Manuscript `ar-2024-40` (Pichelstorfer et al.) presents a new methodology to derive chemical mechanisms that describe auto-oxidation reactions. This class of reactions has gained attention recently because of their role in the oxidation of volatile organic compounds and in the formation of secondary organic aeerosol.  Because of the complexity of the chemistry the representation of these reactions in chemical models is a difficult problem to solve. This study proposes a possible solution to the problem and the results are very promising. The manuscript is well written and the conclusions are well supported. Therefore I recommend publication after the authors have addressed the following points.

MAIN POINTS

The methodology described in this manuscript is complex and I fully appreciate that it is difficult to explain, but I think the paper could benefit from a bit more high-level explanation, in simple terms. As I understand it, for a given chemical system the model chooses a set of rate coefficients for the auto-oxidation reactions. Using this set, a certain distribution of reaction products is obtained that can be compared to the distribution of masses observed by the nitrate-CIMS. This may be too simplistic of an explanation but is it more or less correct? How is the best fit to the experimental data determined?

The assumption of the method, if I understand it correctly, is that each mass measured by the nitrate-CIMS corresponds to a product of reactions R1-R6. My first question is: are you trying to keep a mass balance? In other words is the composition of these products in the model tracked, so that their mass can be calculated and matched to a measured mass? If this is the case is it a problem that you are coupling this methodology with the MCM, a mechanism which doesn't not keep mass balance?

How do you deal with different molecules that have the same mass? Mass spectrometric methods are often unable to distinguish between those and that may introduce a substasntial bias in the methodology. Likewise, fragmentation of molecules in the mass spectrometer may cause masses to be incorrectly assigned to a molecule, and that will also bias the results. Can the authors comment on these points?

Fragmentation of the reaction products is mentioned on page 7, and I agree with the authors that it has a potentially large impact on the final results. It would be good to add a comment on how much of a bias these processes may introduce in the methodology. Are the fragmentation channels simply ignored? This may be acceptable as an approximation in a method that is still being developed, but needs to be clarified.

Another concern I have is that the methodology described here relies on the assumption that the RO2 sum calculated by the MCM is correct, not to mention the distribution of the individual RO2. This is far from a given, and in fact I would argue is a major uncertainty of the MCM, especially for some compounds. Can you comment on this point?

MINOR POINTS

Lines 75-80: is there way to interpret the ion counts other than concentrations?

Lines 89-91: check punctuation and open/closed brackets.

Line 299: correct "datat".

Supplement: ensure MCM is capitalized.

General comments

Overall, this is a very well written and clearly structured manuscript about a novel semi-automated method used to constrain autoxidation reaction schemes, including both unimolecular peroxy/alkoxy radical reactions and all related biomolecular reactions that influence the autoxidation reaction mechanisms. The presented novel autoCONSTRAINT tool seem to be a potentially very useful software for the construction of realistic, theoretically consistent and clearly documented and reproduceable peroxy/alkoxy radical autoxidation mechanisms for a large number of VOC + oxidation systems. Currently such a tool is not existing and hence this manuscript provide a substantial contribution to scientific progress within the scope of atmospheric chemistry and secondary organic aerosol formation.

Specific comments

L105 “Reactions R2a to R2c do only change the reacting peroxy radical and have no effect on the ΣRO2•.” Consider to reformulate this sentence.   Reactions R2a to R2c only influence the concentration of the reacting peroxy radical and has only minor effect on the ΣRO2•

I think that reacting peroxy radical is also part of ΣRO2, so some minor impact R2a to R2c should also have on the ΣRO2•or am I wrong?

Page 4: Why do you consider that fragmentation products can form from RO2• + HO2•and RO2• + NO•reactions but not RO2• + ΣRO2•?

L260: “In the current work we assumed k_autox,high = 2 s^-1. We chose this conservative upper limit as most H-shifts are significantly slower”. What would the consequences be if you would allow considerably higher autoxidation reaction rates?  

Page 9: The description and use of the potential initiation flux (P), equ. 4-5 need to be described more clearly. It is not easy to understand how equ. 4-5 was derived and what these equations represents. I guess that they are derived from equ. 3 or?  These equations do not seem to represent the potential initiation flux (units of molecules cm^-3 s^-1) but ratios (potentials) of how much RO autoxidation and RO2 autoxidation may contribute to the production of a specific RO2 peak. Should not equ. 3 also have a separate term for the RO autoxidation source of RO_2,k or is the RO autoxidation source included in S_k? I guess you don’t need to constrain the  RO autoxidation rate since this is assumed to be very fast. Is this why it is omitted in equ. 3-5?       

Technical corrections

L34: “a drop of the saturation vapor pressure”. Consider if it maybe better to write a decrease in the saturation vapor pressure.

L106-107: ... those equations difficult to constrain.  Change to: those equations difficult to constrain that are difficult to constrain.

L203: “Although direct inclusion of the fragmentation products is beyond the scope of this work, the effect of this reaction can be investigated.” Change to:

“Although direct inclusion of reactions leading to fragmentation products is beyond the scope of this work, the effect of such reactions can be investigated.”

L272: “see Fig. Worklfow_1.pdf”. Change to see Fig. 2

L272-273: “The autoCONSTRAINT tool reads in a chemical scheme with no rate coefficients, together with a NO₃^- obtained mass spectrum” I am not exactly sure what you want to state with this sentence, but would it not be better to write:

The autoCONSTRAINT tool reads in a chemical scheme with no rate coefficients, together with a mass spectrum obtained e.g. with a NO₃^- CIMS.

L299: “datat” should be data