The SAPRC Atmospheric Chemical Mechanism Generation System (MechGen)

Carter, William P. L.; Jiang, Jia; Wang, Zhizhao; Barsanti, Kelley C.

doi:https://doi.org/10.5194/egusphere-2025-1183

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https://doi.org/10.5194/egusphere-2025-1183

Preprints

09 May 2025

| 09 May 2025

The SAPRC Atmospheric Chemical Mechanism Generation System (MechGen)

William P. L. Carter, Jia Jiang, Zhizhao Wang, and Kelley C. Barsanti

Abstract. MechGen is a software system designed to derive gas-phase reaction mechanisms for reactive organic compounds under atmospherically relevant conditions for use in chemical models and for data analysis and interpretation. It has been used to derive versions of the SAPRC mechanisms used in airshed models, with SAPRC-22 being the most recent. MechGen derives fully explicit mechanisms for many types of organic compounds and their oxidation products when they react in the atmosphere in the presence of oxides of nitrogen and other pollutants, and then uses these explicit mechanisms to derive reduced or lumped mechanisms more suitable for use in airshed models. This paper gives an overview of the system, describes the procedures it uses to generate explicit and reduced mechanisms, and presents several types of applications. The assignments and estimates used to derive individual chemical reactions and assign rate constants are discussed in a separate companion paper. The system is publicly accessible for generating explicit mechanisms for single compounds and viewing associated documentation using a web-based interface. A separate terminal login is available for deriving mechanisms for multiple compounds, multi-generation mechanisms, and portions of lumped mechanisms for airshed models, as well as for system programming and management. MechGen is designed to accommodate updates to the chemical estimates and assignments that it uses to reflect our evolving knowledge of and ability to estimate atmospheric reactions of organic compounds.

Received: 12 Mar 2025 – Discussion started: 09 May 2025

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William P. L. Carter, Jia Jiang, Zhizhao Wang, and Kelley C. Barsanti

Status: closed

RC1: 'Comment on egusphere-2025-1183', Rolf Sander, 23 May 2025

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.

Citation: https://doi.org/10.5194/egusphere-2025-1183-RC1
RC2: 'Comment on egusphere-2025-1183', Anonymous Referee #2, 27 May 2025

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.

Citation: https://doi.org/10.5194/egusphere-2025-1183-RC2
AC1: 'Comment on egusphere-2025-1183', Kelley Barsanti, 18 Aug 2025

We thank the reviewers for their thoughtful comments. We have attached our responses to those comments and associated edits, here.

Citation: https://doi.org/10.5194/egusphere-2025-1183-AC1

Status: closed

RC1: 'Comment on egusphere-2025-1183', Rolf Sander, 23 May 2025

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.

Citation: https://doi.org/10.5194/egusphere-2025-1183-RC1
RC2: 'Comment on egusphere-2025-1183', Anonymous Referee #2, 27 May 2025

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.

Citation: https://doi.org/10.5194/egusphere-2025-1183-RC2
AC1: 'Comment on egusphere-2025-1183', Kelley Barsanti, 18 Aug 2025

We thank the reviewers for their thoughtful comments. We have attached our responses to those comments and associated edits, here.

Citation: https://doi.org/10.5194/egusphere-2025-1183-AC1

William P. L. Carter, Jia Jiang, Zhizhao Wang, and Kelley C. Barsanti

Supplement

https://doi.org/10.5194/egusphere-2025-1183-supplement

Data sets

User Manual William P. L. Carter et al. https://github.com/SAPRC/MechGen/blob/master/docs/MechGenMan.pdf

William P. L. Carter, Jia Jiang, Zhizhao Wang, and Kelley C. Barsanti

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Short summary

The SAPRC Atmospheric Chemical Mechanism Generation System (MechGen) generates explicit chemical reaction mechanisms for organic compounds. MechGen has been used for decades in the development of the widely-used SAPRC mechanisms. This manuscript, detailing the software system, and a companion manuscript, detailing the chemical basis, represent the first complete documentation of MechGen. This manuscript includes examples and instructions for generating explicit and reduced mechanisms.


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