Dear Peter Huszar and co-authors,
Thank you very much for promptly letting me have a revised copy of your manuscript. I am happy with the content, but would like to recommend quite a long list of changes to aid clarity. These changes are listed below. Once these changes are made, I hope we can move quickly to acceptance,
Sincerely,
Rob MacKenzie

Corrections:
I don’t insist, but I think that if you presented some typical numbers for eddy diffusivity coefficient somewhere in the Introductory material, you would help readers understand when the effects you see are small or large. Perhaps you could report some measured values for situations readers would recognise, like a still night and a convective cloud.

Abstract, line 9: I suggest “plays a role too, reducing” or “plays an important role too, reducing”

Abstract, line 18 and ff. Is the symbol for the vertical eddy diffusion coefficient as clear as it could be? It reads to me like two separate parameters, K and \nu.

Abstract, line 20 or thereabouts. I feel it would be good to have a sentence here explaining why you’ve focused on ozone and PM2.5, which have regional sources and sinks, rather than, say, NO2 and PM1, which would be more closely tied to the urban areas. The abstract is your opportunity to entice the reader into reading the detail of the paper and I think you miss a bit of that from a chemical perspective.

Abstract, line 22: maybe the following is more explicit, as so helps avoid doubt “cascading domains (of 27, 9, and 3 km horizontal resolutions), which further”

Abstract, p2, line 2. The well-known difficulty of describing ranges of negative numbers arises here. Since -3 m/s is less than -2 m/s, I don’t think we can use ‘up to’. How about either “decreases of up to 2 m s-1”, or “wind (anomalies as negative as -2 m s-1”? This is a pedantic point but is probably worth trying to fix to help those with shaky English and maybe also not too much experience in meteorology.

Page 2, line 3. “a few 0.5” doesn’t work in English I feel. Either simple “from a few” or “from less than one”

Page 2, line 4. I suggest “methods. The turbulent” or “methods; the turbulent”

Page 2, line 6-9. How about putting equivalent relative changes in parentheses, to help the reader be sure they understand the magnitude of these changes in ozone and PM?

Page 2, line 12. Replace “counterweights” with “counterbalances”

Page 2, line 18. This kind of use of ‘while’ is a bit clumsy in my book. It looks like you tend to use it instead of a full stop or at least a semi-colon. I would encourage you to simplify your writing by replacing this use of while with a full-stop predominantly.

Page 2, line 23. I think we need to acknowledge the contribution of researchers other than yourself and Maria Kanakidou in understanding the sources of pollutant emissions in cities. Please replace these citations with at least three wide-ranging reviews reaching back to the 1970s at least.
Page 2, line 26. This gives a slightly better view of urban climate studies reaching back to the 1980s, but I’d still recommend providing some other reviews that would inform a reader who wants to track down some of the historical development of our understanding. There is a whole series of reviews by AJ Arnfield that would help - eg
Arnfield, A.J., 2003. Two decades of urban climate research: a review of turbulence, exchanges of energy and water, and the urban heat island. Int. J. Climatol. 23, 1–26. https://doi.org/10.1002/joc.859
There is Chandler’s classic: Chandler, T.J., 1966. The climate of London. By T. J. Chandler. London (Hutchinson), 1965.
Also: Duckworth, F.S., Sandberg, J.S., 1954. The Effect of Cities upon Horizontal and Vertical Temperature Gradients. Bull. Am. Meteorol. Soc. 35, 198–207
The more fluid dynamical perspective of Steve Belcher — S. E. Belcher, Mixing and transport in urban areas. Phil. Trans. R. Soc. A. 363, 2947–2968 (2005) — could perhaps support sentences which follow.

Page 2, Line 30. Should be “drag triggers mechanical turbulence, which enhances vertical mixing …and contribute to an increase of…” I’ve reversed the order because I think logically it is the mixing [of heat and momentum] that induces the PBL height change.

Page 3, line 3. I think “current” rather than “up-to-date”

Page 3, lines 5-6. I think a spatial scale is required here: “forcing on local-to-regional scale meteorological variables”? Or just local scale?

Page 3, lines 6-7. The changes you’ve made haven’t helped. I suggest deleting the first clause and starting the sentence at “Modifications in…”

Page 3, lines 9-10. Can’t say “many authors” and then cite only yourself and one other. How about taking out everything from “as already shown…” just leaving in the citations but adding some of the other refs you already have: Baklanov et al, Chen et al, Falasca and Curci, Fallman et al, and so on.

Page 3, line 13. The influence of temperature on reaction and nucleation rates is direct; that on deposition is more indirect I’d say. Perhaps add ‘direct’ and ‘indirect’ at the relevant places in the sentence?

Page 3, line 18-19. You need to be more careful here. Did Tao et al. attribute the dry deposition change to increased temperature, or is this your surmise? Surely change in leaf area is a more plausible driver of urban rural change?

Page 3, line 26. I suggest “stilling, or stagnation,” to help readers as yet unfamiliar with the term stilling.

Page 3, line 33. “It has to be noted here…” should be the start of a new paragraph. The preceding two sentences should summarise the foregoing arguments that changes to Bowen ratio and changes to drag increase turbulence over cities and alter the PBL.

Pages 3-4. I think you weaken your own arguments here unnecessarily. Ozone and PM2.5 cannot be properly understood without diagnosis of processes occurring on the regional scale.

Page 4, lines 1-34. Please split by topic into at least three paragraphs.

Page 4, line 4. Should be “ground-level primary pollutant concentrations”. See also line 9. ‘Reduction of NOx’ is a poor grammatical construction on two grounds: (i) reduction could mean chemical reduction; and (ii) the NOx is still present, just dispersed through a greater volume of atmosphere.

Page 4-5. You need to acknowledge that the urban canopy meteorological parameters are very tightly coupled, which probably explains why they have not been studied separately by previous authors. You should then introduce your argument for studying turbulence in isolation, and how you propose to do this in a logically consistent way. Perhaps one of the logical gaps in your argument is that you don’t distinguish clearly enough between online (eg WRF-Chem) simulations, in which it would be very difficult to separate out vertical eddy diffusivity, and offline (eg CAMx) studies in which the eddy diffusivity can be treated as a separate parameter. Please consider how you might make this point clearer in your argument to this point.

Page 5, line 13ff. I suggest phrasing as questions: “The questions arises here: how does the uncertainty…propagate to species concentrations? Does the dominant role of turbulence hold…calculation?” The next para is then “Our paper is motivated by the questions above…”

Page 5, lines 20-22. This repeats one of the questions in the previous para. Delete.

Page 6, line 4: should be “…2012; referred to below as RegCM4), serving…”

Page 6, line 6. Need a citation for a description of MM4 or describing the conversion of MM4 into RegCM4, even if the citation is Giorgi et al. (2012).

Page 6, line 6. Replace ‘It’ with ‘RegCM4’

Page 6, line 9. Should be “…, the scheme from the NCAR…”

Page 7, line 2. Should be (ENVIRON, 2018)

Page 7, line 34. “through” not “trough”

Page 8, line 15. Provide an approximate equivalent height for 50 hPa, based on a standard value for the scale height.

Page 8, line 19ff. I could not be sure how the chemical domains were set up in the vertical. Please provide more detail in text or in a figure showing how the domains map onto each other.

Page 9, line 12. Delete ‘while’: “MEGAN. For each gridbox, …”

Page 9, line 18. Change to: “particular city (i.e., crops predominantly).”

Page 10, line 19. “at each resolution…”, not resolutions

Page 11, line 5. A more concise version might be: “Below, we use the term ‘modeled surface values’ to mean…”

Page 11, line 9. Expand: “(i.e., conform to the FAC2 criterion)” and cite a source for that criterion as a measure of model-data goodness-of-fit.

Page 11, line 18. Repetition of words and grammar glitch. Should be maximum is or maxima are.

Page 11, line 31. Metric not metrics

Page 11, line 33. “The FAC2 statistic…”

Page 11, line 34. I don’t understand why the following clause is included “it is usually higher for urban stations”. Is this your opinion? Based on what? I think a citation or further explanation is needed. It should be separated by a semi-colon from the preceding clauses.

Page 13, line 5. Expect should be except?

Page 13, line 18. Can I suggest using the 24-hour clock to be absolutely explicit (because 12 midnight is ambiguous)? So “(22:00 to 24:00 local time)”. It’s not ambiguous in the following sentences but you might convert all local times to the 24-hour clock for consistency.

Page 15, line 19. “supremacy” is not the right word. “These two methods still produce the largest values…”?

Page 15, line 21 and line 28. Full stops before however.

Page 15, line 27. Where should be were

Pages 15-16: quotation marks are wrong – please check placement of start-quote and end-quote marks. See also page 16, line 25.

Subsection 3.3.1. Please report relative changes in chemical constituents, as a percentage, as well as absolute changes.

Page 19, line 13ff. Please split this paragraph into two or three paragraphs, by topic.

Page 21, line 31. Outweigh, not overweight

Page 22, line 2. Capital k in K

Page 22, line 10. “emissions were…” not “emission where…”

Page 22, line 29. Perhaps “reaching” rather than “up to”?

Page 23, line 4. Span not spawn. This sentence doesn’t really work. The two order of magnitude are spanned in the upper levels. So, I suggest “Near surface Kv modifications range from 0.5 to 30 m2/s. Over higher model levels the impact spans two orders of magnitude, i.e., 1 to 100 m2/s”

Page 23, line 30, Full stop instead of while. Semi-colon instead of while in line 31.

Page 23, line 34-35. I can’t understand the sentence beginning “The more important role”. Could you re-phrase, please, trying to avoid confusing combination of “stronger…more important…reduced…higher.”

Page 24, line 9. “eddy diffusion removal” does not make physical sense. I think you mean “due to the dominance of dispersion by increased eddy diffusion”

Page 24, line 31. This sentence is almost impossible to follow because of all the increases and decreases. Please gather together factor increasing ozone concentrations and those decreasing ozone concentrations into two separate sentences.

Page 25, line 1. Outweighed, not overweighted

Page 25, line 9ff. Has already been said. No need to repeat.

Figures 10, 12, 29, 31 captions. You must acknowledge the two y-axes. So “Solid lines (left-hand axes)…experiment; dashed lines (right-hand axes)…”