From the journal Environmental Science: Atmospheres Peer review history

09-Jul-2023

Dear Dr Shields:

Manuscript ID: EA-ART-06-2023-000087
TITLE: The Driving Effects of Common Atmospheric Molecules for Formation of Clusters: The Case of Sulfuric Acid, Formic Acid, Hydrochloric Acid, Ammonia, and Dimethyl Amine

Thank you for your submission to Environmental Science: Atmospheres, published by the Royal Society of Chemistry. I sent your manuscript to reviewers and I have now received their reports which are copied below.

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Dr Tzung-May Fu
Associate Editor
Environmental Science: Atmospheres
Royal Society of Chemistry

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Reviewer 1

Review attached

Reviewer 2

Review on the manuscript: “The Driving Effects of Common Atmospheric Molecules for Formation of Clusters: The Case of Sulfuric Acid, Formic Acid, Hydrochloric Acid, Ammonia, and Dimethyl Amine” by Olivia M. Longsworth, Conor J. Bready, and George C. Shields.
Olivia M. Longsworth et al. reports a computational study on the interactions between a variety of important acid and base molecules (sulfuric acid, formic acid, hydrochloric acid (HCl), ammonia, and dimethylamine) using quantum chemical calculations. They concluded that the hydrogen bonding topology is the key factor affecting the prenucleation clusters rather than the acid-base strength. In addition, they also investigated the effect of hydration on cluster growth and found that HCl-containing clusters are more prone to hydration. These findings are valuable for understanding the underlying formation mechanism of neutral prenucleation clusters, which clearly falls within the scope of Environmental Science: Atmospheres. And this paper is clearly written and well designed, with sufficient details to support the claims. Hence, I recommend its publication after considering my comments below.
Comments:
1. Page 2, Section 2：Is there any literature support for the prediction of the monomer concentration in the top of troposphere (‘…reduced by a factor of 1000 at 217 K’)? And the monomer concentration at 298 K does not seem to be given in the corresponding literature.
2. Page 3, Section 3.3: What is the foundation for defining ‘strong hydrogen bonds’? Is there any support in other literatures, and in addition, the difference in hydrogen bond strength may be more accurately assessed quantitatively by means of wave function analysis than by the criterion of bond length and bond angle.
3. Page 10, Conclusion: The original expression "The detailed hydrogen bonding topology is more important than any conventional notions such as acid/base strength…" is somewhat absolute and could be toned down. In fact, it is not quite appropriate to be able to consider the acid/base strength and hydrogen bonding topology completely separately, because with the difference in acid-base strength, the resulting cluster structure has a different hydrogen bonding topology. The acid/base strength is the nature of the monomer, and the hydrogen bonding topology is the cluster characteristic of the two when combined.
Minor Comments:
1. Page 4: Please check if the AC/DC expression is correct. Is it ACDC?
2. Page 4 & 6: Please ensure that bond length values are retained with the same precision throughout the text; it is often inappropriate to retain only one decimal place.
3. Page 8: Please ensure uniformity in the presentation of values for monomer concentrations, for example, ‘5 x 104’ is used in page 8 and 5.00E4 in Tables 6 and 7. In addition, the precision of the values in the headings of the two tables is not uniform.
4. Please make sure that the numerical accuracy of energy is uniform.

Response to Reviewers and Editor:

Manuscript ID: EA-ART-06-2023-000087
TITLE: The Driving Effects of Common Atmospheric Molecules for Formation of Clusters: The Case of Sulfuric Acid, Formic Acid, Hydrochloric Acid, Ammonia, and Dimethyl Amine

12 July 2023

Dear Dr. Fu,

Thank you very much for the comments from the reviewers. We have made all the changes, and I have provided a point-by-point response. I have outlined what we have added in red font below after each of the comments and suggestions. I have uploaded two versions of the paper, one with all changes in red font and another with the red font changed to black. You can see the color change in the Response to Reviewers file I uploaded (color does not show up below).

We are excited to publish this second paper in Environmental Science: Atmospheres!

Sincerely,

George
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09-Jul-2023

Dear Dr Shields:

Manuscript ID: EA-ART-06-2023-000087
TITLE: The Driving Effects of Common Atmospheric Molecules for Formation of Clusters: The Case of Sulfuric Acid, Formic Acid, Hydrochloric Acid, Ammonia, and Dimethyl Amine

Thank you for your submission to Environmental Science: Atmospheres, published by the Royal Society of Chemistry. I sent your manuscript to reviewers and I have now received their reports which are copied below.

After careful evaluation of your manuscript and the reviewers’ reports, I will be pleased to accept your manuscript for publication after minor revisions.

Please revise your manuscript to fully address the reviewers’ comments. When you submit your revised manuscript please include a point by point response to the reviewers’ comments and highlight the changes you have made. Full details of the files you need to submit are listed at the end of this email.

Yours sincerely,
Dr Tzung-May Fu
Associate Editor
Environmental Science: Atmospheres
Royal Society of Chemistry

************
REVIEWER REPORT(S):
Referee: 1

Comments to the Author
Review attached

Review of Longsworth et al for Environmental Science: Atmospheres
Longsworth et al. study the cluster formation between three acid molecules (sulfuric acid (SA), hydrochloric acid (HCl) and formic acid (FA)), two base molecules (ammonia (A) and dimethylamine (DMA)) and up to three water molecules (W) using quantum chemical methods. The authors study all the combinations of the acid/base molecules from dimers to pentamers. This is the first work to study the importance of HCl in atmospheric cluster formation.

The authors employ their well-tested configurational sampling technique, which is based on a funneling approach. The final cluster configurations are optimized and thermochemical parameters are calculated at the ωB97X-D/6-31++G(d,p) level of theory. The final binding energies for the most stable clusters are calculated using a high level DLPNO-CCSD(T)/CBS calculation. Overall, the quantum chemical calculations are carried out according to state-of-the-art in the field.

The cluster structures and hydrogen bonding patterns are discussed in high detail. The calculated thermochemistry is used to explain the stability between the various cluster compositions and compared with previous work of the authors and others in the field. The calculated thermochemistry is applied to calculate the cluster equilibrium concentrations at realistic precursor concentrations. The cluster concentrations are then used to derive the most optimal cluster formation paths.
Interestingly, the authors find that nitric acid might be more important for dry pre-nucleation cluster formation, whereas HCl might be more important for hydration of a given pre-nucleation cluster. It is stressed that hydrogen bond topology is more important than the notion of acid-base strength.

Overall, the manuscript is well written, it is nicely structured and is easy to follow. I believe the calculated structures and thermochemistry are of high value to the field and the study is of broad interest to the atmospheric chemistry community. The paper should be published after the following minor comments are addressed.

Comments:
Page 1: ”Many studies have demonstrated the driving effect of sulfuric acid (SA) in forming CCN, especially in the presence of other atmospheric acids and bases.7-73 ”
I guess the authors mean clusters or new particles here, instead of CCN? Yes, we changed “CCN” to “prenucleation clusters”.

Page 2: GFN2 should be written as GFN2-xTB throughout the manuscript. Done.

Page 3, abstract: “This is because DMA is more favorable for pre-nucleation,123 especially in dry clusters”

I would suggest the authors cite the original Kurtén et al, Atmos. Chem. Phys., 2008 paper for the difference in cluster stability between ammonia and dimethylamine (DMA). Could the authors briefly comment on why DMA leads more stable clusters than ammonia? Is it basicity or hydrogen bond topology?

An excellent suggestion. We made this change throughout the paper, citing Kurten etal. It is the new reference #10, and has been cited four times where we discuss cluster stability of ammonia and DMA. We also commented on why DMA forms more stable clusters than ammonia, because of basicity. (Elsewhere in the paper, section 3.3, we had already stated that ammonia is better at hydration since the ammonium cation can donate four hydrogen bonds while the DMA cation can only donate two.) The new text in section 3.1 is:

“Every HCl-DMA-W0-3 minima undergoes proton transfer from the acid to the base, and have G values roughly 10 kcal mol-1 (9.47-11.19 kcal mol-1 at 217 K and 8.96-11.27 kcal mol-1 at 298 K) more positive than the SA-DMA-W0-3 complexes (S4,T4), resulting from DMA’s well known nucleating ability in the presence of SA.10 DMA and other amines higher gas-phase basicities than ammonia,131 and this explains why studies of these small complexes have more negative Gibbs free energies of binding relative to ammonia.10, 24, 132-134.”

The relevant text in section 3.3 is:

“Ammonium has four hydrogen bonding sites, which allows the water molecules that are added to form more stable hydrogen bond geometries than are possible with the geometry of protonated DMA, which is restricted by only having two possible sites for hydrogen bonding.”

Page 4: “Elm and co-workers have used AC/DC to predict that …”

I believe AC/DC refers to the band. The Atmospheric Cluster Dynamics Code is just abbreviated ACDC.

Yes, done.

Page 4, Figure 2: Is it possible to improve the quality of the figure? It is a bit grainy, both on screen and in printed version. Same applies to Figure 3, 4 and 5.
Page 8, section 3.7: What relative humidity (or water concentration) was used in the equilibrium cluster calculations at 298 and 217 K? This is important and we have addressed it twice, first in section 2 and again in section 3.7, Equilibrium concentrations and pathways for formation: We have also added it to the table captions for Tables 6-8 which are in section 3.7
In section 2, Methodology:
“We used a water concentration of 7.7 x 1017 cm-3 at 298 K and 9.9 x 1014 cm-3 at 217 K, which corresponds to 100% humidity at the bottom and top of the troposphere.120”




Referee: 2

Comments to the Author
Review on the manuscript: “The Driving Effects of Common Atmospheric Molecules for Formation of Clusters: The Case of Sulfuric Acid, Formic Acid, Hydrochloric Acid, Ammonia, and Dimethyl Amine” by Olivia M. Longsworth, Conor J. Bready, and George C. Shields.
Olivia M. Longsworth et al. reports a computational study on the interactions between a variety of important acid and base molecules (sulfuric acid, formic acid, hydrochloric acid (HCl), ammonia, and dimethylamine) using quantum chemical calculations. They concluded that the hydrogen bonding topology is the key factor affecting the prenucleation clusters rather than the acid-base strength. In addition, they also investigated the effect of hydration on cluster growth and found that HCl-containing clusters are more prone to hydration. These findings are valuable for understanding the underlying formation mechanism of neutral prenucleation clusters, which clearly falls within the scope of Environmental Science: Atmospheres. And this paper is clearly written and well designed, with sufficient details to support the claims. Hence, I recommend its publication after considering my comments below.
Comments:
1. Page 2, Section 2：Is there any literature support for the prediction of the monomer concentration in the top of troposphere (‘…reduced by a factor of 1000 at 217 K’)? And the monomer concentration at 298 K does not seem to be given in the corresponding literature.

We have added the literature values for the monomer concentrations. The water concentration is reduced by 3 orders of magnitude from the bottom to the top of the troposphere, and lacking experimental measurements of these molecules in the upper atmosphere we assumed that these concentrations would be reduced by a factor of 1000 as well. This is clearly just an estimate and will most likely change as measurements get better in the upper atmosphere. To reflect these ideas, we have added the following text to Section 2:

“We used a water concentration of 7.7 x 1017 cm-3 at 298 K and 9.9 x 1014 cm-3 at 217 K, which corresponds to 100% humidity at the bottom and top of the troposphere.120 Initial monomer concentrations from the literature22, 120-128 at 298 K were reduced by three orders of magnitude at 217 K to compensate for the reduction of CCN-forming particles in the upper troposphere. This is a rough estimate based on the three orders of decrease in concentration of water, and we resort to this approximation since experimental concentrations of these monomers in the upper troposphere are difficult to measure.”

In addition, as these is a key point in modeling, we also added this text in section 3.7:

“Initial starting concentrations of the monomers were 5 x 107 cm-3 for SA, 2 x 1011 cm-3 for FA, 1 x 109 cm-3 for HCl, 2 x 1011 cm-3 for A, and 2 x 109 cm3 for DMA at 298 K. These concentrations were chosen because they are atmospherically relevant over inland and urban areas. 120 30 118-125 We chose a water concentration of 7.7 x 1017 cm-3 at 298 K and 9.9 x 1014 cm-3 at 217 K, which corresponds to 100% humidity at the bottom and top of the troposphere.120 Initial monomer concentrations from the literature22, 120-128 at 298 K were reduced by three orders of magnitude at 217 K to compensate for the reduction of CCN-forming particles in the upper troposphere. This rough estimate is based on the three orders of magnitude decrease in water concentration, and we used this approximation since experimental concentrations of these monomers in the upper troposphere are difficult to measure.”

2. Page 3, Section 3.3: What is the foundation for defining ‘strong hydrogen bonds’? Is there any support in other literatures, and in addition, the difference in hydrogen bond strength may be more accurately assessed quantitatively by means of wave function analysis than by the criterion of bond length and bond angle.

This is a good point. A quantitative analysis of hydrogen bond strength is beyond the scope of this paper, so we have removed the word “strong” in every occurrence, such that we talk about “hydrogen bonds” and “van der Waals interaction” without labeling any hydrogen bonds as strong.

3. Page 10, Conclusion: The original expression "The detailed hydrogen bonding topology is more important than any conventional notions such as acid/base strength…" is somewhat absolute and could be toned down. In fact, it is not quite appropriate to be able to consider the acid/base strength and hydrogen bonding topology completely separately, because with the difference in acid-base strength, the resulting cluster structure has a different hydrogen bonding topology. The acid/base strength is the nature of the monomer, and the hydrogen bonding topology is the cluster characteristic of the two when combined.

This is a really good point. We have toned down the language to reflect the nuanced nature of these clusters. The new language that replaces the hydrogen bond topology sentence above is:

“Many subtleties are at play in the beginning stages of pre-nucleation and the importance of different factors changes with the system being investigated. Hydrogen bonding topology, acid/base strength, and complex structural interactions all play an important role in structure energetics and atmospheric relevance. Sometimes detailed hydrogen bonding topology is as important as conventional notions like acid/base strength, which makes a priori prediction of which atmospheric species will be most important for driving prenucleation growth quite difficult. Complexes with DMA and various acids form stronger dry complexes than does ammonia, yet the sequential hydration energies favor ammonia since the ammonium cation can form up to four hydrogen bonds while protonated DMA can only form two.”

We changed the last line in the Abstract to reflect his point as well:

“The results presented in this paper add to the conclusions that hydrogen bond topology and the detailed structural interactions that are subtle interplays between enthalpy and entropy are as important as conventional ideas such as acid/base strength.”

And we changed the second to last sentence in the Conclusion as well:

Taken as a whole, the results presented in this paper add to the conclusions that hydrogen bond topology and the detailed structural interactions that are subtle interplays between enthalpy and entropy can be as important as conventional ideas such as acid/base strength.

Minor Comments:
1. Page 4: Please check if the AC/DC expression is correct. Is it ACDC? Yes, fixed.
2. Page 4 & 6: Please ensure that bond length values are retained with the same precision throughout the text; it is often inappropriate to retain only one decimal place. Done. Two decimal places throughout. See red font in paper.
3. Page 8: Please ensure uniformity in the presentation of values for monomer concentrations, for example, ‘5 x 104’ is used in page 8 and 5.00E4 in Tables 6 and 7. In addition, the precision of the values in the headings of the two tables is not uniform. Fixed. See red font in paper.
4. Please make sure that the numerical accuracy of energy is uniform. Done.

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28-Jul-2023

Dear Dr Shields:

Manuscript ID: EA-ART-06-2023-000087.R1
TITLE: The Driving Effects of Common Atmospheric Molecules for Formation of Clusters: The Case of Sulfuric Acid, Formic Acid, Hydrochloric Acid, Ammonia, and Dimethyl Amine

Thank you for submitting your revised manuscript to Environmental Science: Atmospheres. I am pleased to accept your manuscript for publication in its current form. I have copied any final comments from the reviewer(s) below.

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Environmental Science: Atmospheres
Royal Society of Chemistry

Reviewer 1

The authors have adequately addressed the minor comments from both reviewers. The paper should now be accepted for publication.