs yet still greater than zero-the occurrence of 𝑤𝑠 = 0 was minimal.” Please rephrase, this sentence was very hard to parse.

Line 255: It would be helpful to indicate the CTR SOAS site on the plots shown in Figure 2 since you reference it here.

Line 261: “The frequency of time that the organic coating of an aerosol is in a liquid phase in layer 1 (i.e., ground level, GL) across the whole modeling episode when an appreciable amount of ALW is present in the organic coating (when 𝑤𝑠 > 0.1) and when 𝑤𝑠 ≤ 0.1, corresponding to 𝑇𝑔(𝑤𝑜𝑟𝑔): 𝑇 and 𝑇𝑔,𝑜𝑟𝑔: 𝑇, is shown in Figure 3.” Please clarify if this is the same modeling episode as Figure 2 (June 1 – July 15, 2013).

Figure 3: It would be helpful to add subheadings for the model used on the columns and water content condition for the rows, also please fix the legibility issues.

Figure 4: What was the normalization process? Additionally, what fraction of the time was w_s > 0.1?

Figure 7: From your caption, it seems like a and b are from CTR and c is from LRK. However, the text states that b and c are both from LRK. Please clarify this in both the text and figure caption. Also, please address why these are all not from the same site, I assume it is due to what data was collected at each site but please be explicit. Also, if you only have one site for each species comparison, how confident are you that the addition of phase separation into the model will be consistent with underpredicting IEPOX-SOA and organosulfates, and overpredicting 2-methyltetrols?

Line 474: You have already introduced AIEOS and AIETET as acronyms previously.

This study continues the work in Schmedding (2020), implemented three different glass transition temperature T_g parameterization in a newer version of CMAQ that uses parameterized organic hygroscopicity parameter kappa. This manuscript presents new advancement in improving organic aerosol phase state resolving in atmospheric chemistry modeling. However, several issues remain. I recommend major revision before acceptance.

Major Comments:      

1. Aerosol liquid water and water uptake are central to this manuscript. The newer CMAQ can model organic-layer water uptake, which is the main advance over Schmedding (2020). Please expand Results/Discussion to compare directly with Schmedding (2020) using the same Shiraiwa et al. 2017 parameterization and to show how different water uptake schemes affect the results. Also move the statement about no water transfer between core and shell in the phase separation setup earlier in the manuscript.
2. Kappa parameterizes equilibrium water uptake. The manuscript notes that aerosol can become semi-solid or solid at higher altitudes. Please discuss the potential bias from applying the same Kappa and equilibrium water uptake to semi-solid or glassy aerosol, and outline what observations and modeling are needed to represent non-equilibrium water uptake in such phases.

Specific Comments:

1. Line 98: Please use em dash (—) instead of hyphen (-)
2. Line 103–115: Please acknowledge other T_g parameterizations that might not be O:C ratio or volatility based (e.g., Galeazzo and Shiraiwa, 2022, "Predicting glass transition temperature and melting point …"). Explain why they are not included, and justify selecting the three used here.
3. Line 159–160: The resistor term for IEPOX uptake is central to later discussion and should be included, at least in part, in the main manuscript. The rate constant k_particle should be introduced here. k_particle was never formally introduced in the main manuscript, but only later discussed on page 18 and page 22. In addition, it is stated in earlier texts that the implementation of phase separation and phase state follow Schmedding (2020), is the IEPOX reactive uptake in this study handled differently?
4. Figure 1: The equations and conditions (red texts) are hard to read in the figure. Since they follow Schmedding (2020), re-define the full equations in the Supplement and reference them in this schematic only. The flowchart should present each step clearly without the full equations. The three different T_g parameterization should be shown in three parallel steps instead of in one step.
5. Line 168–172 is unclear and requires clarification. I also don't see why the case w_s = 0 needs special treatment, as the Gordon-Taylor equation (eq.2) is fine when one component’s (in this case water) mixing ratio is 0. Additionally, please use em dash (—) instead of hyphen (-) for in sentence explanatory phrases. What does it mean by switch equations?
6. Figure 3 is ineligible. It looks like it is related to the conversion during manuscript upload. Please re-upload the figure in the rebuttal.
7. Table 2. Species description is ineligible. For the T_g comparison, a three-panel scatter plot (one scheme to scheme comparison in each panel) would be better, with points color coded by O:C or volatility, a 1:1 line, and RMSE in each panel.
8. Line 390–394: I don’t see why it is important to note that water diffusion from core to shell was not considered given the sensitivity of 𝛾_IEPOX to k_particle. Please explain. Can you elaborate further on these sensitivity studies?
9. Line 477: what is the rationale in increasing k_particle from 0.0001s⁻¹ to 0.001s⁻¹? Please elaborate. Additionally, also avoid using “/s” and use the standard unit “s⁻¹” or “s⁻”
10. Line 497: the atmospheric implication section is rather general and more suitable for introduction. Please tie the atmospheric implication to your results.