This manuscript developed a new chemical mechanism for 3D chemical transport modeling, CRACMM, which represents a major advance compared with the chemical mechanisms used in previous versions of CMAQ. I believe that the new mechanism will benefit the air quality modeling community, especially the researchers working on O3 and SOA simulations. The manuscript is clearly written. I think it can be accepted for publication after the authors address the following minor comments and suggestions.

(1) CRACMM builds on the implementation of RACM2 chemistry coupled with aerosol chemistry of AERO6. As we know, AERO6 treats both organic and inorganic aerosol chemistry, but this manuscript describes only organic chemistry. Did you treat inorganic aerosol chemistry within or outside of CRACMM?

(2) You simulated aging in addition to the initial oxidation of alkane-like species. Aging changes SOA yields. Are the simulated SOA yields of alkanes still consistent with chamber experiments after aging is considered?

(3) Line 138: Do you mean gaseous L/S/IVOC emissions only, or both gaseous and particle-phase L/S/IVOC emissions?

(4) Line 140: Are any SVOC emissions considered here?

(5) Line 154: What kinds of compounds are these? Can they be IVOC?

(6) Line 180: You assumed equal RO2 reaction rates with HO2 and NO here, but what is the amount of RO2 reacted with HO2 vs NO? The latter determines whether this is a high-NOx or low-NOx condition and hence determines the SOA yields.

(7) Line 190: Which of the three methods did you actually use? Multiple linear regression, exponential/logarithmic equation, or averaging?

(8) Are these alkane-like L/S/IVOC species emitted into just the gas phase, or both gas and particle phases?

(9) Line 372: “The decrease in 𝑙𝑜𝑔10(𝐶𝑖∗) per oxygen in the 2-D VBS box model was set at -2.3”. This is likely the largest volatility decrease one oxygen addition might bring. This is a stronger volatility decrease than the default assumption in the 2D-VBS box model. The authors may want to note this in the manuscript.

(10) Line 387-390: How did you select these species?

(11) Line 401-403: Some products are mapped to aldehydes and some are mapped to ketones. Any science behind this assumption?

(12) Line 459-461: Among the products of furan, the model assumes that only furanone leads to SOA production. Is this true?

(13) Line 516: From R9-R13, it is not clear how furanone was produced from aromatics oxidation.

(14) Line 522-523: Will setting the yields to match high-NOx experimental results lead to an underestimation of SOA yields under low-NOx conditions?

(15) Line 651: It is not clear from the text if the organic peroxide products (OPB) lead to any SOA in the model.

(16) Line 712-714: Does this mean the SOA yields from API oxidation will be much higher under high-NOx conditions than under low-NOx conditions?

(17) Line 772-784: Does this section have anything to do with SOA formation?

(18) Line 1141-1142: I don’t think it is appropriate to define this metric as saturation ratio. I think saturation ratio typically means the ratio of vapor concentration to saturation vapor concentration.

This paper aims to describe a new tropospheric organic-chemistry mechanism for use by the US EPA for understanding the concentrations of air pollutants such as O3, particulate matter and compounds hazardous to health. 

It builds on a number of previous mechanisms but extends them to be more comprehensively relevant for SOA and compounds hazardous to health. It also provides a formal description of the chemistry and the choices made to develop this chemistry. This activity has been a substantial and thoughtful piece of work. It is very useful to the community to have the thoughts used in the development of the mechanism catalogued in a single location. 

I don’t have any real comments about the description of the mechanism. It is based on a number of well-regarded other mechanisms and brings them together. There will be by very necessity some inconsistencies between these mechanisms but I’m not to concerned about that. 

I have one comment for the editor about whether this paper is best published in ACP rather than GMD. The paper is a description of a model mechanism and the choices that went into developing it. It doesn’t evaluate the mechanism against previously used mechanisms or against other mechanisms. Thus there isn’t much in the way of “new science” here more documentation of a new mechanism. It would seem that this is ideally suited for a GMD paper whereas it’s less clear that this is an ACP paper. What have we learnt from this paper? This is however an editorial decision rather than one for a reviewer so I would leave it at that. 

My major comments can be split into a number of categories. 

1. The introduction is written from a particularly EPA perspective. This is quite US-centric at times. The discussion around O3 bias in models (line 63) seems to suggest all models suffer from the same problems and only discusses the US. I appreciate that the development work here has been done with the US in mind. Still, I think the introduction should be looked at to make it clear that the comments are nearly always relevant only to the US and mainly comes from the perspective of people running EPA models.  
2. The paper focuses on the completeness of the mechanism developed but it should be clear that it ignores some important aspects. There is no representation of much of sulfur oxidation chemistry (DMS), halogen oxidation chemistry, or representation for HO2 uptake etc. These might be seen as boundary conditions for the primary objective here but there should be some explanation for why they have not been included, especially for things like chlorine chemistry which has been shown to have an impact on ozone in coastal locations etc.   I think the introduction should spend some time putting some context around the developed mechanism. Why does it what it does but also what does it exclude things and why? Again in the section discussing future developments it would be worth including some description of the plans for including some of these other aspects of chemistry in future versions of the mechanisms. 
3. Peroxy-radical self reactions. Historically these reactions have not been considered too important in these kinds of models as there is usually enough NO around for the fate of the peroxy radicals to be dominated by the reaction with NO rather than the reactions with other peroxy radicals. However, as NO emissions drop that assumption may be less convincing. However, including the reaction between each peroxy radical and each other add enormously to the number of reactions if implemented explicitly. It would be useful to have some comments here about the choices made for the fates of peroxy-radicals in the mechanisms and why the choices were made as they were.  

Figure 1,2,3 Many of the figures are extremely data rich which is excellent however this can make understanding the detail of these rather hard. I find the use of the violin plots quite difficult to get my head around as its suggests compounds with non-integer values for the number of carbons. I think the overlain box plots show the 25th,50th and 75th percentiles of the carbon number not the emitted mass? Are the colours representing the new species added to the system above the RACM2 mechanism, if so I think they should come below the grey bar in the key to signify they are additional to the base. What is the difference between the RACM2 systems and the CMAQv5.3.3. I think these graphs are really informative but I have found it quite confusing to understand what exactly they were telling me. I’d suggest the authors go back and think about the figure and figure caption and from the perspective of a reader who is more detached from the figure than they might be. 

There are some minor typos in the brackets etc of some of the rate constants.