From the journal Environmental Science: Atmospheres Peer review history

13-Aug-2022

Dear Dr Farnik:

Manuscript ID: EA-ART-07-2022-000094
TITLE: Molecular-level insight into uptake of dimethylamine on hydrated nitric acid clusters

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Dr Nønne Prisle
Associate Editor, Environmental Sciences: Atmospheres

************

Reviewer 1

Review attached.

Reviewer 2

The authors performed the reaction between DMA and hydrated HNO3 resulting in (DMA)k(HNO3)m(H2O)n clusters, which provided important molecular-level details of the prelude of new particle formation. These neutral clusters were subsequently ionized into positively and negatively charged cluster ions for MS analyses. For neutral clusters, the acid and base were found to be in 1:1 ratio. Both positively and negatively charged cluster ions were found to be dehydrated and the major ions observed were (DMA)k(HNO3)mH+ and (DMA)k(HNO3)mNO3−. The authors demonstrated that the formation of the dehydrated clusters were due to energy release upon the DMA uptakes, inducing rapid water evaporation. For the positively charged cluster ions (DMA)k(HNO3)mH+, the molecular ratio of DMA and HNO3 of k=m+1 was attributed to the poor binding of HNO3 but strong in DMA uptake, hence, resulting that the evaporation of HNO3 was energetic preferable. On the other hand, the negatively charged cluster ions (DMA)k(HNO3)mNO3- showing m >=k was rationalized by the high binding energy of HNO3 and poor binding of DMA. Overall, both experimental and computational studies were in good agreement and the scientific arguments were well discussed and justified. I support its publication in Environmental Science: Atmospheres.

Comments:
For those positively charged cluster ions, the single DMA attachment is highly exothermic and sufficient to evaporate water molecules. Given the convergence of DMA evaporation at ~130 kJ mol-1, one would expect that the heat release may not sufficient to dehydrate a large cluster completely. Could the observed cluster dehydration only hold for small clusters?

For the positively charged cluster ions that satisfying k=m+1, the thermodynamics equations were as followed.
(DMA)x+2(HNO3)x(H2O)n -> (DMA)x+1(HNO3)x(H2O)n + DMA
(DMA)x(HNO3)x(H2O)n -> (DMA)x+1(HNO3)x-1(H2O)n + HNO3
Since water molecules were evaporated, would the binding energy be consistent at any number of x?

For the negatively charged cluster ions, the evaporation of DMA was more probable than evaporating HNO3 and resulted in m >= k. From n=2 to n=3, the second DMA update (purple line) was almost thermal neutral, but the update of third DMA enthalpy (blue line) became a lot favorable. Perhaps, the authors might commend on this observation.

Minor correction:
Page 3. Under 2.2 Theory. “We gathered these structures from snapshots from the previously calculated trajectories” -> “snapshots of”
Page 3. Under 2.2 Theory. “We preformed all quantum chemical calculations
in the Gaussian 16.” -> “performed”
Figure 5: Label of the y axis should be “Evaporation enthalpy”

Dear Dr Prisle,

thank you for your positive evaluation of our manuscript:
Molecular-level insight into uptake of dimethylamine on hydrated nitric acid clusters
Andriy Pysanenko, Karolína Fárníková, Jozef Lengyel, Eva Pluhařová and Michal Fárník

We have revised it according to the reviewers’ comments and answered all their questions below. We hope that you will now find our revised manuscript suitable for publication in the journal Environmental Sciences: Atmosphere.

Sincerely yours,
Michal Fárník
___________________________________________________________
Reply to reviewers
Reviewer: #1
Comments
1) It is mentioned in the abstract, as well as the conclusions that the formation of (DMA)K(HNO3)M(H2O)N clusters is atmospherically relevant. Furthermore, in the environmental significance section nitric acid and DMA is being directly linked to NPF. I believe that this is an excellent model system for understanding acid-base chemistry, but to the best of my knowledge there are no indications that this exact type of cluster favourably forms in the ambient atmosphere, nor being directly relevant for NPF by itself. Normally a stronger acid such as sulfuric acid is required. Perhaps the authors should further stress that this is used as a model system for understanding atmospheric processes instead of claiming their direct relevance.

Answer: We thank the reviewer for her/his careful reading of our manuscript and all his comments. Concerning this first one, we have modified the corresponding text in the abstract as well as on p. 2 in the following way:

Abstract: Mixed nitric acid/water clusters with dimethylamine (DMA) represent a suitable model system for understanding acid-base chemistry in atmospherically relevant clusters. We investigate these clusters in a detailed molecular-beam experiment accompanied by ab initio calculations…
P2. Left: “…These species [nitric acid and ammonia] are more abundant in polluted areas and thus nitric acid can be responsible for urban smog. Although, there are no indications that clusters of nitric acid HNO3 with dimethylamine (CH3)2NH (DMA) are directly involved in NPF in atmosphere, they represent an excellent model system for understanding detailed acid-base chemistry in the NPF process. Nanoparticle formation and growth from the nitric acid and dimethylamine was investigated before in a flow tube experiment accompanied by theoretical modelling.13…”

2) The configurational sampling was performed using Born-Oppenheimer MD. Is the simulated 20 ps trajectory sufficient to explore a representative part of the configurational space? I would suspect that the MD will confine the sampling to clusters very close to the starting geometry. Could the authors further comment on the quality of the configurational sampling. Furthermore, only 20 structures were used for the subsequent DFT optimizations at the M06-2X/aug-cc-pVDZ level of theory. How different did these 20 configurations look? Are they close in (free) energy?

Answer: The configurational sampling is certainly important and we apologize for not being precise enough in the description of computational methods. We generated one trajectory for smaller clusters containing one HNO3 unit, two for dehydrated clusters with more HNO3 units and three for larger clusters. The energy span of resulting configurations was 20 – 90 kJ/mol. We extended the text in the Methods section on p. 3:

“We generated at least one 20 ps trajectory at 300 K for each of the systems, specifically one for clusters containing one HNO3 unit, two for dehydrated clusters with two HNO3 units and three for larger clusters.
…
The energy span of the resulting structures was 20 – 90 kJ/mol.”

3) The finally applied M06-2X/aug-cc-pVDZ level of theory warrants a bit further justification. Usually, a double-zeta basis set does not lead to well converged binding energies. However, for the current study at hand where only the trends are of interest, I believe that it should give qualitatively correct results. Why did the authors use the M06-2X functional? I agree that it is an excellent choice, but perhaps refer to a benchmark study or review article (https://doi.org/10.1016/j.jaerosci.2020.105621) to further strengthen that it one of the recommended functionals for studying the binding energies of atmospherically relevant molecular clusters.

Answer: We have chosen the M06-2X functional in order to be consistent with the previous studies of systems with hydrated HNO3 (https://doi.org/10.1039/C7CP01205E, https://dx.doi.org/10.1021/acs.jpclett.0c00207) that contain comparison with CCSD(T). We have not performed any benchmarks calculations in the present study. We agree with the reviewer that we are interested in getting the trends. The choice of the basis set does not influence our conclusions. We have added justification of our choice of the functional in the Methods section on p. 3:
“The DFT functional has been chosen in order to be consistent with previous studies of systems containing hydrated nitric acid36,39 where it was benchmarked against CCSD(T). M06-2X has been shown to provide reliable results for atmospherically relevant clusters50.”

4) The authors mention the evaporation of different molecules from the clusters throughout the manuscript. Generally, evaporation coefficients are related to the free energies of the clusters and not the enthalpies (https://doi.org/10.5194/acp-12-225-2012). Hence, normally when discussing the stability of clusters, one would refer to the free energy. Could the authors comment on the importance of entropy and temperature effects in their current study. I.e., do you see the same trends when analyzing the free energies?

Answer: We used enthalpies rather than free energies to make a closer comparison with the experiment where the clusters are presumably generated with a low internal temperature (though, its exact value cannot be measured). In addition, another study (https://doi.org/10.1021/acs.jpca.9b03326) reports positive free energies of formation of small hydrated nitric acid clusters – i.e., instability against evaporation – but these clusters are observed in our mass spectra. As we performed the vibrational analysis, we checked the free energy differences at ambient conditions. Indeed, the effect of entropy is important and it decreases the binding strength, but the differences between water, DMA and HNO3 are preserved. We explain the choice of enthalpy in the revised manuscript at the beginning of Computational results on p. 5:

“Note that, throughout the whole manuscript, we use enthalpies rather than free energies52 to allow for easier comparison with the experiment where the clusters have presumably a low temperature, though its exact value is challenging to determine experimentally.”

5) The binding (free) energies/enthalpies are normally given as a negative quantity, as it is calculated as the cluster minus its isolated constituents. I assume the authors flipped the sign? It would be beneficial if this is clearly stated in the manuscript.

Answer: We use “binding strength”, “binding energy” or “energy released” without the negative sign so that stronger corresponds to larger number. Values reported in Figs. 4, 5 and 7 correspond to enthalpy change for the process of evaporation (unbinding of a molecule) as is listed in the description of the figures. We now state this explicitly on p. 5:

“We use "binding strength" or "binding energy" without the negative sign, i.e., the enthalpy change associated with the processes listed in captions of Figs. 4, 5 and 7.”
_________________________________________________
Reviewer: #2
Comments
1) For those positively charged cluster ions, the single DMA attachment is highly exothermic and sufficient to evaporate water molecules. Given the convergence of DMA evaporation at ~130 kJ mol-1, one would expect that the heat release may not sufficient to dehydrate a large cluster completely. Could the observed cluster dehydration only hold for small clusters?

Answer: We thank the reviewer for her/his careful reading of our manuscript and all his comments. Concerning this first one, it ought to be mentioned that in our experiment, the DMA is attached already to the neutral clusters and the ionization of the mixed DMA/HNO3/H2O cluster follows. Therefore, the relevant energy to consider is the energy released upon the attachment of a single DMA to the neutral HNO3/H2O cluster. This energy is not sufficient to evaporate all water molecules from the clusters, as has been discussed on p. 7-8 in the original manuscript. At the beginning of the corresponding paragraph, we argue that the number of water molecules in an average neutral HNO3/H2O cluster in our experiment is large (>=6), then we discuss the processes responsible for evaporation of these molecules:

“…The comparison of the binding energies suggest that the uptake of one DMA and subsequent acid-base reaction is sufficient to evaporate about two water molecules. In addition, the average collision energy of DMA molecules with clusters in our experiments corresponds to about 58 kJ/mol, which could lead to another single water molecule evaporation. However, this is not quite sufficient for the complete dehydration of the clusters, thus, the remaining water molecules are evaporated by both, positive and negative ionization processes.”

2) For the positively charged cluster ions that satisfying k=m+1, the thermodynamics equations were as followed.
(DMA)x+2(HNO3)x(H2O)n -> (DMA)x+1(HNO3)x(H2O)n + DMA
(DMA)x(HNO3)x(H2O)n -> (DMA)x(HNO3)x-1(H2O)n + HNO3
Since water molecules were evaporated, would the binding energy be consistent at any number of x?

Answer: Fig. 5 shows a relatively large difference between evaporation enthalpy of DMA and HNO3 for the case x = 1,2 (for clusters with different number of water molecules). We believe that it is reasonable to assume these trends preserved in clusters with a larger number of DMA and HNO3 molecules. However, since we have not done the calculations for these larger clusters, we do not comment on this point in the manuscript to avoid speculations.

3) For the negatively charged cluster ions, the evaporation of DMA was more probable than evaporating HNO3 and resulted in m >= k. From n=2 to n=3, the second DMA update (purple line) was almost thermal neutral, but the update of third DMA enthalpy (blue line) became a lot favorable. Perhaps, the authors might commend on this observation.

Answer: The reviewer is right that the presence of the third water molecule seems to stabilize the third DMA in the negative clusters However, as we do not have results for larger clusters and we do not know whether it is just a fluctuation for n(H2O) = 3 or whether it is a trend we decided not to speculate about it in the manuscript.

Minor correction:
Page 3. Under 2.2 Theory. “We gathered these structures from snapshots from the previously calculated trajectories” -> “snapshots of”
Page 3. Under 2.2 Theory. “We preformed all quantum chemical calculations in the Gaussian 16.” -> “performed”
Figure 5: Label of the y axis should be “Evaporation enthalpy”

Answer: We thank the reviewer for spotting these typos and correct them.

19-Aug-2022

Dear Dr Farnik:

Manuscript ID: EA-ART-07-2022-000094.R1
TITLE: Molecular-level insight into uptake of dimethylamine on hydrated nitric acid clusters

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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Reviewer 1

The authors have fully addressed my minor comments. This is an excellent manuscript and I advise publication as is.