Sunday, May 5, 2013

Manuscript review: The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties

The reviews are in for +Jimmy Charnley Kromann's  MolCalc paper. Five reviewers!  I think the combined reviews may be longer than the manuscript.  Some preliminary thoughts.

Reviewer 3
"brief example of its use in their hands and some evidence of the positive impact the exercises have had on their students’ learning"

According to the author guidelines, Technology Reports only needs to describe "intended use".  However, Reviewer 5 offers some text and examples which we could quote (remember to acknowledge and check word count max 1600 words):

"I found the software to be clear, intuitive, and user-friendly, ... I also found the software to be a powerful teaching tool providing students with opportunities to: (1) visualize three-dimensional molecular shapes, (2) create their own molecules following simple rules of valence, and (3) explore structure-property relationships in molecules in more interesting and profound interactive ways.

In order to test students’ reactions, I had students in Physical Chemistry II carry out some lab/simulation exercises in two separate weeks within an introductory unit on molecular quantum mechanics/computational chemistry (see attached handouts Supplementary Materials). The students took well to the assignments; they were able to navigate the software with relative ease; and they were impressed with the power and utility of molecular orbital theory as implemented in these programs to answer questions regarding molecular properties. The students realized the limitations of the software imposed by the low level of theory needed to speed the calculations, and yet they were able to learn how compositional and structural parameters affect molecular properties in a relative way and to understand some basic chemical principles on a deeper level."

Other stuff: we need to redo the references, check ref 4 and add a reference to SMILES.  Not sure what auxiliary software is being referred to.

We need to add something the accuracy of the heat of formation (also the fact that molecules like H2 don't have a zero heat of formation) and frequencies.

Reviewer 4: We should address those 5 points

Reviewer 5

This person really went above and beyond and we will be using the comments and worksheets!

We are working on the CO2 bug.  I think we should remove the common names until it works right.  We address nonzero elemental heats of formation when talking about the accuracy.

We should fix the small errors.

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30-Apr-2013

Journal: The Journal of Chemical Education
Manuscript ID: ed-2013-00164n
Title: "The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties"
Author(s): Jensen, Jan; Kromann, Jimmy

Dear Dr. Jensen:

I have carefully evaluated your manuscript with the aid of three reviewers, and I would like to request that you make minor revisions to the manuscript to incorporate the reviewers’ comments, which appear at the end of this letter. Three reviewers suggest publication without revision, but please address the concerns expressed by reviewer 3, as well as the set of Additional Comments listed at the end of this letter.

Please submit your revision no later than 14-Jun-2013.

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I look forward to receiving your revised manuscript for publication in Journal of Chemical Education.

Sincerely yours,

xxx


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Reviewer(s)' Comments to Author:

Reviewer: 1

Recommendation: Publish as is.

Comments:
The paper was well written and offers instructors and students readily available access to simple calculations to useful information on a variety of platforms. The calculations are nothing new when compared to existing programs that are available, what is new here is access through the new generation of platforms.

The video provided, and I assume available to instructors and students, really demonstrates the ease by which the program can be utilized. We use Spartan with our organic course and there are, at times, issues as to student access.  This problem would seem to be resolved with Jensen and Kromann's approach.

A new approach to an established tool. I would encourage the publication of the manuscript.


Reviewer: 2

Recommendation: Publish as is.

Comments:
A very nice program.  This is a great and simple tool for introducing students and faculty to software like Spartan and Gaussian - and for illustrative purposes may actually be better because it runs so easily and quickly.  I can't wait to see it developed to include more options.  Personally I would love to be able to see output of the AO coefficients in the MO expansions for small molecules like diatomics for teaching purposes.


Reviewer: 3

Recommendation: Major revision.

Comments:
The authors have developed a free-access web-interface, MolCalc, that operates in conjunction with the Java-independent JSMol editor and the GAMESS computational code to permit students to construct a range of structures and to obtain ‘rough’ estimates of a variety of molecular properties rapidly.

As is the case with other student-level molecular modeling programs, the speed of the calculations is related to the size and complexity of the structure submitted; this interface can accommodate up to 11 non-H atoms, and elements up to Ar.

Having viewed the video (link provided) and read much of the information provided in the accompanying references, this reviewer is of the opinion that the MolCalc interface (plus the required auxiliary downloads required) does not have a steep learning curve even for students new to modeling, that the most ‘demanding’ preparation for using the interface may be accessing the several auxiliary software packages it requires, that it could serve as a useful instructional tool, and that it would be well-received by instructors who may still find the costs of at least some of the other commercially available computational software for student use prohibitive.

The authors envision this tool as an aid for both classroom instruction and for out-of-class assignments with the primary goal being the enlivening of students’ ‘chemical intuition’ for structure-property relationships. They have written, and cite, a modeling/computational monograph (reviewed earlier by JCE and others) that provides some useful examples of what the MolCalc can do [note: the www link provided in Ref. #4 in the ms was dead as attempted by this reviewer. I did access information about the text by an alternative route.] However, this ms does not provide an example - nor any indication at all- of how, and ‘how much’ the authors have used/use the MolCalc interface in their own instruction. This gap is especially important in that they assert its primary value – despite the approximate nature of the data obtained - as a productive means of improving students’ ‘chemical intuition’. While that assertion may seem self-evident, absent more detail, the assertion leaves an impression akin to reading a ‘pitch’ rather than learning about a tested pedagogical approach. It would be helpful to interested readers to have more information about how, and with what students, the authors employ this system in their own institution.

It would also be important to learn just how approximate various, but typical, calculations are, i.e., are the approximations ~10% deviation or an order of magnitude? Are related values (e.g., vibrational frequencies) in the ‘correct’ relative order?

The potential utility of MolCalc notwithstanding, as submitted, this ms seems unsatisfactory for publication in this Journal. This reader has inferred that the text is at least in part cut-and- pasted from some other manuscript or text, perhaps from the www sites given in the first few references, as the wording and claims are the same as seen there. This supposition helped explain why the assignment of reference numbers throughout is irregular, and not at all standard. There seems to be no ref. #3; #6 precedes #5; #8 is placed between numbers 10 and 12, and ref. #11 follows #9. This apparent clumped-together composition renders the text uneven and not cohesive. Also, with regard to literature citations, while most instructors involved with computational work even at a ‘low level’ may likely be familiar with SMILES notation, including a citation for its use is required (p. 3, line 39).

It is not clear to this reader why the screenshot that follows the Abstract is placed there. It is not labeled as a Figure relevant to the text of the ms, and the screenshot that precedes the entire ms, as received, is redundant – perhaps a simple oversight.

Two other typographical errors: line 48 on p. 4 repeats the word ‘separately’ unnecessarily, and the end “Note” should read “.... no financial interest....”.

Author Guidelines for a TechnoIogy Report limit the word-count. Compared to several others in this category in recent issues of this Journal, the length of this ms may exceed that limit - but I did not ‘count’. Those guidelines also indicate that a submission should make [more] clear (beyond ‘faster’ access to ‘estimates’ of molecular properties), what learning/skills have been (documented) improved. The use of on-line-only Supplementary Material section might be the most appropriate way to address this and could permit the published text to be condensed accordingly.

In summary, if the authors are willing to redraft and restructure this text, clean up the citation format (order & numbering), include at least a brief example of its use in their hands and some evidence of the positive impact the exercises have had on their students’ learning - besides rapid access to estimated properties, the ms can make a positive contribution to the instructional literature.


Reviewer: 4

Recommendation: Publish as is.

Comments:
This brief manuscript reports the first version of an application involving the use of JSmol, and deserves to be published.  As has been reported by Hanson and others, and stated by the authors of this paper, JSmol's principle advantage over Jmol is that Java is not required - everything is based on JavaScript, allowing many more operating systems to easily run the programs.  The Molecular Calculator provides us with a very nice example of the use of JSmol on a limited set of possibilities, but that set can be expanded as more people develop JSmol examples.  I for one find the limited set to be less constraining than I had originally thought it to be, and suspect that this application will be heavily used by people in a number of different courses, either as a build-up to a more sophisticated set of models, or as the stand-alone structure and calculation program used in those courses.

Additional Comments:

1. Please number the references sequentially in the text.
2. Please add the names of the Web sites in the references with URLs.
3. Please add the titles of the articles to the references.
4. TOC graphic: A small inset containing the MolCalc name would, if possible, be a nice addition to the TOC graphic.
5. Figure 1: The control buttons are not visible in this figure when the molecule portion is made normal size for publishing. Because these buttons are important aspects of this figure (they represent the controls for the molecule editing module) enlarged versions of these controls are needed, perhaps as insets or maybe separate panels with indications showing where in the original screenshot these enlargements were taken

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30-Apr-2013

Journal: Journal of Chemical Education
Manuscript ID: ed-2013-00164n
Title: "The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties"
Author(s): Jensen, Jan; Kromann, Jimmy

Dear Dr. Jensen:

After I sent you my decision letter a reviewer (Reviewer 5) belatedly sent me review comments, and,  in addition, two student hand-outs that the reviewer prepared for students in a physical chemistry course. I am attaching these documents to this letter and request that you also consider the comments and suggestions of Reviewer 5. If you would like to make the hand-outs available to JCE readers, I suggest you upload those files, edited as you deem necessary, with your revision as Supporting Information, and refer to these instructional resources in your manuscript. It would be accordingly appropriate for you to acknowledge the role of a reviewer in the Acknowledgement section of the manuscript.

Please let me know if you have any questions.

Sincerely yours,

xxx

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Reviewer: 5

This technology report describes web-based software for constructing and visualizing relatively small molecules composed of atoms no larger than argon, and viewing some of their calculated molecular properties. The calculated molecular properties include some thermodynamic properties (enthalpies and entropies), molecular orbital energies and shapes, and vibrational modes and frequencies. I found the software to be clear, intuitive, and user-friendly, as the authors claim on line 57 of the text. I also found the software to be a powerful teaching tool providing students with opportunities to: (1) visualize three-dimensional molecular shapes, (2) create their own molecules following simple rules of valence, and (3) explore structure-property relationships in molecules in more interesting and profound interactive ways.

In order to test students’ reactions, I had students in Physical Chemistry II carry out some lab/simulation exercises in two separate weeks within an introductory unit on molecular quantum mechanics/computational chemistry (see attached handouts). The students took well to the assignments; they were able to navigate the software with relative ease; and they were impressed with the power and utility of molecular orbital theory as implemented in these programs to answer questions regarding molecular properties. The students realized the limitations of the software imposed by the low level of theory needed to speed the calculations, and yet they were able to learn how compositional and structural parameters affect molecular properties in a relative way and to understand some basic chemical principles on a deeper level.

The students also discovered some glitches in the software that might be addressed by the authors in their editing for publication. For example, they could not successfully build a CO2 molecule in JSmol. The software insisted that this molecule did not have a closed-shell electron configuration (probably because of the way it was constructed from methane). They could build the molecule and “Minimize” its structure using MMFF, but they could not “Calculate” further. Secondly, the calculated enthalpies of formation of elements were not zero. It was unclear how these quantities were determined by the software, and this made it difficult or impossible to determine calculated enthalpies of reactions. Finally, many of the common names determined by the software were unusual. Outside of these small concerns, the students found the software to be a very accessible, useful, and instructive tool, and I agree.

The following minor editorial changes are suggested:
1. Line 34—use “estimate” not “estimates”
2. Line 57—add a comma after “clear”
3. Line 72—insert “be” after “then”
4. Line 90—delete one “separately”
5. Modify reference numbering to be sequential.

I believe that this technology report and software is a valuable contribution to the pedagogy of molecular modeling/computational chemistry. I found it quite useful to help students understand molecular orbital theory and learn how to apply it to simple molecular systems. The report should be published after consideration of the above comments and suggestions.
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