Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GC-MS ANALYSIS OF PHYTOCHEMICAL COMPOUNDS OF OPUNTIA MEGARRHIZA (CACTACEAE), AN ENDANGERED PLANT OF MEXICO
Review round: 2
Reviewer: 2

Output:
Basic reporting: The author has substantially improved the manuscript and incorporated major of the reviewers' suggestions. However, regarding the extracts identification, the identity of five compounds was tentatively confirmed by correlation with standards.  However, the remaining 48 compounds were identified based only on the mass spectra comparison. With the possibility to easily apply the Linear retention index analysis, I keep the suggestion to use it.
More important, even with the use of the pure standards, the mass spectra for the standard benzothiazole (Figure S5-A) are not comparable to the spectra of the benzothiazole in the extract (Figure S3-A). The fragmentation patterns are very different. The same occurs to the heneicosane. In addition, for a better comparison, the retention times should be informed in the standard cromatograph spectra.
The spectra presentation and analysis still is the main concern and requires attention.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In addition, it is still possible to identify some typos.
Line 121. I suggest replacing the expression “These solutions were mixed by centrifuge one hour” with “These solutions were vortex mixed one hour “. I believe that in this case, a centrifuge was not used once it accelerated particle sedimentation. Thus, this procedure has to be checked.
The nomenclature of the compounds still requires revision. The library software has some limitations regarding to the way how the nomenclature is displayed. Thus, in the main manuscript, the prefix such cis or trans, (Z) or (E) has to be italicized. Also, the prefix (R)-, (S)-,  n-, tert-. The nomenclature en the Tables also has to be revised.
In this way, I strongly suggest revising de nomenclature of the compounds following the IUPAC rules. Otherwise, I suggest including in the experimental Section that the Chemical Abstract nomenclature is used.
Line 208: CHCl3 and not CHCL3. In the line 2019 and 220 also.
Line 213: For retention time, I suggest using tR or RT instead of Tr. The abbreviation for minute is “min” and does not require de dot.
Line 217, 218, and 219. It is missing the open parenthesis in the acetone formula.
In the Figure 2 caption, the representation of methanol must be corrected. MeOH and not MeOTH. In addition, the Figure 2 caption mentions the CH3CN extract. According to the main text, it should be chloroform (CHCl3) and not acetonitrile. It has to be checked.
Figure 3. replace MeOTH with MeOH, and the use or not of CH3CN has to be checked.
In Figure S2, the chemical structure shown in the spectra (B) does not represent the Phenol, 2,4-bis(1,1-dimethylethyl-), but its silyl ether derivative. It is also observed in Figure S4, spectrum A. Please revise it.
In Figure S5, the spectrum F comes after spectrum D. The retention times for each standard should be informed for comparison with the extract chromatograms.
Also, the mass spectra for the standard benzothiazole (Figure S5-A) are not comparable to the spectra of the benzothiazole in the extract (Figure S2-A).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GC-MS ANALYSIS OF PHYTOCHEMICAL COMPOUNDS OF OPUNTIA MEGARRHIZA (CACTACEAE), AN ENDANGERED PLANT OF MEXICO
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The major revisions request were considered by the authors and now the manuscript is suitable for publication.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NEW INSIGHTS INTO THE MECHANISM OF SCHIFF BASE SYNTHESIS FROM AROMATIC AMINES IN THE ABSENCE OF ACID CATALYST OR POLAR SOLVENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article appears to meet the stated standards.
Experimental design: This article appears to meet the stated standards.
Validity of the findings: I have concerns about the results. While the calculations were rather straightforward, the conclusions seem to be drawn on particular orientations of a single water molecule. To my mind, the authors would need to sample a multitude of possible orientations to assure that configuration space is adequately covered to draw meaningful conclusions. In addition, I worry about carrying out such sampling in the presence of a continuum rather than a large number of explicit solvent molecules.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NEW INSIGHTS INTO THE MECHANISM OF SCHIFF BASE SYNTHESIS FROM AROMATIC AMINES IN THE ABSENCE OF ACID CATALYST OR POLAR SOLVENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Manuscript is very well written. I suggest addition of discussion to the introduction regarding importance of understanding Schiff base formation. I would also suggest substituting "apolar" for "nonpolar" throughout.
Experimental design: Methods are likely to be adequate. However, I suggest the authors add discussion on the appropriateness of the PBE0 method for such systems.
Validity of the findings: All data provided are appropriate.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NEW INSIGHTS INTO THE MECHANISM OF SCHIFF BASE SYNTHESIS FROM AROMATIC AMINES IN THE ABSENCE OF ACID CATALYST OR POLAR SOLVENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a purely computational study investigating pathways towards imine synthesis with specific emphasis on solvent effects. Prior work has been referenced appropriately. I have no problem with this being an entirely computational study without any experimental evidence, however, as outlined further below, I do have some concerns regarding the methodology that has been used and the reliability of the results. I also find the discussion relatively short and feel the author could elaborate more on the findings. A few things, which I will mention below, are not quite clear and hence it would be difficult to reproduce the results. I think a major revision is warranted.
Experimental design: The positive thing is that the author took into account London-dispersion interactions, something that has been often ignored in computational organic chemistry in the past. That being said, it is surprising that the author uses an outdated version of the DFT-D3 correction instead of the more reliable and accurate 2011 version with Becke-Johnson damping. There is also no reason given why PBE0 was chosen as the functional (more on this in the next point). The basis sets seem to be OK. The author mentions explicit solvation, but even after rereading various sections of the manuscript multiple times, I would not be able to reproduce those results if I wanted to. How many explicit solvent molecules were included? Only one? If that is the case, this would not qualify as a reliable study.
Validity of the findings: 1)I already commented on how difficult it was to understand how exactly solvent molecules were treated explicitly? The author does not mention any sampling of the solvent shell, how many molecules were included etc.

2) The discrepancy between experiments and calculated high activation barriers could not only be due to the postulated reaction mechanism (see ll. 71-74), but due to the chosen methodology. However, such critical analysis is missing. In fact, The reliance on PBE0 is a bit worrying. Major benchmark studies have shown that it is only a mediocre functional for reaction energies and barrier heights (see the GMTKN55 and MGCDB84 databases and subsequent recommendations and insights). While I can accept this functional for geometry optimisations, the systems (at least in the gas phase) are not prohibitively large for dispersion corrected double hybrids or at least the better hybrid functionals recommended in the aforementioned studies. As such, I do not agree that PBE0-D3/aug-pcseg-2 can be considered a “high level” (line 49). If the author decides to stick with the chosen methodology, then a paragraph is needed that puts it into context with larger benchmark studies. An expected error range should be provided and it should be made clear that this is only a very qualitative study.

3) What type charges are reported in l. 78 and the lines thereafter? Mulliken charges or more reliable ones?
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NEW INSIGHTS INTO THE MECHANISM OF SCHIFF BASE SYNTHESIS FROM AROMATIC AMINES IN THE ABSENCE OF ACID CATALYST OR POLAR SOLVENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I would add a brief description of the MD test on solvent mentioned in the response letter.
Experimental design: I still have concerns about using single solvent molecules but I am okay with readers deciding whether or not they believe the results. It is at least clear what was done.
Validity of the findings: See point #2.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NEW INSIGHTS INTO THE MECHANISM OF SCHIFF BASE SYNTHESIS FROM AROMATIC AMINES IN THE ABSENCE OF ACID CATALYST OR POLAR SOLVENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: This manuscript has addressed all of my concerns and there are only two minor things for a very minor revision.
Experimental design: The computational strategy has improved. Choosing a double hybrid was a very good move to give the study more credibility. What is not clear is why the first sentence in the Computational Methods section reads that PBE0 was used to investigate the reaction mechanism if the final energies were based on DSD-BLYP? Maybe it would be better to say that a combination of two levels of theory was used to explore the reaction mechanism? PBE0-D3(BJ) for the geometries and thermal corrections, DSD-BLYP-D3(BJ) for the electronic energies?
Validity of the findings: The findings appear to be valid
Additional comments: PBE0 was published around the same time as PBE1PBE by Scuseria and co-workers, which is exactly the same functional. It is common practice to cite both papers.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND BIOLOGICAL ACTIVITY OF 1,4-PENTADIEN-3-ONE DERIVATIVES CONTAINING TRIAZINE SCAFFOLDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, the authors described clear and professional English, however, there are some mistakes and deficiencies.
1.line 65: "chemists studies"
2.line 29: "besides"
3. line 96-99: 12mmol, 10mmol, et al, add spaces for numbers and units, and check the full article.

The authors provide sufficient literature references, and professional article structure, figures, tables.
Experimental design: Plant diseases, such as citrus canker, rice bacterial leaf blight and tobacco bacterial wilt and TMV, can be very serious and difficult to manage in agricultural production. Thus, exploring novel lead compounds with potent agricultural bioactivities is very crucial in the agricultural chemistry. In this manuscript, the authors described “Novel 1,4-pentadien-3-one derivatives containing a 1,2,4-triazine moiety: design, synthesis, antibacterial and antiviral activities”, which is the first report on the antibacterial and antiviral activities of this series and important for agricultural production. 1,4-pentadien-3-one derivative, derived from plant metabolic products curcumin, found to have a good range of biological activities(Zhang et al., 2018). In order to highlight the importance of 1,2,4-triazine moiety, the authors should add the discussion by contrasting the data, or apply compound 2 or the intermediates of 2 to evaluate their activities.
Validity of the findings: Bioassay results demonstrated that several of the target compounds exhibited better antibacterial activities against Xoo, R.s or Xac and higher activity than ningnanmycin against TMV. Authors  provide all underlying data  and conclusion are well stated.
Additional comments: By comprehensive consideration, I think this manuscript meet the criteria of this journal and should be accepted for publication after minor revise.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND BIOLOGICAL ACTIVITY OF 1,4-PENTADIEN-3-ONE DERIVATIVES CONTAINING TRIAZINE SCAFFOLDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this paper, antiviral and antibacterial activities have been investigated for a series of penta-1, 4-diene-3-one derivatives containing a 1, 2, 4-triazine moiety. A series of novel curcumin compounds have been synthesized and exhibited remarkable activities against plant virus and bacterial, and the activities were comparable to the existing drug bismerthiazol and ningnanmycin. And molecular docking studies for 4a with tobacco mosaic virus coat protein (TMV-CP) have been conducted. The authors have also described the synthesis of analogues in detail, and are reliable. References are properly introduced, including recent ones. Overall, this work broadened the scope of application of curcumin and provided reliable support for the development of novel agrochemicals. As a result, this paper deserves publication in the journal Peer J after following revise.
The comments are as follows:
1. There are some grammar problems in the article that need to be carefully corrected, for example the sentence “In addition, tobacco mosaic virus (TMV) can cause more than 885 plants to infected the virus, resulting in a worldwide loss of $100 million worldwide.”;
2. The first letter of each sentence should be capitalized. Please carefully check the upper and lower case of the text;
3. In the Line 28 and 29: BT and TC first appeared, should be give full name;
4. In the Line 91: the sentence “A synthetic route to 1,4-pentadien-3-one derivatives containing
a triazine moiety was designed and is shown in Scheme 1.” tenses should be consistent;
5. In the Line 116: “Molecular docking.” should be delete;
6. In the article, author should pay attention to the Tables and Figures should be unified format;
7. The sentence “Table 1. Inhibition effect of the sme title compounds against Xoo, R.s and Xac.
a” pay attention to spelling;
8. Figure 5 sick spots can't be seen clearly, please provide a clear picture;
9. Figure 6 of docking research the caption for the interaction is too small. A correction is
necessary for the descriptions of “Conventional Hydrogen Bond”, “Carbon Hydrogen Bond”, “Pi-Sulfur”, “Pi-Pi T-shaped” and “Pi-Alkyl” in the lower left and lower right in the figure.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND BIOLOGICAL ACTIVITY OF 1,4-PENTADIEN-3-ONE DERIVATIVES CONTAINING TRIAZINE SCAFFOLDS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The work is sound and provides new molecular scaffolds to treat plant infections. However, the results on the biological activity should be provided in international units, i.e. microMolar and nor micrograms/mL, which does not allow for comparison purposes.
Another major concern is the presentation of the actibacterial data (Tables 1 and 2) in non conventional units. The widely accepted parameter to measure antibacterial activity is MIC, and not EC50.
Experimental design: The experimental design is appropriate, although the results were not given in the adequate units.
Validity of the findings: Since the results are not given in international units, it is not possible to anticipate the value of the findings, which rely on the potency of the compounds when compared to the reference drugs.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND BIOLOGICAL ACTIVITY OF 1,4-PENTADIEN-3-ONE DERIVATIVES CONTAINING TRIAZINE SCAFFOLDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout.
Literature references, sufficient field context provided
Experimental design: Methods described with sufficient detail & information to replicate.
Validity of the findings: All underlying data have been provided; they are robust.
Additional comments: This paper deserves publication in the journal PeerJ Organic Chemistry without further revisions.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE DETERMINANTS OF CHEMORECEPTION AS EVIDENCED BY GRADIENT BOOSTING MACHINES IN BROAD MOLECULAR FINGERPRINT SPACES
Review round: 1
Reviewer: 1

Output:
Basic reporting: A very good well-written paper that will attract the attention of scientists.  The basic premise is well-chosen and the methodology and execution justifies the hypothesis
Experimental design: The design is sound and I believe that the author has justified his hypothesis well
Validity of the findings: I believe the article to be well-researched; the investigations are sound> These findings could find broad utility in research
Additional comments: I like the basic premise of the paper.  I found it to be interesting .


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE DETERMINANTS OF CHEMORECEPTION AS EVIDENCED BY GRADIENT BOOSTING MACHINES IN BROAD MOLECULAR FINGERPRINT SPACES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Numbered points are in order of precedence, bullets signify points to be
addressed in no order of precedence.

1. The abstract does not contain details of the study and needs to be re-written
   to include the results. Specifically, the AceK insights should be a part of
   the abstract.
2. Machine learning in the title is too vague. Consider being more specific,
   e.g. "as evidenced by machine learning" -> "as evidenced by gradient boosting models in molecular fingerprint spaces"

- 156: "Well known" should be backed by a citation.

Minor Spelling and Grammar issues (indicative, non-exhaustive):

- 15-18: the sentence is overly long
- 30: "the cues drawn" -> "cues drawn"
- 36: "It appears" -> "It has been reported"
- 41: "used as a flavoring" -> "used as a flavoring agent"
- 47: Unclear why nevertheless is used
- 54: "have a taste-chemosensory capacity" -> "have taste-chemosensory capabilities"
- 90: "a ChemSpider" -> "ChemSpider"
Experimental design: Numbered points are in order of precedence, bullets signify points to be
addressed in no order of precedence.

1. 98-100: The scaffold process needs to be described in more detail, including
   the SAHN algorithm and how this is relevant to reduce and cluster the
   underlying chemical structures.
2. 109: Why has the gradient boosting model been used? How has the model been
   generated? What is the rationale behind the parameters? How was the data
   validated? What were the hyper-parameters? Figures 1. and 2. need more of an
   explanation in the text.
3. What is the relation between the RQI and LD50.human? (Table 3) Has the LD50
   been correlated with the RQI in this study or others? Has it been factored
   into the model development? The scaling is clearly non-linear (RQI v/s LD50)
   so the correlation should be described in more detail.
4. 82-89: The data-set used should be described in more detail, including at
   least the description of how many data points were obtained.
5. 104-111: This section should be expanded on with an example, detailing the
   transformation, descriptor generation and other transformation metrics.
6. 107-108: Why have the low and zero variance vectors been removed?
7. 127: Further comment on why the regressed model correlates well with the
   observations would add to the manuscript.
Validity of the findings: Numbered points are in order of precedence, bullets signify points to be
addressed in no order of precedence.

1. Figure 2 is unclear. What do the hollow dots and the filled in dots signify?
2. 184: 3 data points which do not show linear ordering is insufficient to
   confirm a hypothesis. Consider using different language if more data is not available.
3. 130: It is unclear as to how the Predicted RQI performs here without
   information on the actual RQI. Table 2 should include the actual RQI.

- 162: Though a reasonable conclusion from the data, any supporting evidence
  would help in terms of establishing the distinction between after tastes and
  initial taste sensations.
Additional comments: The authors have explored computationally, an abstracted input space of chemical
structures and have regressed over a model (details unclear) to obtain insights
into the RQI index, a measure of bitterness. The work presented is very
interesting and the details surrounding the necessity of the study have been
presented in a compelling manner. The conclusions drawn from the data are also
largely consistent, not-with-standing the issues listed above. The model
description is inadequate, but after these have been addressed this will be a
very timely addition to the existing literature.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE DETERMINANTS OF CHEMORECEPTION AS EVIDENCED BY GRADIENT BOOSTING MACHINES IN BROAD MOLECULAR FINGERPRINT SPACES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The reporting style and flow of the language in the manuscript make it an engaging and compelling read. However, despite being well-written in general, there are a few minor grammatical issues/typos to be addressed, listed below in no particular order.

1. The first line of the abstract (lines 15:18) is a little long and could be split into two sentences. Similarly, the sentence in lines 98:103 could be broken into two.

2. The following replacements are suggested: line 17 ("have" --> "has"); line 19 ("ability for intensely bitter molecules" --> "ability of intensely bitter molecules"); line 31 ("are a range" --> "is a range"); line 35 ("showing the systemic responses..." --> "showing that the systemic responses..."); line 47 ("to believe the bitterness receptors..." --> "to believe that the bitterness receptors..."); line 69 ("The ability for" --> "The ability of"); line 75 ("questions on the precise a molecular theory" --> "questions regarding the precision of a molecular theory"); line 90 ("using a ChemSpider" --> "using ChemSpider"); line 131 ("given they" --> "given that they"); line 133 ("Give the model could sufficiently..." --> "Given that the model could sufficiently..." or "Since the model could sufficiently..."); line 134 ("it reasons" --> "it stands to reason" or "it is reasonable to suppose" or "it can be inferred"); line 136 ("relative the" --> "relative to the");

3. The expansions of the acronyms RQI (line 124), R2 (line 125), RMSE (line 125) should be included once.
Experimental design: I was wondering how the bitterness index quantifies the gradations of bitterness, and more details of the same could be provided in the Methods or Results sections.
Validity of the findings: The sample size of the data, controls and scientific methods adopted in this work are adequate. The bitterness index and the relationship between RQI and the results could be expounded further.
Additional comments: I think the manuscript has been written in professional, unambiguous language, with several compelling points made. Slightly more description in the Methods and Results might improve the manuscript further.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FAST AND AUTOMATED IDENTIFICATION OF REACTIONS WITH LOW BARRIERS USING META-MD SIMULATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is an excellent paper, methods described clearly, results should be of utility to the community.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FAST AND AUTOMATED IDENTIFICATION OF REACTIONS WITH LOW BARRIERS USING META-MD SIMULATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is clear and well-referenced, with a suitable level of recognition of alternative strategies for reaction path finding. The article is well structured and logically laid out, and offers a self-contained narrative linking the aims, methods, results, analysis, and conclusions. The figures are clear and of generally high quality. Raw data is available via a link at the end of the manuscript.

Minor comments on the basic reporting of the manuscript are listed in the attached PDF.
Experimental design: The investigation carried out in this work is rigorous and to a high technical standard. The aims of the investigation are clearly set out, and the approach employed is mostly well-described for those who would choose to replicate their findings.

Minor comments on the experimental design are listed in the attached PDF.
Validity of the findings: All data used or generated in this work are provided, as are the scripts used to generate these data. The conclusions answer the questions proposed in the introduction, and are justified by the methods employed and the results presented. These conclusions are clear and are limited to the content of the work presented.

Minor comments on the validity of the findings are listed in the attached PDF.
Additional comments: The manuscript is well-written and well-presented. The scripts and data used and generated in this manuscript are openly available, however would benefit from more extensive documentation to facilitate their widespread use. The minor comments listed above are intended only to improve an already thorough piece of work. I do not believe any new primary data need to be generated, and many of my comments relate only to justification of the chosen methods and parameters rather than any fundamental issues with the work. I am therefore suggesting that only minor corrections are required before publication.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FAST AND AUTOMATED IDENTIFICATION OF REACTIONS WITH LOW BARRIERS USING META-MD SIMULATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well written and enjoyable to follow. However, some aspects could be improved, making the article accessible to a broader scientific audience:

1) Figure 1 would benefit from including the explanation of abbreviations, and the meaning of colors used for the products (not all cultural backgrounds see red as unfavorable and green as positive). Also, I would suggest not using a combination of red and green concerning the colorblind readers.

2) Since the estimates with RMSD-PP method are critical in the screening stage of the workflow, it would be helpful to have a short, 1-2 sentences, explanation of its principle with its first mention.

3) On lines 142-143, adding info on the fact that the estimates come from RMSD-PP would make the distinctions between the estimates and the actual semi-empirical barriers easier.

4) Figure 9 would report the reaction path in a more comprehensive way when supplemented by data on reaction energies as well as barriers.

5) Figure S2 is missing the caption.
Experimental design: The dataset used is rather extensive, given the methodology used, and the extension towards also evaluating bimolecular reactions with meta-MD is valuable. Although, the description of the experimental procedures could be enhanced by providing more details on the following two issues:

1) on line 63, the authors provide an additional set of hyper-parameters used for meat-MD, which were found as in this study. However, there is no data on how were these parameters found, what other sets were used etc.

2) on line 77, the algorithm checks for changes in atomic connectivity every 5 ps. How is this performed? Do such checks rely on semi-empirical energy minimization as described on line 74?
Validity of the findings: I wonder if the authors have tried more meta-MD runs, in particular, for bimolecular reactions where the odds of enumerating all expected low-barrier reactions are relatively low. Given the computational costs, it should be feasible to markedly increase the number of runs at least for some of the problematic cases.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FAST AND AUTOMATED IDENTIFICATION OF REACTIONS WITH LOW BARRIERS USING META-MD SIMULATIONS
Review round: 1
Reviewer: 4

Output:
Basic reporting: Overall, the manuscript is well-written. However, some phrases are in the abstract and conclusion 1:1 copies: “In addition, we find 34 new […] until a reaction is observed.” Some variation would be better here.

Mostly, the literature references also appear to be appropriate. Yet, in the beginning, a number of references is given in the context of “computational methods for exploring reaction space in an automated manner”. I suggest to add the paper from the Martínez group (https://doi.org/10.1038/nchem.2099) that also falls into this category. I think that it is worth noting that their “piston-like” pushing of molecules is a harsher predecessor to the here suggested cavity reduction.

Minor issues:
line 313 and abstract: “at an” -> “an”
line 87 "is" -> "are"
line 178 "GFN-xTB" -> "GFN2-xTB"
Experimental design: The used methodology is described quite well in chapter 2.
Due to the additional biases applied, the comp. cost is increased roughly by a factor of 3 compared to a minima search (cf. line 215)?

line 99-101: About testing only 5 structures. Is there a fall-back option, if more than just these 5 structures are found within a certain energy window?

line 126: To make the comparison with the previous work of Grambow better possible, the authors might consider to compute wB97X-D3 single-point calculations (for example, using ORCA) on the wB97X-D geometries.

line 284: an average atom number for the investigated systems should be given.
Validity of the findings: The data has been provided in an external repository, which is very good.
I personally would favor an (additional) upload together with the paper SI to have all the data available in the same place.

line 280: It is stated that the manual proton transfers could easily be automated. But the authors should comment on this - would an automatic procedure (exploring all paths) not grow dramatically in comp. cost?

Overall, the manuscript “Fast and automated identification of reactions with low barriers using meta-MD simulations” by Rasmussen and Jensen presents a computational approach to automatically identify low-energy barriers by means of a previously established and herein adjusted metadynamics approach. The adjustments include mainly adjusting the parameters of the RMSD potential, but all cross-usage of different products in the metadynamics simulation.
The results in this manuscript are of large interest to the computational chemistry community, as automated search for transition states is a, yet, unsolved problem. The presented approach will thus be of significance in automated determinations of reaction barriers that are used microkinetic modeling.
Additional comments: About line 126: A warning: wB97X, wB97X-D, wB97X-D3, and wB97X-V all have different XC functional parameters! So, wB97X-D3 is not simply the D3-corrected version of wB97X.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFICIENT SEQUESTRATION OF LEAD FROM AQUEOUS SYSTEMS BY PEANUT SHELLS AND COMPOST: EVIDENCE FROM FIXED BED COLUMN AND BATCH SCALE STUDIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This submission deals with the adsorption of lead from water onto a biosorbent based on peanut shells. Some equilibrium batch tests were conducted and conventional models were applied to the data. The approach applied is very conventional and the only new aspect is the use of a relatively new biosorbent for a specific contaminant. I think that it is a normal approach in a laboratory to evaluate a commercial product and to propose it for the treatment of a specific type of water. There are many studies and textbooks giving detailed research and insights about the experimental evaluation of adsorbents. I don’t see any advancement in the science in this aspects.
It can further not be excluded that such a waste product may have the potential to contaminate the treated water because of pesticides or other heavy metals used in various part of the world.
Because of its low informative value and no innovative approaches proposed, I have to recommend to reject the submission.
Experimental design: -	Line 125: in this research a synthetic wastewater was used, based on a very simple composition by the dilution Pb in distilled water. This is one of the main concerns in this research, because the use of synthetic wastewater does not permit to evaluate the effects of non-competitive and competitive adsorption and desorption (mutual interference effects, multiple adsorption mechanisms, ...).
-	Please reconsider the extensive use of the words "biosorption" - they refer to filling materials able to develop a microbial community or biofilm.
Validity of the findings: -	Figure 4: It is very questionable to apply these models on 3-4 data points.
-	A very important aspect which is not covered by the authors is that distilled water was examined. If, as the authors suggest, the tested material should be useful for contaminant removal from wastewaters etc. why were no tests carried out on such waters? This would be highly necessary because in real/ natural waters, competition for adsorption sites occurs, reducing the available adsorption capacities for single adsorbates by orders of magnitude.
-	With the extremely high dosages reported here (for instance see figure 4 with 25-100 mg/L), it appears largely unrealistic that the tested material could be applied in practice.
Additional comments: no comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFICIENT SEQUESTRATION OF LEAD FROM AQUEOUS SYSTEMS BY PEANUT SHELLS AND COMPOST: EVIDENCE FROM FIXED BED COLUMN AND BATCH SCALE STUDIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is written in an English that needs improvement. It's not bad, but there are some mistakes that need to be corrected. Just one example: line 468 <<The more Pb sequestration onto PSB is attributed to its improved surface characterization>>. Some words are spelled wrong (e.g., line 177 concertation instead of concentration).
Literature references look fine, and sufficient field background/context is provided.
The article structure, figures, and tables are fine, but a few things should be corrected:
•	Figure 3: the caption is incomplete: (b) effect
•	Figure 3a: The experimental data symbols for Q = 5.0 ml/min (CCB) are missing - there is only the curve.
•	Figure 5a: the line connecting the experimental points must be made either broken (straight lines) or curved: not a mix of the two options.
Experimental design: The experimental design is fine, even if basic. The scientific and methodological approaches are fine. Methods are well described.
Validity of the findings: Findings are OK, although often quite trivial.
I do not see any statistics on the experimental data: it seems all the tests have been performed only once. However, considering the type of tests carried out, I think this can be accepted.
Conclusions seem fine.
Additional comments: Abstract: Indicating the pump flow rate has no physical meaning if the value of other parameters is not reported: bed volume and/or vessel cross-section.
Line 64: define the CNS acronym.
Line 110: if possible, report about the residual biomasses used to produce the commercial compost.
Line 134: specify what do you mean with steady state – I guess the fluid-dynamics.
Line 144: avoid @
Line 177: the IC acronym should be defined.
Line 203 << Table 1 shows the values of k1, qe (calculated from model), qe-experimental,>>. In Table 1 I do not see any experimental data.
Line 225 <<Kp>>: in Table 1 the authors wrote <<Kdif>> referring to the same variable: decide which symbol to use. The IPD acronym should be defined.
Line 326 <<capacity decreased from 10.26 to 9.9015μg g−1>> too many values after the comma in the second data.
Line 374 << The maximum values of Pb ion sorbed on PSB and CCB surface were found at mass of 1.25 g/L of contaminated water. Overall, Pb adsorption showed a decline with the increase when adsorbent dose was increased.>>. Looking at the Fig, the trend seems reversed.
Line 447: << for PSB and CCB was 2.27 and 1.92>>. The values were reversed.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFICIENT SEQUESTRATION OF LEAD FROM AQUEOUS SYSTEMS BY PEANUT SHELLS AND COMPOST: EVIDENCE FROM FIXED BED COLUMN AND BATCH SCALE STUDIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript deals with the very serious problem of aqueous systems contamination by lead, a very toxic and hazardous contaminant. The solution investigated to obtain pure and safe water for drinking is based on the adsorption performance of a peanuts shell biosorbent.
In the latest years many papers, aiming at finding an efficient, economically feasible and environment-friendly adsorbent, have been published, the most of them addressed to claim very high adsorption capacity. Less attention was addressed to verify the performance of such adsorbents in flow systems based on adsorption packed columns for contaminated water remediation.
The authors claim that main goal of the study was to assess the biosorption potential of peanut shells wastes (PSB) to remove Pb from wastewater through experimental and modeling approaches, using batch and flow systems, operated under various conditions in terms of adsorbate concentration, adsorbent dosage, solution pH and contact time. A comparison with a commercial compost biosorbent (CSB) was also performed.
Experimental design: Experimental characterization of PSB has been carried out through FTIR, SEM, and nitrogen adsorption for surface area/pore volume size.
Really, the results obtained in the latter case (surface area of 226.8 m2 /g, average particle and pore size 26.5 and 3.3 nm, respectively, 5.11% porosity) are not presented as adsorption isotherms, while they are essential to support the reported, rather surprising, size values.
Validity of the findings: The work is medium quality, and could be improved by adding some results, discussion, especially concerning the potential application, following the below suggestions.
Concerning the adsorption equilibrium measurements and modeling:
line 404…… “The removal onto PSB increased from 49.4 to 73.0 % when the contact time was changed from 15 to 60 min. Moreover, only 6.8% removal was increased when the contact time further increased from 60 to 180 min”
Comments : If the purpose is to determine the real equilibrium values, further 6.8 % increase of adsorbed amount is not negligible. The approach to the equilibrium can be very slow, especially in the experiments in which the amount of lead is not enough excess with respect the amount of adsorbent, resulting in a rather high reduction of lead concentration and then driving force to adsorption. Moreover, I suggest that the Authors  don’t use the term contact time along all the manuscript to indicate the run time. The modeling approach is acceptable; the same for choosing R2= 0.99 as acceptable values for supporting a model.
Concerning the flow column experiments and modeling :
I believe an introduction to the comments is necessary. The challenge of using adsorption to remove Pb from wastewater containing 10-100 ppm and over is really very much arduous, if one considers that the current limit for drinking water is 10 ppb. This means that you need a very large amount of very high capacity adsorbent or a very large scale adsorption column. Cheap adsorbent can surely help, but how much the adsorbent cost influences the final cost of the treatment ? And, looking at the above premise, how frequent is the necessity of column regeneration ? How much the operation influences the final cost, compared to the effect of adsorbent cost ? Moreover, the discussion and interpretation of the breakthrough curve sas depending of the operating parameters should be less qualitative.
Coming back to the right comment of the Authors on the low attention addressed in the most papers to verify the performance of adsorbents in flow systems, however their experimental approach is rather far from answering the above considerations. First of all, the scale of the experiments : the column is too small and the adsorbent bed geometry is questionable. A too large diameter with respect the height also results in a radial profile of velocity very non uniform, and the entrance effects are critical.
From the experimental data it can be seen that to reach the limit of 50 ppb (higher than the current regulation limit) 99.8 or 99.9 % removal are the values fot the breakthrough curves to be stopped. One simple parameter to be evaluated is the corresponding BV (bed volume) number at that value, i.e. the ratio between the total amount of liquid fed to the bed and the adsorbent volume. Few BVs means a very high frequency of regeneration, resulting in high operation cost.
One more aspect, the importance of regeneration, underlined by the Authors, is not investigated. The comparison with CCB is winning in terms of adsorption capacity and shape of breakthrough curves, however the flow column behavior of CCB is very poor. It seems difficult to imagine the practical utilization of CCB for lead sequestration in a flow system on the base of the results found by the Authors.
English language is of acceptable quality.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFICIENT SEQUESTRATION OF LEAD FROM AQUEOUS SYSTEMS BY PEANUT SHELLS AND COMPOST: EVIDENCE FROM FIXED BED COLUMN AND BATCH SCALE STUDIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: It seems to me that the paper has been improved by introducing further experimental tests (as requested by other reviewers) and accepting the observations / suggestions / requests for changes highlighted by me in the first round of review.
Experimental design: It seems to me that the paper has been improved by introducing further experimental tests (as requested by other reviewers) and accepting the observations / suggestions / requests for changes highlighted by me in the first round of review.
Validity of the findings: It seems to me that the paper has been improved by introducing further experimental tests (as requested by other reviewers) and accepting the observations / suggestions / requests for changes highlighted by me in the first round of review.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CRYOPROTECTIVE ACTIVITIES OF FK20, A HUMAN GENOME-DERIVED INTRINSICALLY DISORDERED PEPTIDE AGAINST CRYOSENSITIVE ENZYMES WITHOUT A STEREOSPECIFIC MOLECULAR INTERACTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript reports cryoprotective activities of three human-genome derived IDPs and their truncated peptides for LDH and GST. CD analysis by using D-enantiomeric isoform suggested that FK20 might not interact to GST and not affect the GST's structure during the cryoprotection. FK20 could also successfully cryopreserve two mammalian cell systems.
Experimental design: The experimental design is modern and appropriate.
Validity of the findings: I have major difficulties to understand this finding. Details are shown in the following "General comments."
Additional comments: 1) It is my doubt thorough the manuscript that the information of the gene (protein) is limited. The gene information supports readers to correctly understand this work. First, it is needed to note the reason why authors used these protein sequences. More than 10% of open reading frames in eukaryotic genomes have been estimated as intrinsically disordered proteins or proteins containing intrinsically disordered regions. Authors should show the intension of choosing the gene from abundant IDPs existing in the human genome in the "Introduction" section or the "Results" section. Second, it is highly recommended that the accession number, the function (unless it has determined, putative), and the expression patterns (organ, age, stress specificities) of the protein are documented in the text.

2) Figure 1. This figure is difficult to understand. What does the green, blue, and magenta bars represent? Although some bars have amino acid sequences above them, they did not fit to the lengths of the corresponding color bars (or each amino acid sequence is a part of the original sequence that was exhibited by a bar?). Are these sequences parts of some proteins? if so, show which part is taken from the original protein.

3) Figures 2, 3, and 5. Please show basic information in the legends to understand the figures. How many times the experiments are repeated? What is the mean of error bars? Statistically significant?

4) Figure 6. A) the paper (Chakrabortee et al. 2012) proposed two types of molecular shield models, original one and extended one. Figure 6A seems to show the extended one. However, applying extended model needs weak association between cryoprotective peptides and protected proteins. Authors should describe the reason why they adopted the extended molecular shield model to their results. B) I think that relevance of the data is not enough to make Figure 6B.

5) The title is somewhat ambiguous. A title which directly represents the cryoprotective activities of FK20 for cryosensitive enzymes and mammalian cells seems to be better.

6) L45-46. The phrase "but also non-functional proteins" can be omitted because the following sentence mentioned "IDPs are widely associated with biological processes".


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CRYOPROTECTIVE ACTIVITIES OF FK20, A HUMAN GENOME-DERIVED INTRINSICALLY DISORDERED PEPTIDE AGAINST CRYOSENSITIVE ENZYMES WITHOUT A STEREOSPECIFIC MOLECULAR INTERACTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript contains numerous small grammatical errors that needs correction by a native English speaker. Below are corrections for text that are not necessarily grammatically incorrect:

Line 29 Change “if all-D-enantiomeric” to “of all-D-enantiomeric”
Line 34 Change “IDPs larger than 20 amino acids” to “IDPs longer than 20 amino acids”
Line 46 What is meant by “non-functional” proteins? Is this in the sense of not yet identified, or that they have zero biological function?
Line 49 Not all IDPs will fold into a stable structure, or gain any structure, when bound to a ligand. Please reword this sentence to reflect that.
Line 91-104 This section could be shortened since it reads like a very detailed summary of the results. I would also suggest using the present tense to avoid confusion.
Line 213 “It is generally saying that proving non-existence is always difficult.” To be clear, it is impossible to prove something does not exist because we cannot distinguish between something not existing or that we cannot observe it. Please rewrite this sentence.
Line 222 “atmospheric” - perhaps the author means environmental?
Line 216+ I assume the equimolar mixture concentration is the total concentration of the protein?

There are several problems with the figures. Fig. 1 is very confusing to me - the protein sequence text is not the same length as any of the coloured bars, making it difficult for me to tell which sequence corresponds to what bar. PONDR is mentioned in the text on line 185, but I could not find any such plot (Fig. S1 is actually a Uversky plot). The supplemental filenames should be revised to make it clearer which files correspond to Fig. S1 etc.
Experimental design: No comment
Validity of the findings: The paper has a considerable amount of interesting data and the use of all-D amino acids is a very clever way to address the molecular shield mechanism of IDPs, and an especially smart way to eliminate the IDP signal in the GST CD studies.

I am having some difficulty interpreting Fig. 2C and 2D. Normalized activity is not defined in the Methods and I do not see the calculation in the Excel files. Because of the sigmoidal shape of the LDH cryoprotection curves, using a single protein concentration does not provide an accurate view of the efficiency. I would strongly suggest plotting the normalized activity as PD50 (concentration of protein required to recover 50% of LDH activity) to get a hopefully better view of how these IDPs are working.

The cell cryoprotection data are interesting, but I think they are very out of context in this manuscript. I think the data should be removed, because at this point it is not clear if the protection is due to the protein stabilization effect seen in the in vitro experiments, or due to membrane stabilization. The membrane stabilization is a possibility, because the IDPs were added to the culture media and there is no specific evidence that these peptides are internalized.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CRYOPROTECTIVE ACTIVITIES OF FK20, A HUMAN GENOME-DERIVED INTRINSICALLY DISORDERED PEPTIDE AGAINST CRYOSENSITIVE ENZYMES WITHOUT A STEREOSPECIFIC MOLECULAR INTERACTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have made all of the appropriate changes based on my review.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THEORETICAL INSIGHTS INTO THE MOLECULAR MECHANISM OF I117V MUTATION IN NEURAMINIDASE MEDIATED REDUCTION OF OSELTAMIVIR DRUG SUSCEPTIBILITY IN A/H5N1 INFLUENZA VIRUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a clearly written manuscript that highlights the relevant literature in the introduction. The figures are relevant, clearly labelled and of high quality. There was no raw data supplied, which would be the simulation trajectories and secondary data derived from trajectory analysis. These raw data would take a lot of space and re-analysis would be beyond the scope of this review.
Experimental design: The experimental design is evident of original primary research. It is made clear how the research question fills the knowledge gap of understanding how mutations outside the active site of an enzyme can influence the binding affinity of an inhibitor. The Methods are state-of-the art and described with sufficient detail that an expert would be able to replicate the methods.
Validity of the findings: All relevant data have been provided, however no statistical analysis was provided. It should be assessed, if the difference in hydrogen bond occupancy in figure 2 is statistically significant. At least error bars based on confidence intervals should be shown in figure 2 as well as in figure 3. The description of the hydrogen bond results in lines 213, 214 (and elsewhere) should distinguish between thermodynamic and kinetic effects by using the correct terms stable/unstable and inert/labile.
Relevant and clear conclusions are made, which are linked to the research question. However, the discussion lacks depth as pointed out in section 4.
Additional comments: The discussion is quite limited in scope. It is completely focussed at the results, without references to the wider literature and comparison with similar computational and/or experimental studies. Furthermore, the discussion should refer to the significance of the finding for the future prospects of OTV as an anti-influenza drug and any implications for future drug discovery. An appreciation that the mutation may affect viral fitness (with references to literature) as well as opportunities for further work should be shown. With regards to viral fitness, the present study may even be extended to include a comparison of the computed binding affinities of the natural sialic acid substrate to the mutant and wild-type enzyme.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THEORETICAL INSIGHTS INTO THE MOLECULAR MECHANISM OF I117V MUTATION IN NEURAMINIDASE MEDIATED REDUCTION OF OSELTAMIVIR DRUG SUSCEPTIBILITY IN A/H5N1 INFLUENZA VIRUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	The manuscript is clearly written. Only in the introduction around lines 66-68, I would suggest to use the present tense, as the residues are still located at the described positions, this was not only the case when the structures were reported.
Experimental design: 2.	The authors report that they performed four independent simulations, with different starting conformations. How were these different starting conformations obtained?
3.	I am typically not a fan of MM-PBSA calculations, but I laud the authors for the clear description of the methodology. Could they still say something about how the SA term was obtained and (more importantly) why they think a single-trajectory approach is appropriate? This is typically only the case if no conformational changes upon binding are to be expected. However, as the whole manuscript is about conformational changes due to the mutation, it is not unlikely that the indicated sidechains would perform very differently in an apo simulation of the protein? The argumentation that the triple trajectory approach leads to a lot of noise does not make the single-trajectory approach more appropriate.
Validity of the findings: 4.	At the end of the introduction, the authors make a rather bold statement that in previous studies the ‘simulations were too short to reach reliable statistical results’. This may be true, but after such a harsh statement, I would expect that the authors would go out of their way to show proper statistical tests for their analyses. As you have done four independent simulations, you could add error bars to the bar plots of figures 2 and 3. Is the decrease of the secondary structure elements of 12% or the change in the occurrence of hydrogen bonds by 10% or 30% actually statistically relevant?
5.	For the free energy differences in table 1, the authors may want to emphasize what the difference in free energy is for an effect of a factor 3-50. This would be between 0.6 and 2.3 kcal/mol.
6.	The authors may also want to emphasize that, based on table 1, they predict that the difference in binding affinity is mostly enthalpy driven and not entropy driven. Based on that analysis, it makes sense to focus on direct interactions, such as hydrogen bonds.
Additional comments: 7.	In what kind of interactions does D151 engage when it is not hydrogen bonded to OTV?
8.	The authors may want to spend a few thoughts on how their newly derived knowledge on the mechanism of the I117V mutation can be put to practical use. Do they expect that drugs that rely less on the interactions with E119 and D151 would suffer less from this mutation? Could they give suggestions of such molecules?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THEORETICAL INSIGHTS INTO THE MOLECULAR MECHANISM OF I117V MUTATION IN NEURAMINIDASE MEDIATED REDUCTION OF OSELTAMIVIR DRUG SUSCEPTIBILITY IN A/H5N1 INFLUENZA VIRUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have responded to my comments and have made modifications to the manuscript. It is basically acceptable for publications, but I would urge the authors to make a few small clarifications.

Let me follow my original comments:
1.	OK
Experimental design: 2.	The authors write that the four independent simulations started from randomly selected conformations from the initial 10-ns equilibration. Were the velocities reassigned completely? If not, then you have actually performed the same simulation 4 times with a slightly different shift in starting time: picking a random configuration (positions and velocities) and starting a simulation is basically the same as continuing the simulation at that point. I guess you have reassigned velocities for the four simulations, but this is not stated in the manuscript.
3.	The authors seem to brush away the argumentation that the single-trajectory approach in MMPBSA may not be appropriate when conformational changes are involved by stating that it is widely used and that it leads to results that match the experimental values. I would like to emphasize that this still does not make the single-trajectory approach appropriate. For the current manuscript and the aims of the authors, it may be sufficient, and I appreciate that the authors at least mention the possibility that the single-trajectory approach is sometimes not reliable. If they really want to make me happy, they would add ‘because it assumes that no significant conformational changes occur upon ligand binding’ to that statement.
Validity of the findings: 4.	OK
5.	Here, I think that the authors should be more careful. The IC50 is a property that depends on the experimental setup (protein and substrate concentration), and the equation that the authors give (ΔG ~= RT ln IC50) is not correct. If experiments are done under the same conditions, however, a similar equation often does hold for the relative binding free energies: ΔΔG ~= RT ln [IC50(1) / IC50(2)]. This is also what the authors actually use in the manuscript.
6.	OK
Additional comments: 7. OK
8. OK


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THEORETICAL INSIGHTS INTO THE MOLECULAR MECHANISM OF I117V MUTATION IN NEURAMINIDASE MEDIATED REDUCTION OF OSELTAMIVIR DRUG SUSCEPTIBILITY IN A/H5N1 INFLUENZA VIRUS
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: the authors have satisfactorily addressed my final concerns
Validity of the findings: the authors have satisfactorily addressed my final concerns
Additional comments: no comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: USING A GENETIC ALGORITHM TO FIND MOLECULES WITH GOOD DOCKING SCORES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Steinmann et al. demonstrate the use of a genetic algorithm to design new structures in drug discovery using docking. Compared to traditional approaches such as high throughput virtual screening, the authors demonstrate superior performance in light of synthetic feasibility of generated molecules. I recommend acceptance of this article after incorporation of the following minor edits:

- In one of the experiments, the authors report the following fitness function “In the score modifier approach, the docking score is multiplied by a modified Gaussian function that ranges from 0 to 1 for high and low values of the SA score”. Here, it is my opinion that explicitly stating the fitness functions (using equations) for all experiments will help a reader. I found it challenging to understand the equation for this particular example.

- “the mutation rate is 50%”: Can the authors please clarify how the mutation rate is determined?. For example, for a given molecule, are 50% of the atoms and bond modified?. In my opinion, this will help readers that have not read the GB-GA paper. Additionally, was this 50% mutation rate also used for crossovers?.

- “While these results are encouraging visual inspection of some of the best scoring molecules (first column of molecules in Figure 1) show that they do not resemble drug-like molecules, indicating that they may be unstable and/or synthetically inaccessible.” For better readability, please add a comma after “encouraging” (or break the sentence into a few parts).

- “ and the fraction of the 100 best-scoring molecules with a Molecule.one score below 10 is shown in Column 2 of Table 4” In the previous part of this sentence, the authors state that Molecule.one returns a score between 1 and 10. As such, re-stating that “100 best-scoring molecules with a Molecule.one score below 10” might be redundant. Maybe the authors wanted to convey something else?

- “ The only case for which a non-negligible fraction of molecules may be synthetically viable is DDR1 with 26% while for the rest that fraction is very close to 0%.”. Please consider rewriting this sentence. It is hard to read.

- “A similar plot of the Tanimoto similarity to the best scoring molecule for each target vs docking score (Figure 2b) also shows no correlation”. The authors should explicitly state which fingerprint was utilized for calculating the similarity.

AkshatKumar (Akshat) Nigam
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: USING A GENETIC ALGORITHM TO FIND MOLECULES WITH GOOD DOCKING SCORES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the manuscript ‘Using a genetic algorithm to find molecules with good docking scores’ the authors Steinmann and Jensen present a graph-based genetic algorithm (GA) based approach to identify highly scoring molecules) from the ZINC database for different receptor targets. The approach combines a functional group filter with a docking score modifier (based on a heuristic synthetic accessibility score, SA) (GA+Filter+SA approach). The authors compare their results to standard screening of large molecular datasets.
The paper tackles the challenge of efficiency for virtual screening techniques of millions of docking compounds with the target to select lead structures that are possible to synthesize chemically. The introduction refers to several recently developed and applied methodologies, mostly based on fragment-based techniques in combination with GA search algorithms. The authors highlight, that their approach is different as it is not based on a fragment-based approach and focuses on better selection of synthetic assessable molecules.
The basic reporting in the manuscript is clear and coherent.
Experimental design: The design of the study and the computational methodology of the paper is sound. It could be considered if a flow diagram for the methodology might help the reader in the methodology section. Some minor questions on the details might be interesting to add to the methodology section as listed below:
Is there a specific reason that Glide has been chosen as docking software?
It might be valuable for the reader to briefly comment on the difference between Glide’s HTVS and SP (and XP) scoring.
Why have five conformations been generated for each molecule at the start and how does this compare to e.g. a standard combination of Glide SP + Glide XP conformational search and optimisation approach? (also in terms of computational costs). Also in relation to the different number of flexibly rotating bonds in different molecules, could this fixed number lead to a bias in conformer selection?
“the docking score is multiplied by a modified Gaussian function that ranges from 0 to 1 for high and low values of the SA score”: Would it be possible to inform very briefly on the type of modification?
On the receptors: Do the receptors contain any “specialities” like metal ions or water molecules in the binding pockets and have they been treated (or removed)? Has a docking grid been defined and what was its centroid and size?
Validity of the findings: The findings are valid and relevant. Independent from the fact that a zoo of virtual screening methodologies is published in literature a focus on including synthetic accessibility better into high throughput methods is valuable.
Additional comments: As the authors might know, this referee is a strong supporter of open and FAIR data sharing principles. Thus, I appreciate that github links have been included in the supporting information. However, the links seem to be broken and might need corrections. (Is the interface with graph-based GA algorithm for this application also included there?)
The link between the new approach and the Covid Moonshot project could be established (on page 7) a bit better. It appears that “An early incarnation of the GA+Filter+SA approach” has been used for this part of the study and it might be good to better understand why this then has been added to this manuscript and if the developed approach would result in different outcomes.
Other minor comments:
Please add units to values in Tables
Figure 1 Caption: Replace “Highest scoring” with “best scoring”?
Page 6 (Comparison to…): “equally good results can obtained” … “can be obtained”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: It is not a particularly innovative work. However the work is complete and well written. So it deserves publication.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: NO comment and NO changes necessary. The article was written in conformity with any required professional standards and in accordance to the stated aim of the journal itself. Technically correct, clear and professional English was used throughout in the article. The abstract provides a concise and a complete summary of the content of the paper. Besides, the introduction provides a good, generalized background of the topic that quickly gives the reader an appreciation of the wide range of applications for this technology. Anyway, the study objectives, scientific data are clear, understandable and explicitly defined. The conclusions are mostly well supported by the results.
Experimental design: The experimental design and the scientific methods used are appropriate to the aims of the study. The article provides sufficient information for another capable researcher to reproduce the experiments described.
Validity of the findings: NO comments and NO any additional experiments are necessary to validate the results presented here. The conclusions of the study are supported by appropriate scientific-technical methods. The data on which these conclusions are based are solid, statistically sound, and controlled.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Throughout the manuscript, the writing needs to be professional and consistent.
a.	There are several incomplete or fragment sentences (e.g. lines 49, 398).

b.	There are many inconsistencies with spaces (e.g. for wt.% and wt. % in lines 94 and 107, for “°C” in line 105 and 113, for “=” in lines 198 and 205, for “Fig.” in lines 166 and 192, after “CS-” in lines 402 and 409).

c.	Inconsistency in subscript fonts for parameters (K1 in line 135, qm in Table 1).

d.	The font of parameter symbols is not consistent with italic vs non-italic fonts. (e.g. qe in line 135 and 137).

e.	Theme and bold font dissimilarities in line 138.

f.	First bracket missing in equation (line 141).

g.	Be consistent with theme fonts for all the equations (e.g. lines 138, 147 and more).

h.	Degree symbol is missing (lines 197, 198).

i.	Capital and small letters (Adsorption in line 72).

j.	The period or full stop mark was twice used (lines 129).

k.	Re-write the sentence in line 296-297.

l.	FT-IR and FTIR (lines 120, 164, 166 and more).
Experimental design: It was mentioned that the proteins in the eggshells were denatured, washed, dried, and made into powder (line 102). The authors need to clarify the type of eggshell they used in the section of Synthesis of the Adsorbents and Characterization.

At end lines in section Adsorption Isotherms Study, the authors mentioned that the adsorption capacity of an adsorbent depends on “so many parameters” and included only three factors. The authors are suggested to provide more factors for the adsorption capacity of an adsorbent.
Validity of the findings: The authors need to provide the justification for this study in more details. Synthesis of bio-calcium carbonate from the source that this study used is not novel, as demonstrated by below mentioned papers among others. The knowledge gap being filled in this study should be clarified in Introduction section.

•	Morsy, F. A.; El-Sheikh, S. M.; Barhoum, A., Nano-silica and SiO2/CaCO3 nanocomposite prepared from semi-burned rice straw ash as modified papermaking fillers. Arabian Journal of Chemistry 2019, 12 (7), 1186-1196.
•	Hassan, T. A.; Rangari, V. K.; Jeelani, S., Value-added biopolymer nanocomposites from waste eggshell-based CaCO3 nanoparticles as fillers. ACS Sustainable Chemistry & Engineering 2014, 2 (4), 706-717.
Additional comments: General comments:
The authors synthesized bio-based adsorbing materials silica/calcium carbonate (CS-SiO2/CaCO3) from nature-based waste materials for removal of one of contaminant chemicals phenol from water. Though the principle behind the synthesis is not quite new, there are novelty in design and demonstration of usage for the adsorbing materials for practical phenol removal applications.

The writing needs to be more scientific and technical. There is a high chance that the reader may misinterpret or cannot understand what the authors want to explain and report. The plots in the figures have major scopes to be improved both in quality and presentation.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 1
Reviewer: 4

Output:
Basic reporting: The paper is well written and interesting. The materials are not very new the synthesis is well known in the literature but the application part can be useful for the readers.
Experimental design: The experiments were well designed and executed.
It was not clear: on line 107 A solution of 5 wt. % ESCaCO3 was prepared under vigorous stirring at 3000 rpm for 30 min. What was the solvent used to prepare the %wt% solution.

It would be added advantage if authors could provide the surface area measurements of all the samples to see pore volume of the particles.

Add the CS : chitosan in the abstract
Validity of the findings: The research finding are validated with several experiments and data collected.
From the experiments its not clear that the CaCO3/ SiO2 is a physical mixture ? or any formation of calcium silicate traces. Also in XRD of composite with Chitosan the peaks related to the Chitosan are missing, pl explain the reasons.
The percentages CaCO3 and  SiO2  in the mixture are advised to report
The percentage of mixture of CaCO3/ SiO2 in Chitosan should be reported.
Additional comments: The paper is well thought and experiment are well designed
It is advised to address all the comments before final publication


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 1
Reviewer: 5

Output:
Basic reporting: This manuscript is well organized. It was well written with clear and unambiguous, professional English used throughout.
Experimental design: Original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Validity of the findings: Obtained results are original. The conclusions are appropriately stated based on investigated data.
Additional comments: 1. Some specific words should be corrected or explained, such as: ESCaCO3, RHSiO2, what are ES and/or RH meaning?
2. A subsection “Chemicals and Reagents” is needed to add for indicating purity and listing of all chemicals used.
3. A subsection “Characterizations” is needed to add for listing all techniques have been used for characterization of synthesized materials.
4. All equations should be numbered and cited into body text.
5. A table must be added to compare the working conditions and the maximum adsorption capacity (Qmax) of the CS-SiO2/CaCO3 nanocomposites to other pervious reports.
6. Authors must check again the manuscript to correct all mistakes for examples: line 147, “


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Pervious comments have been addressed properly. No further comment.
Experimental design: Pervious comments have been addressed properly. No further comment.
Validity of the findings: Previous comment has been addressed properly. No further comment.
Additional comments: The manuscript is better shape both in technicality and in writings. I recommend to publish the current edition without major changes.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ADSORPTION OF PHENOL OVER BIO-BASED SILICA/CALCIUM CARBONATE (CS-SIO2/CACO3) NANOCOMPOSITE SYNTHESIZED FROM WASTE EGGSHELLS AND RICE HUSKS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Literature references, sufficient field background/context provided.
Clear and unambiguous, professional English used throughout
Experimental design: Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled.
Additional comments: N/A


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HIGH THROUGHPUT VIRTUAL SCREENING OF 230 BILLION MOLECULAR SOLAR HEAT BATTERY CANDIDATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well-written and the background is well represented with appropriate citations.

1. The GitHub link is broken: https://github.com/jensengroup/dha should be https://github.com/jensengroup/dha_htvs

2. It is a bit confusing that compound 9 in Table 3 and compound 10 in Table 4 have storage energies and reaction barriers that are not comparable. As I understand it, the properties of 9 are predicted by the DFT calculations, while those of 10 are given by the linear model, but a quick look might lead to the belief that 10 is actually better than 9.
Experimental design: The research is scientifically sound and the research question well stated. All the code and modelling notebooks and data are made freely available online. The technical details are described in sufficient detail in the manuscript, and further details are available by inspection of the provided code. The QM methodology is very well benchmarked in the supporting information and it is obvious that a lot of work has gone into this manuscript. It combines many different aspects such as library enumeration, machine learning and  automatic transition state searching with conformational search and the final product is very complete.

1. Regarding the machine learning, it is not clear to me what is the result of the train, validation and test sets. I would assume that the data in Figure 5, Figure S6 and Figure S8 is for the test set, but this should be clarified in the figures or the captions.
Validity of the findings: The presentation of the results and conclusions is very balanced, where the authors discuss also the limits of their methodology and the challenges associated with the synthesis of compound 9.

1. The molecules in Table 2 (6-7) are said to have low barriers for back reaction due to the hydrogen-bonding favoring the s-cis VHF form. Compound 10 has the same substitution pattern with an amine at position 2 and an aldehyde at position 1. Is compound 10 expected to have a similarly inflated reaction barrier as 6-7? In this case it should be highlighted as a limitation of the approach. This especially in light of the suggestion to replace the high-throughput virtual screening approach by the GA, which could get stuck in a false minimum.

2. The conclusion that “The overall methodological approach outlined in this paper is generally applicable to lead optimisation of properties involving chemical reactivity.” is too strong and should be qualified. Not all reactivity problems will be amenable to semi-empirical methods, particularly if challenging quantum-mechanically or if there are strong solvent effects. Also, it’s not certain that similar machine learning models employed will be equally successful to other reactivity problems.

4. The GA model finds compound 10 74% of the times, but it would be interesting to know the difference in predicted performance between 10 and the best molecule in the  rest of the runs. If something nearly as good is found, that would increase the perceived usefulness of the GA even more.
Additional comments: I have read the report by Koerstz et al. with significant interest. They describe a computational high-throughput study for finding better molecular solar heat batteries of the photo-switch dihydroazulene/vinylheptafulvene. The goal is to find molecules with both a higher energy storage density and a higher energy for the back reaction (longer thermal half-life) than the parent compound. They first identify the most promising molecules with 1-2 substituents, for which it is possible to test all different combinations with quantum chemistry, using a combination of semi-empirical methods and DFT. They then go on to investigate molecules with 3-7 substituents, which is a too large set for QM calculations (ca. 230 billion molecules). Instead, they train machine learning models (linear regression and LightGBM) based on the semi-empirical results of a smaller set and use the predictions of the machine learning models to single out ca 30 000 candidates for SQM calculations. Of these, the ca 1000 most promising are subjected to more accurate but time-consuming DFT calculations. The DFT calculations identify a particular candidate, molecule 9, which has promising properties in terms of a higher barrier for back reaction and a greater energy storage density than the parent compound. However, it also has lower absorption in the visible region and is challenging to obtain synthetically. Finally, the authors demonstrate that a genetic algorithm can be used together with a linear regression model to assess both the energy storage and energy of back reaction. The GA is able to quite consistently recover (72% of the runs) the best molecule in the set predicted by the linear regression model and could therefore potentially serve as a more economical alternative to the high-throughput screening that led to the discovery of molecule 9.

As a suggestion for future work (does not need to be added to this paper!): For the NBD-QC photo switch, the energy barrier of the back reaction and the absorption spectrum are closely related in that an increased energy storage density leads to a lower barrier for back reaction (10.1021/acs.accounts.0c00235). It would be interesting to see if this trend broadly holds true also for the DHA/VHFs studied in this set and if so, if there are ways to break the relationship. Already the fact that 9 is predicted to absorb at a similar wavelength as the parent compound is an indication that the connection might be less strong. Potentially it could also be investigated with semi-empirical methods such as sTDA or INDO/S.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HIGH THROUGHPUT VIRTUAL SCREENING OF 230 BILLION MOLECULAR SOLAR HEAT BATTERY CANDIDATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors performed a high-throughput virtual screening from a combinatorial library they generated from DHA to find a suitable thermocouple pair. This methodology used semiempirical methods, DFT calculations, and machine learning methods. They found the best candidate has an energy density of 0.38 kJ/g and a half-life of 10 days 4 hours.

The English through the text is clear and unambiguous. I consider that it has a well-provided context and pertinent references. The Figures are overall clear and well described in the text; with the exception of figure 3, the graph labels slightly differ from what is defined in the text. I consider that the manuscript is written in a professional way, its structure is clear, and has a concise methodology.

I consider that this manuscript meets the standard of the journal, its pertinence is well documented and the methodology is clear and unambiguous.
Experimental design: The authors defined the research question in a clear way; they establish the methodology to find the best possible candidate using a scaffold analysis, they first consider single and double substitutions on the DHA core to calculate energy barriers and storage energies using PM3 Hamiltonian and screening the 10 best molecules from there to be calculated using DFT M06-2X/6-31G(d) level of theory. From these results, the authors trained a linear regression model to screen the energy barriers and storage densities of the 42^7 compounds; then focusing on storage density values greater than 0.3 kJ/g, they reduced this library to 421 M molecules.

Following the results in this reduced library, the authors trained a gradient boosted model with new PM3 calculations and performed a binned sampling to get 957k molecules which energy barrier and storage density are above 165 kJ/mol and 0.4 kJ/g, respectively. They further performed a refinement to get 34241 unique molecules to be calculated using PM3 and found around 22 k molecules with storage density above 0.4 kJ/g and perform on these a PM3 adiabatic scan, giving 1177 suitable candidates that went under DFT refinement to find the best candidate having a storage density of 0.38 kJ/g and a barrier height of 130 kJ/mol.

This methodology design heavily relies on PM3 calculations, which are suitable for the organic molecules considered in this library. I consider that the ML methods used (linear regression and gradient boosting decision tree) are well implemented. The authors bound the capabilities of their approach and give the community a deep insight into the energetics and storage density of these parent couples. Furthermore, they applied a genetic algorithm and get comparable results to the screening process.
Validity of the findings: I consider that the findings of this work are well supported by the computational evidence the authors provided.

The methodology is clearly discussed. I consider that the conclusions are insightful and well supported by the evidence provided.

The authors perform a well-organized methodology to answer their research question.

They shared their datasets and code as public repo (github).
Additional comments: I would suggest that the authors please be more explicit in how is the process of vectorizing the molecules to be feed to the ML methods are. Or if they are using a standard algorithm such as Morgan fingerprints.

On synthetic accessibility, I’m aware that a quite small number of the possible combinatorial functionalizations could lead to synthetic viable molecules. I may suggest that, at least for the small screening library (the one tested using PM3 and TB methods), the authors could evaluate the synthetic complexity score (https://github.com/connorcoley/scscore) to have a complexity metric that can enrich the discussion of their results.

In Figure 3, the labels of electronic barriers and storage energies do not coincide as the same variables in the first paragraph of the Computational Methodology, please uniform the notation.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HIGH THROUGHPUT VIRTUAL SCREENING OF 230 BILLION MOLECULAR SOLAR HEAT BATTERY CANDIDATES
Review round: 1
Reviewer: 3

Output:
Basic reporting: - The computational pipeline introduced in this paper is very impressive and clearly well thought out and implemented. However, it is complex, with several steps involved, each using different subsets of data with different methods and models. Therefore perhaps a schematic diagram of the entire pipeline, either as a main or SI figure, would help guide the reader.
- In the manuscript, when the authors mention the number of substituents considered, they sometimes write “42” and other times “41” Please make this consistent.
Experimental design: no comment
Validity of the findings: - Can the authors add a comment somewhere in the main text on the possibilities or outlooks for comparing the predictions to experimental data? The project hinges on the assumption that the quantum chemistry calculations are an accurate representation of the ground truth values for storage energies and reaction barriers. So additional comments on how those DFT calculations are expected to correlate with experimental data would be valuable. (More specifically: I have read the section “Synthetic considerations”. However, what I’m referring to is the possibility of connecting the predicted thermodynamic/kinetic parameters to a database of experimental data.)
- In the summary and outlook, pg. 15, the authors mention “For example, their absorption profiles are not optimum.” Can they add an extra sentence/phrase to explain why?
Additional comments: - [OPTIONAL] One really nice part of the paper is when they select 109 molecules for further study with DFT. They demonstrate that the majority of the selected molecules have higher energy storage densities than the parent compound. While this is a very promising result, their argument/evidence would be strengthened even more if a statistical measure was attached to this finding. More specifically, what is the probability of finding a similar fraction of compounds with higher energy storage (than the parent compound) for random sets of 109 molecules (sampled several times). In other words, a p-value for the observed enrichment of high energy storage compounds. I’m not sure if this is computationally prohibitive, so that is why I’m tagging this as “optional”.
- In summary and outlook, pg. 14, third paragraph, there is a typo: “421 molecules” should be “421 million molecules”.
- Figure S6: The acronym “ML” appears in the figure legend, but the exact meaning of ML is not specified in the caption. Please fix this.
- Figure S2: Fig. S2 (A) has green data points that are circled in black. However, no mention of what this means appears in the figure legend. I know this is mentioned in the SI text, but adding this to the figure legend might help with clarity.
- I think it’s great that the authors provide access to the code through a repository.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HIGH THROUGHPUT VIRTUAL SCREENING OF 230 BILLION MOLECULAR SOLAR HEAT BATTERY CANDIDATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: All my concerns have been adequately addressed.
Experimental design: All my concerns have been adequately addressed.
Validity of the findings: All my concerns have been adequately addressed.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HIGH THROUGHPUT VIRTUAL SCREENING OF 230 BILLION MOLECULAR SOLAR HEAT BATTERY CANDIDATES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thanks for responding to my comments. I consider the manuscript is in good shape to be published in this journal.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: HIGH THROUGHPUT VIRTUAL SCREENING OF 230 BILLION MOLECULAR SOLAR HEAT BATTERY CANDIDATES
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed my previous comments and I have no further suggestions for improvements. The article should be accepted as is.