Estimation of Rate Constants for Reactions of Organic Compounds under Atmospheric Conditions

Round 1

Reviewer 1 Report

The manuscript describes a new structure and reactivity (SAR) method for estimating the reaction rate coefficients of free radicals with hydrocarbons under atmospheric conditions. Although other SAR methods have been developed, the newly designed method uses a recently published database for atmospheric reactions, allowing estimating rates for more types of compounds. Overall, the RAS gives satisfactory results and compares well with other methods. The main limitations are the need for “expert judgment” for the choice of parameters to adjust or estimate and the lack of methods do derive uncertainty ranges. Still, the proposed SAR is an improvement due to its used of an extensive rate coefficient database. Although I am not an expert in the development of SAR for reaction kinetics, I understand the need for their development and validation. The author goes through a very exhaustive description of the method and its validation. I also appreciate the discussion of the method limitations and the mention of the SAR evaluation working group. Overall, I strongly recommend publication of the manuscript in Atmosphere. I only have some minor syntax comments:

Line 260 the sentence does not read well

Line 268 “This is used all cases” missing in

Line 292 “were found significantly” missing to

Line 599 add a . before The

Line 892 “the author in” missing is.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

This manuscript describes a set of structure-activity relationships (SARs) that help predict the rate coefficients for the reactions of VOCs with OH, Cl, O3, and O(3P). These SARs are useful in the generation of (near)explicit atmospheric kinetic models, and are implemented in the SAPRC software suite. The SARs are derived based on an extensive database of experimental rate coefficients (i.e. no product or theory-based data were used) and aim primarily to reproduce total rate coefficients at room temperature. Still, some site-specific information is given by virtue of the constituting individual rate coefficients summed into the total rate, where minor channels may be ignored by the SAR. Likewise, some T-dependencies are given, helping to span the temperature range in the atmosphere where most VOC oxidation occurs. The SARs are found to have good predictive power, even if the reliability is somewhat less for more complex multi-functionalized species. These SARs will be of use primarily in the software-assisted derivation of models ; manually predicting rates seems too elaborate to do on a regular basis given that the predictive expressions are complex and require a lot of parameters. At the same time, in view of the complexity of the application, I don't feel that the SAR can or should be simplified as the parameters are mostly chemically meaningful, and removing parameters for the sake of simplification would negatively impact the predictive power.

 

I have no remarks that impact the core of the paper, and nearly all of the comments below pertain to typographical or linguistic aspects. Many of these are mere suggestions on minor things and it is up to the author whether he incorporates modifications to address these suggestions. I support publication of this paper.

 

Below, references are given by line numbers as provided by Atmosphere in the preprint.

 

* General comments:

 

The manuscript would benefit from having a few elaborate examples on the use of the SAR, i.e. referencing the equations and parameters used, listing the values of those parameters and the results of the intermediate calculations, name the tables where those parameters can be found, etc. I propose adding such examples in section 4, or at least refer to examples in the SI at that point.

 

It would be useful to mention early on that the SAR does not try to cover ALL pathways, only the main ones, and that the others are assumed negligible.

 

There is little to no mention of stereo-specificity, and while most compounds are not affected some will have a different rate of abstraction / addition for different sides of the molecule (a-pinene, b-pinene,...). This should be commented on. It could also be worthwhile to add a short section specifically discussing how well the SARs work for stereo-specific compounds that are considered explicitly in the underlying database (e.g. Z/E-alkenes).

 

The scope and rate constant database section mentions peroxy groups (line 86), but their treatment is not clear in the SAR, e.g. Table 1 has no -OO- entry, and no parameters are given explicitly dealing with peroxy groups. This should be discussed more explicitly.

 

O3P is used as notation, while electronic state information is usually enclosed in brackets: O(3P)

 

ipso/ortho/meta/para ; cis / trans : not always italicized

 

There are a few instances where a reaction mechanism is "assumed" (e.g. p. 23 in SI "We assume that the initial reaction is transfer of an O atom from O3 to the amino group, forming O2 and an amine oxide"). While I acknowledge that the SAR is derived based on experimental data only, it would make sense to look at some theoretical studies to see if such mechanistic assumptions of addition (or strong complex formation) vrs. abstraction are warranted, without having to resort to a full literature overview.

 

line 159 and beyond: "Although the limited database of O3P rate constants can be fit about as well by either method, the method used for O3 was employed", and similarly for line 388-392.

This wording is vague and thus hard to interpret. I feel the text could be made more readable by using terminology like "cycloaddition" for O3 and O(3P), while using H-abstraction and chain addition for OH / Cl.

 

line 669-675: -C(O)-O- has an sp2-hybridized carbon (planar center with angles of 120 degrees), while -O- does not (tetrahedral angles of ~107-115 degrees). The geometric difference may explain the large difference in correction factor.

 

line 799: "Rate constant measurements for targeted compounds could reduce the number of instances where estimated parameters that could not be experimentally verified had to be used".

Any suggestions for such compounds ?

 

* Specific comments:

 

line 8: "Structure and reactivity (SAR)". SAR is usually taken as the acronym for "structure-activity relationship"

line 33: "Predictions the lifetimes" : insert "of"

line 64: "for estimating initial reactions of" : insert "rates"

line 90: "an attempt was initially made to also include compounds with...". Superfluous, just mention that the methods employed do not work satisfactorily and that they are not covered.

line 105: "greatly reducing greatly reducing" : remove repetition

line 119: "used in previously" : remove "in"

line 145: "Summary of numbers of numbers" : remove repetition

line 148: "estimates are made in include" : remove "in"

line 150: "rings, and additions..." : remove "and"

line 167: "presence of these group by the reaction site" : replace "by" with "on" or "near"

line 169: "due to characteristics of the molecule". All parameters refer to characteristics of the molecules. Perhaps "compound-specific" or "unique" characteristics?

line 228: "the order they were derived" : add "in which"

line 256 and elsewhere: non-consistent use of "non-hydrocarbon", "non-alkyl", ...

line 260: "insufficient data to overall correction factors" : replace "overall" with "derive" ?

line 266: "individual groups their product" : insert "when"

line 267: "susbsituents" : correct to "substituents"

line 268: "This is used all cases" : insert "in"

line 277: "also the values so derived are significantly different" : change to "and where the values so derived are also significantly different."

line 287: "by NO3 radicals, and better results" : insert "are needed" before comma

line 292: "were found significantly improve" : insert "to"

line 306: "-C<" : correct to "-CH<"

line 354: "No structural correction where used" : correct to "were"

line 484: "substation" : correct to "substituent"

line 566: "298⁰K" : Remove degree symbol

line 574: "ignoring knows temperature" : correct to "known"

line 595: "performance or our" : correct to "of"

line 605-606: indicate how many compounds these worst 1% / 10% are represent

line 623: Header 4.3 is not on its own line

table 4 : gamma-crotonolactone, beta-caryophyllene : use greek letters

line 683: "reactions or organcis" : correct to "of" and "organics"

line 686: "atomsphereic" : correct to "atmospheric"

line 693 : "there are published estimate" : correct to "estimates"

line 699: "ethyl methacrylate, for O3, allyl acetate" : remove comma before "for O3"

line 699: "notroethene" : correct to "nitroethene"

line 702: "performace" : correct to "performance"

line 706: "distributons" : correct to "distributions"

line 732: move "(e.g., [28.29]" to the comma just after "with OH" for better readability

line 733: "Jenkin et al [30,31]. Kerdouci et al [32]" : change period to comma

line 758: "reactions, a relationship" : insert "or"

line 764: "given uncertainties and in rate" : remove "and"

line 805: "compounds that are difficult to make or study experimentally". Replace "make" with "synthesize"?

line 889: "should undergo through peer review" : correct to "thorough"

line 892: "the author in a SAR evaluation" : add "is"

line 896-898: Remove "S1", S2", "S3" in this sentence, as they is not needed here and make the sentence harder to read.

line 996: "last accessed August 9" : add year

 

* Comments on the supplementary information

 

p. 4 : "in the reviews of Calvert et al (2000, 2002, 2011, 2015) and the IUPAC (2019) and JPL (2015)," : replace last half of sentence with "...2015), IUPAC (2019), and JPL (2015)"

p. 4: "and results from a number of publications" : rephrase to "and supplements these with results from a number of publications"

p. 5, 6, 23 : "section 0" : correct section number.

p. 6: "could be affected experimental difficulties" : insert "by"

p. 6: "with the with the method" : remove repetition

p. 6: "Only these few compounds were excluded" : provide the number of compounds omitted thus.

p. 8 was empty

p. 12 : "FHnhr" : correct to "FHnbr"

p. 12: "Base rate constant for addition if a radical to group G1" : correct "if" to "of"

p. 12: "G2 by a double by a double bond, where" : remove repetition

p. 13: "Based on these results in and other consideration" : remove "in"

p. 14: "compared to those for OH or Cl reactions, where the kinetic database" : remove comma

p. 14: "from - [linebreak] CH3 group" : keep "-CH3" on a single line

p. 14 table on bottom : inconsistent number of significant digits

p. 15: "In the case of additions amine or amide groups" : insert "on"

p. 16: "based on and the ~5% yield of furan products" : remove "and"

p. 17 footnote 4 : "is the same the base rate constant" : remove "the"

p. 18: "but available are sufficient to derive group parameters" : correct "available" to "the available data"

p. 19 table S9 bottom : "X = - [linebreak] CO-O-" : keep "-CO-O-" on a single line

p. 21 bottom: "after an H shift by from the alpha hydrogen" : remove "by"

p. 21 bottom: "G1=G2 + O3 -> *G1-G2-O* Epoxide" : oxidant should be "O(3P)"

p. 23: "it is performs much better than" : remove "is"

p. 23: "where both is possible" : correct to "are"

p. 23: "we roughly that abstraction" : insert "estimate"

p. 25: Start section S2 on a new page

p. 28 note (3): "Usedthe same A factor as for the..." : insert space between "used" and "the"

p. 30 top: "Table S11 (continued)" : This is table S12

p. 32 top : "Table S11 (continued)" : this is table S13

p. 34 top : "Table S12 (continued)" : this is table S14

p. 37 top : "Table S17 (continued)" : this is table S16

p. 37 footnote (1) : "are assumed to half of the base rate constant" : insert "be"

p. 38 top : "Table S17 (continued)" : this is table S16

p. 39 top : "Table S17 (continued)" : this is table S16

p. 41 top : "Table S16 (continued)" : this is table S17

p. 41 footnote 1 : "and nitro or nitrato compounds" : correct "nitrato" to either "nitrate" or "nitrooxy"

p. 43 top : "Table S17 (continued)" : this is table S18

p. 44 top : "Table S17 (continued)" : this is table S18

p. 44 footnote (2): "between the number of substitutnts" : correct "substituents"

p. 45 top : "Table S17 (continued)" : this is table S18

p. 47 footnote (8) : "furan corrections for for furans" : remove repetition

p. 49: Start section S3 on a new page

p. 95 footnote [b] : "sources of experimental data are as follows" : add "(see section S4)"

 

Table S12, S13, S14, S17, S20 : Notation "-BR" instead of "-Br", inconsistent with notation of "-Cl" and bromine substituents in other groups

 

Inconsistent use of capitalization on "Saturated":

p. 27: "Acyclic Saturated oxygenates"

p. 32: "Acyclic Saturated xxxxxx" (multiple lines)

 

Table S21, S22, S23, S24: inconsistent spacing, capitalization, greek letters, stereo-indication

"2,2-Dimethyl Pentane" to "2,2-dimethylpentane"

"2,2-Dimethyl Hexane" to "2,2-dimethylhexane"

"2-Methyl Octane" to 2-methyloctane"

"4-Methyl Octane" to "4-methyloctane"

"2,3,5-Trimethyl Hexane" to "2,3,5-trimethylhexane"

"2,6-Dimethyl Octane" to 2,6-dimethyloctane"

"2-Methyl Nonane" to "2-methylnonane"

"3,4-Diethyl Hexane" to 3,4-diethylhexane

"1,1,3-Trimethyl Cyclohexane" to "1,1,3-trimethylcyclohexane"

"Hexyl Cyclohexane" to "hexylcyclohexane"

"2-Octanol", "3-Octanol", "4-Octanol" to "2-octanol",...

"trans / cis" versus "(Z) / (E)" notation (many compounds)

"Methyl Isopropyl Carbonate" : lowercase

"iso- butyl nitrate" : remove space

"e-2-pentenal" to "(E)-2-pentenal"

"e-3-methyl-3-penten-2-one" to "(E)-3-methyl..."

a-phellandrene, a-terpinene, b-phellandrene, b-pinene, g-terpinene, a-pinene, beta-caryophyllene, a-copaene, gamma-butyro-lactone, beta-butyro-lactone, delta-valero-lactone, gamma-crotonolactone, beta-ionone, trans-beta-methylstyrene : use greek letters

"1-Methoxy-2-Propyl Acetate" : correct caps and space

"Methoxy Acetone" : caps

"trans-1-methyl-1.2-dinitrooxycycloohexane" : remove space before compound name, replace period with comma, remove second "o" in "cycloohexane"

"3-methyl--2-buten-1-ol" : correct doubled hyphen

"z-butenedial", "3(e)4-methylhex-3,5-dienal", "4-methylhex-3(z),5-dienal", etc... : stereospecifier should be capital

Missing stereospecifier : "4-hexen-3-one", "4-methyl-3-penten-2-one", "3-methyl-3-pent-2-one", 3-hepten-1-ol", "3-octen-1-ol", "1-chloro-2-butene"

"Methylamine", "Dimethyl Amine", "Trimethyl Amine" : caps and spaces

"3h-furan-2-one" to "3H-furan-2-one"

 

p. 96-97: Inconsistent reference notation :

add brackets around publication year: Atkinson 1997, Atkinson 1978, Deslauriers 1986, Lauraguais 2016, Yang 2016, Zhang 2016

Jenkin 2020 : remove "2" after "Valorso2"

JPL 2015: "ocrober" : correct to "October"

Yang 2016: add comma before journal name

 

Author Response

Please see the attached.

Author Response File: Author Response.pdf

Reviewer 3 Report

The paper is well written with important research findings, thus I recomend to accept in present form.

Author Response

I wish to thank the reviewer for the favorable comments. No response is necessary.