Carter et al. present the chemical mechanism generation system MechGen.

I think that MechGen is a very valuable tool for the atmospheric

chemistry modeling community, and the manuscript is well-written. I

recommended publication in GMD.

I only have a couple of minor comments:

- Line 37: "Many hundreds of types of volatile organic compounds" are

  mentioned here but Tab. 1 lists only 12 types. Maybe this should be

  species, not types?

- Line 47: "lumping or condensations" is mentioned here. Lumping is

  explained later in the text but "condensations" is not. Is this the

  same as lumping or something different?

- Lines 113-115: It is announced that MechGen could be migrated to

  Python or another actively supported software platform. I fully agree

  that this is a good idea. However, since this is about future work, it

  should be mentioned in an "Outlook section" near the end of the

  manuscript, not in the introduction.

- Line 203: Remove superfluous "are".

- Table 4: I suggest to replace the non-standard name "2-methyl-2-ethyl

  butane" by "3,3-dimethylpentane".

- Table 4: Why are the radicals denoted as plural? Why not "radical"

  instead of "radicals"?

- Table 4: The acronym "MEK" is used here but not defined anywhere.

- Table 4: The structures use the symbols *, ^ and v which seem to refer

  to cyclo, cis and trans. This should be explained in a table footnote.

- Lines 480-481: It is claimed that "interconversions of

  hydroperoxy-substituted peroxy radicals due to rapid H-shift

  reactions" have been mentioned above. I cannot find this anywhere in

  the text. I can only see H-shifts for alkoxy radicals in Table 2.

- Line 525: Probably change "the minimize size" to "the minimum size".

- Line 552: Should this be Figure 6c instead of 6b?

- Table 8: What is meant by "explicit lumping"? Maybe this should be

  changed to "explicit (no lumping)"?

- Lines 704-705: "1 ppm" is not a "concentration" but a "mixing ratio"

  (or even more precise: "amount fraction". See e.g.:

  https://doi.org/10.1029/00EO00007

- Lines 830-842: The first paragraph of the Discussion section is a

  review about mechanism development which seems out of place. I think

  it can be deleted completely (or moved into the introduction section).

- Lines 851-853: It is speculated that MechGen is not as widely used as

  MCM or GECKO-A because it has not been documented in the peer-reviewed

  literature. While I partially agree, I think there is another reason

  why the MCM is much more popular: The MCM-generated mechanism can

  easily be exported in KPP or facsimile format. These formats are used

  by many atmospheric chemistry models. In contrast, an elaborate

  conversion of the complex MechGen output is necessary in order to

  implement reactions from MechGen. Although probably out-of-scope for

  this manuscript, I suggest to add KPP-export functionality to MechGen

  (Disclosure of potential COI: I am involved in the development of

  KPP).

- Reference "Carter, 2025": I tried to open the web page

  https://intra.engr.ucr.edu/%7Ecarter/MechGen (which leads to

  http://149.165.173.164:8000). Unfortunately, the page was unreachable.

  It should be checked if this is a temporary or permanent problem.

- Throughout the text, the recommended symbol "s" should be used for a

  second, not "sec".

- Throughout the text, a period "." has been used to denote radicals.

  This can be confused with the end of a sentence. Instead, a vertically

  centered dot should be used.

This manuscript describes the MechGen mechanism generator that underlies the SAPRC mechanisms and builds upon the predictive chemistry described in an earlier paper (Carter et al. 2025). This work is an essential part of documenting the MechGen system, making an important contribution to FAIR research software in atmospheric chemistry. The publication is timely, as current atmospheric chemistry research relies on ever more complex kinetic models, and software assisted mechanism creation is gaining strongly in importance. The manuscript is well written, with clear and accessible descriptions despite covering a highly complex software suite.

I recommend publication of this manuscript. My comments are basically only suggestions for different presentation, and can be accepted or ignored by the authors as they please.

Specific comments:

line 89: "for around 298 K and 1 atm" -> "for conditions covering the lower atmosphere, i.e. around 298 K and 1 atm"

Table 2: "Criegee biradicals"

Replace with "Criegee intermediates", as used in the remainder of the text (CI do not behave as biradicals)

line 203: "rate constants are have to be estimated"

remove "are"

line 230: "representing RC(O)O·"

should be "RC(O)OO."

line 244: "because these peroxynitrates are assumed to rapidly decompose at temperatures of interest"

The results from Färber et al. suggest that it might be useful to have these reactions as a selectable option for specific environments (DOI: 10.1039/D3CP04163H)

Table 3:

- No CH2OO intermediate ? It shows up in the mechanism listings.

- Does MechGen support non-carbon backbone chains, e.g. -O--O- (peroxide or even higher length such as the ROOOH from RO2+OH), or (more exotic) -NH--NH-

Table 5: "Note that "RO-alpha-H" refers to the carbonyl formed when an alpha-hydrogen on an alkoxy radical is abstracted."

perhaps make this a separate footnote [d]

Figure 1, lower left: "Reaction not supported" could perhaps read "species not supported"

line 381: "making the fate of the reactant is independent"

remove "is"

line 525: "they determine the minimize size"

minimal size

line 743: "lower limits unless very low values of MGminYld are used.'

perhaps add "... are used to minimize the amount of untreated carbon (negC)"

Table 9: "Rct'd" is a notation used only in this table, where it's not clear why there is an apostrophe. Is it short for e.g. "Reactants reacted"? Perhaps "Rcts", analogous to "Rxns", would be more intuitive?

Figure 8, S10

The 0.5 entry seems to have a superscript "s" on the right. What does this signify ?

Figure 8, 9, S10, S11: The meaning of the "s" after some functionalities needs to be explained. It seems superfluous.

Line 769: "The corrected yields assuming that the distribution of products from unreacted compounds to those that were reacted are also shown."

Sentence seems malformed

Line 780: "Lumping involves representing the many predicted organic products by lumped model species representing groups of products assumed to react similarly, "

This sentence is hard to parse. Perhaps rephrase it as "Lumping involves representing a group of several predicted organic products, selected to react similarly, as a single lumped model species"

line 782: "to reduce the numbers of intermediates"

"number"

page 29: "chemical operators"

"operators" is only used ~5 times and seems equivalent to the more common phrasing "lumped species". Perhaps harmonizing the naming across the text could improve readability.

page S11 top: "If only a red line is seen, then both mechanisms give the same predictions."

Move this note to the caption of Figure S5, where it is more relevant.

page S11 bottom: paragraph of "S3.1. Initial Processing for Interconverting Intermediates"

Perhaps join this title and few text lines with the bulk of the text below ?

page S11 and elsewhere: 'sets of "cyclic" intermediates'

The term "cyclic intermediates" is a bit unfortunate, as it is too similar to cyclic species. Furthermore it implies that the intermediates are connected in a 2-neighbor circle graph with n members, which is also the picture suggested by the descriptions ("intermediates react to ultimately reform themselves"). The graph topology, however, has a more general connectivity here, where connections with more/all set members are possible. I do not object strongly against the use of "cyclic" but then it needs to be clearly defined, and perhaps referred to as "cyclics" (see also below) at all times to avoid connotations of cyclic species.

page S14 footnote [d]: "the fate of unreactive Criegee intermediates"

"unreactive" is perhaps not the right word here, as the CI are still reactive towards bimolecular reactions. I assume the authors mean CI without fast unimolecular reactions?

Page S18 middle: "30 by default, is a property of the lumping object that the MechGen programmer can modify."

Is this user-modifiable without recompilation ? I don't see it in Table 8 in the main text, but it would make sense to have that as an option.

p. S22, middle : "cyclics"

Define 'cyclics' at the start of the paragraph, or even better when the sets of interconverting intermediates are defined.

page S25 bottom: "deg K", "degK"

Temperature in Kelvin does not have "degrees", it's just "Kelvin".

p. S26 top: "Further discussion of vapor pressure and SOA estimation methods is beyond the scope of this work."

Perhaps refer to the papers above for that discussion, rather than leave the reader hanging.