Friday, May 31, 2013
Thursday, May 30, 2013
Wednesday, May 29, 2013
Sunday, May 26, 2013
Taking a chemistry MOOC - part 2
Just submitted the homework problems for week 2 (non-ideal gasses, virial coefficients, intermolecular interactions) in +Chris Cramer's online Statistical Molecular Thermodynamics course.
Just like for week 1, I noticed that I do the exact same thing that I observe in my students. I start with problem 1 and then go hunting for the equation or plot I need, and repeat. Assigning questions that cover all the key concepts is therefore important. Doing a brilliant lecture on a topic is mostly wasted unless followed by at least one homework question. Also, asking questions that checks understanding of concepts rather than equations is important (and Chris does this). Finally, I was happy to see a few questions that touched on last weeks material, which allowed me to brush up on that as well.
One thing I noticed in myself is that when I get a question wrong on the homework (this is a purely hypothetical scenario of course), I would dearly love to be presented with a similar problem and given a chance to redeem myself, even if it didn't "count" for anything. There's a teachable moment going lost here.
After I started this course I came across a blogpost entitled "Is a MOOC a Textbook or a Course?" and further internet-digging let me to the phrase the "MOOC is the new textbook" and I really think that is true. As I have argued before I think modern textbooks have become horribly bloated and overpriced compromises written with the instructor, and not the student, in mind. In this course the textbook is replaced with a set of (free!) Powerpoint slides and corresponding lectures. Much more concentrated and to-the-point material in a much more digestible form.
People who are contemplating writing a new textbook should seriously consider making a MOOC instead: make some Powerpoint slides, use them to make some video lectures, write some multiple choice problems, and put everything up on a website. All the tools you need are freely available: Google docs, Screencast-o-matic, Youtube, and Google Docs or Blogger.com.
Furthermore, if you are a teacher, you should seriously consider writing your owntextbook MOOC for your course. My guess is you're already halfway done.
And remember, the first O in MOOC stands for open.
This work is licensed under a Creative Commons Attribution 3.0 Unported License.
Just like for week 1, I noticed that I do the exact same thing that I observe in my students. I start with problem 1 and then go hunting for the equation or plot I need, and repeat. Assigning questions that cover all the key concepts is therefore important. Doing a brilliant lecture on a topic is mostly wasted unless followed by at least one homework question. Also, asking questions that checks understanding of concepts rather than equations is important (and Chris does this). Finally, I was happy to see a few questions that touched on last weeks material, which allowed me to brush up on that as well.
One thing I noticed in myself is that when I get a question wrong on the homework (this is a purely hypothetical scenario of course), I would dearly love to be presented with a similar problem and given a chance to redeem myself, even if it didn't "count" for anything. There's a teachable moment going lost here.
After I started this course I came across a blogpost entitled "Is a MOOC a Textbook or a Course?" and further internet-digging let me to the phrase the "MOOC is the new textbook" and I really think that is true. As I have argued before I think modern textbooks have become horribly bloated and overpriced compromises written with the instructor, and not the student, in mind. In this course the textbook is replaced with a set of (free!) Powerpoint slides and corresponding lectures. Much more concentrated and to-the-point material in a much more digestible form.
People who are contemplating writing a new textbook should seriously consider making a MOOC instead: make some Powerpoint slides, use them to make some video lectures, write some multiple choice problems, and put everything up on a website. All the tools you need are freely available: Google docs, Screencast-o-matic, Youtube, and Google Docs or Blogger.com.
Furthermore, if you are a teacher, you should seriously consider writing your own
And remember, the first O in MOOC stands for open.
This work is licensed under a Creative Commons Attribution 3.0 Unported License.
Wednesday, May 22, 2013
Quantum Biochemistry: the talk
Here are the slides for the talk I will be giving tomorrow at the DPM3.2 meeting.
Update: now with audio:
Update: now with audio:
Sunday, May 19, 2013
New manuscript: Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
+Anders Steen Christensen's study on protein structure validation is now on arXiv. It was submitted to PNAS but was rejected without review. So now we are trying JACS.
Here is the abstract:
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.
Here is the abstract:
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.
Why is life chiral?
Ingeniøren, the magazine of the Danish society for engineers, has a column where people submit questions, which are then farmed out to scientists who provide short answers.
The question send to me is (translated from Danish)
This is not known but there is some speculation, which can be divided into two general categories: When life began, there were (1) a greater concentration of biologically relevant molecules with the mirror image form that are now found in living organisms, and (2) equal concentrations of mirror-image forms, and the mirror-image form we see now in living organisms was chosen by chance and then copied.
Category 1: It came from outer space
Amino acids with a higher concentration of the mirror-image form that is now found in living organisms have been found in meteorites on Earth. So if a sizable part of life's building blocks came from space, this may be the answer.
The reason for this difference in concentration is likely to result from chemical reactions in space that are affected by "polarized" light from the stars. Light comes also two mirror-image forms and starlight has a little bit more of one kind. This is called polarized light, which kan affect chemical reactions in such a way that as to form more of one mirror-image form than the other. The light must travel long distances to be polarized so that the sunlight that hits the Earth is not polarized.
Beta-decay, a sort of natural radioactive radiation, can also lead to polarized light here on earth, but it is uncertain whether the amount of light is enough to have a practical effect on chemical reactions.
Category 2: That's life
Because the genetic code is the same in all organisms, we assume life as we know it may lead back to a single "primordial cell", as it is unlikely that such a complex system can be created randomly twice. Whether the the reason for this is that life originated only once, or whether this cell happened to survived where other cells (in other biochemical ways to copy object) died, is not known.
The same considerations apply to the molecules and reactions which underlie life. We know that many molecules of the same mirror-image form "clumps together" and that many self-replicating molecules retain their mirror image form. It is therefore possible that a group of molecules of the same mirror-image form by chance clumped together in such a way that they can make copies of themselves, and this is the basis of our primordial cell. If this only happened on one occasion, it may explain why we only see a mirror image form in living organisms.
The question send to me is (translated from Danish)
Chemical substances are found in two variants which are each other's mirror image. In an ordinary chemical reaction in the laboratory, there is formed the same amount of the two mirror image forms. In the natural products and organisms there are only one of the two mirror image forms. Why is there only one mirror-image form of natural substances and living organisms?Once you know the term for this (homochirality) there is plenty of information on the web, including a wiki page. Here's me trying to get my head around some of it and explain it in layman's terms. Comments welcome.
This is not known but there is some speculation, which can be divided into two general categories: When life began, there were (1) a greater concentration of biologically relevant molecules with the mirror image form that are now found in living organisms, and (2) equal concentrations of mirror-image forms, and the mirror-image form we see now in living organisms was chosen by chance and then copied.
Category 1: It came from outer space
Amino acids with a higher concentration of the mirror-image form that is now found in living organisms have been found in meteorites on Earth. So if a sizable part of life's building blocks came from space, this may be the answer.
The reason for this difference in concentration is likely to result from chemical reactions in space that are affected by "polarized" light from the stars. Light comes also two mirror-image forms and starlight has a little bit more of one kind. This is called polarized light, which kan affect chemical reactions in such a way that as to form more of one mirror-image form than the other. The light must travel long distances to be polarized so that the sunlight that hits the Earth is not polarized.
Beta-decay, a sort of natural radioactive radiation, can also lead to polarized light here on earth, but it is uncertain whether the amount of light is enough to have a practical effect on chemical reactions.
Category 2: That's life
Because the genetic code is the same in all organisms, we assume life as we know it may lead back to a single "primordial cell", as it is unlikely that such a complex system can be created randomly twice. Whether the the reason for this is that life originated only once, or whether this cell happened to survived where other cells (in other biochemical ways to copy object) died, is not known.
The same considerations apply to the molecules and reactions which underlie life. We know that many molecules of the same mirror-image form "clumps together" and that many self-replicating molecules retain their mirror image form. It is therefore possible that a group of molecules of the same mirror-image form by chance clumped together in such a way that they can make copies of themselves, and this is the basis of our primordial cell. If this only happened on one occasion, it may explain why we only see a mirror image form in living organisms.
Saturday, May 18, 2013
Taking a chemistry MOOC - part 1
The massively online open course (MOOC)
I, along with almost 8000 other people, am taking Chris Cramers' MOOC Statistical Molecular Thermodynamics, which is officially starting Monday. I am curious how a MOOC works in practice So and what Chris chooses to focus on.
Step 1 is to sign up and get a login to the course, which gets you access to the course material. I signed up in February, but haven't gotten an email yet about the fact that the course material is available. Good thing I follow Chris on twitter.
So far material for the first 3 weeks are available. The topic for week 1 is quantization and energy levels. The material for week 1 consists of 8 video lectures (between 8 and 16 minutes each) with corresponding powerpoint slides, and a homework assignment with 10 multiple choice questions. Five of the videos have one or more multiple choice questions embedded in them, and you can also download detailed answers to these questions.
"The videos are the core content of this course." The idea, according to the website, it is "that you download the homework pdfs and familiarize yourself with the questions early on. As you view the videos, keep the homework problems in front of you so that you can make connections between the lectures, the demonstrations and the problems."
Once you have finished the homework you submit it on the web site. The deadline for submission for week 1 is May 31st, and the answers become available the next day. Update: when you submit your answers, you are immediately told whether it is right or wrong. Also, this week, remember not to confuse De with D0 (happened to a friend of mine ...)
There is also a discussion forum, monitored by instructors.
Some thoughts
Chris made the videos, slides and homework problems. What does Coursera provide? (1) A website that keeps track of users responses to the homework (and later the final exam) needed for the certificate you get at the end and (2) a way to embed multiple choice questions in a video.
If one is not issuing certificates, I'm not sure Coursera is needed, but this is only a first impression. Embedding quizzes in videos can be solved by shorter videos that end in a quiz, i.e. watch this video, then answer this question.
From a teachers perspective I think the main practical difference between regular teaching and a MOOC (as exemplified by this course) is that you don't rely on a textbook with regard to reading and assignments (in addition to making all the videos of course).
I'm not sure how I feel about using Powerpoint lectures vs pencasts. Powerpoint can go a bit fast, but here you can rewind and you get a written record of the lecture through the slides.
I, along with almost 8000 other people, am taking Chris Cramers' MOOC Statistical Molecular Thermodynamics, which is officially starting Monday. I am curious how a MOOC works in practice So and what Chris chooses to focus on.
Step 1 is to sign up and get a login to the course, which gets you access to the course material. I signed up in February, but haven't gotten an email yet about the fact that the course material is available. Good thing I follow Chris on twitter.
So far material for the first 3 weeks are available. The topic for week 1 is quantization and energy levels. The material for week 1 consists of 8 video lectures (between 8 and 16 minutes each) with corresponding powerpoint slides, and a homework assignment with 10 multiple choice questions. Five of the videos have one or more multiple choice questions embedded in them, and you can also download detailed answers to these questions.
"The videos are the core content of this course." The idea, according to the website, it is "that you download the homework pdfs and familiarize yourself with the questions early on. As you view the videos, keep the homework problems in front of you so that you can make connections between the lectures, the demonstrations and the problems."
Once you have finished the homework you submit it on the web site. The deadline for submission for week 1 is May 31st, and the answers become available the next day. Update: when you submit your answers, you are immediately told whether it is right or wrong. Also, this week, remember not to confuse De with D0 (happened to a friend of mine ...)
There is also a discussion forum, monitored by instructors.
Some thoughts
Chris made the videos, slides and homework problems. What does Coursera provide? (1) A website that keeps track of users responses to the homework (and later the final exam) needed for the certificate you get at the end and (2) a way to embed multiple choice questions in a video.
If one is not issuing certificates, I'm not sure Coursera is needed, but this is only a first impression. Embedding quizzes in videos can be solved by shorter videos that end in a quiz, i.e. watch this video, then answer this question.
From a teachers perspective I think the main practical difference between regular teaching and a MOOC (as exemplified by this course) is that you don't rely on a textbook with regard to reading and assignments (in addition to making all the videos of course).
I'm not sure how I feel about using Powerpoint lectures vs pencasts. Powerpoint can go a bit fast, but here you can rewind and you get a written record of the lecture through the slides.
Thursday, May 9, 2013
Frontiers in Theoretical and Computational Chemistry
I was recently invited to be a "Review Editor" for Frontiers in Theoretical and Computational Chemistry. One of the commendable features of FTCC is that the reviews are done by a board review editors and the names of these reviewers are displayed on the published manuscript. I sign all my reviews already, so I think that's an excellent idea. In fact I think they should publish the reviews too.
FTCC is also open access, publishes under the CC-BY license, arXiv-friendly and "significance" is not a review criterion. So what's not to like? Well, the publishing fee is a bit steep: €1600 (though it may be possible to get a fee waiver). Considering the considerably lower fees at PeerJ or even PLoS ONE the size of this fee is a result either of inefficiency or avarice (FTCC is owned by the Nature Publishing Group). But as the fees appear to have been set before NPG took over, it looks like it's just inefficiency.
So I have decided to accept and I might even submit a paper there if I can get a partial fee waiver or land a big grant.
FTCC is also open access, publishes under the CC-BY license, arXiv-friendly and "significance" is not a review criterion. So what's not to like? Well, the publishing fee is a bit steep: €1600 (though it may be possible to get a fee waiver). Considering the considerably lower fees at PeerJ or even PLoS ONE the size of this fee is a result either of inefficiency or avarice (FTCC is owned by the Nature Publishing Group). But as the fees appear to have been set before NPG took over, it looks like it's just inefficiency.
So I have decided to accept and I might even submit a paper there if I can get a partial fee waiver or land a big grant.
Sorry Inorganic Chemistry: I only review for arXiv-friendly journals
From: Jan Halborg Jensen
Sent: Thursday, May 02, 2013 12:38 PM
To: xx
Subject: Re: Invitation to Review Manuscript ic-2013-xx
Dear xx
Does Inorganic Chemistry consider paper that have been deposited on the preprint server arXiv? I ask because I am boycotting (i.e. not reviewing for or submitting to) all journals that don't.
Best regards, Jan
-----
From: xxx
Sent: Friday, May 03, 2013 10:21 PM
To: Jan Halborg Jensen
Subject: Re: Invitation to Review Manuscript ic-2013-xxx
Prof. Jensen, Our policy with regards to arXiv is as follows:
If a submission to IC is essentially the same as a preprint in arXiv, then it will not be considered for publication, but if it differs significantly (and contains significant new work), then it will be considered.
I hope this answers your question.
xxx
IC Journal office
----
From: xx
Sent: Thursday, May 09, 2013 7:48 AM
To: Jan Halborg Jensen
Subject: Reminder: Inorganic Chemistry
09-May-2013
Dear Dr. Jensen:
Recently, I invited you to review Manuscript ID ic-2013-xx. I have yet to hear from you about this.
This e-mail is simply a reminder to respond to the invitation to review. I appreciate your help in accomplishing our goal of having an expedited reviewing process. Please do not hesitate to contact me if I can be of any assistance.
Sincerely,
xx
-------
From: Jan Halborg Jensen
Sent: Thursday, May 09, 2013 10:25 AM
To: xx
Subject: RE: Reminder: Inorganic Chemistry
Dear xx
I am afraid I won't be able to review this paper, because I find Inorganic Chemistry's policy with regard to pre-print deposition on arXiv too restrictive and not in the best interest of science. I urge you to re-consider this policy, in which case I would be happy to serve as a reviewer.
Best regards, Jan
Monday, May 6, 2013
Manuscript review: Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program
The review of +Casper Steinmann 's paper on PCM and semi-empirical methods is back. First impressions
First of all it's a real pleasure to deal with an editor like this. Second:
Accuracy
Not quite sure yet how to address this yet. Some thoughts. I think Chudinov et al. might have implemented D-PCM, which is not guaranteed to get the same result as C-PCM I think. If we increase the number of tesserae do we get closer to Chudinov et al.? Also, what is the RMSD to experiment for our implementation? Any agreement with experiment must be considered fortuitous for both Chudinov et al. and us, since both studies only consider the electrostatic part of the solvation free energy.
Numerical stability
Add at the end of 2nd paragraph in conclusions: "We therefore consider the current implementation a working code for all practical purposes, but welcome feedback from readers who encounter numerical stability problems for large molecules."
It would also be interesting to see how MOPAC performs for these systems.
Clarifications/references
**"Moreover, it is not clear to me why calculations performed with DIIS should be slower than the case with no acceleration."
We should add a sentence saying "The increase in CPU time when using DIIS is due to the extra matrix operations associated with this method, which represent the computational bottleneck for sem-empirical methods."
**"Presenting convergence tests is tedious and not generally interesting to the public, but it is mandatory if the method only converges with very tight parameters and the article only deals with the timing, scalability and implementation issues of standard methods."
When using PCM the SCF converges with all three choices of convergence acceleration. We simply checked all three to see which one is the fastes.
**"As minor points, some of the formulas presented and the jargon adopted are not completely clear. In particular: it is not clear to me why there is a r_A in the denominator of equation (4)"
r_A is clearly defined immediately after equation (3)
**"equation (14) is not usually addressed as the PCM solvation energy, as it lacks wavefunction and geometry relaxation effects (usual PCM solvation energy is defined as the difference between the free energy of the system optimized -nuclei and electrons- in solution and the one of the system optimized in vacuum);"
We should replace "solvation energy" with "electrostatic interaction free energy"
**"it is not clear to me what STO-3G calculations refer to (perhaps Hartree-Fock calculations with STO-3G basis set?);"
We should replace "STO-3G" with "RHF/STO-3G" throughout
**"before equation (16) the authors refer to frequencies, without having introduced before what they are referring to (vibrational frequencies, computed from the diagonalization of the Hessian, as inferred from a following section);"
We should replace "frequencies" with "vibrational frequencies" right before Eq (16).
** "DIIS and SOSCF lack of a proper reference, if not of the full acronym explanation; a reference to GEPOL should be included, as all the other methods have been properly referenced."
Yes, define the acronyms and reference the methods.
----
From: PLOS ONE <plosone@plos.org>
Date: Fri, May 3, 2013 at 10:46 AM
Subject: PLOS ONE Decision: Revise [PONE-D-13-11686]
To: xxx
PONE-D-13-11686
Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program
PLOS ONE
Dear Dr Steinmann,
Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit, but is not suitable for publication as it currently stands. Therefore, my decision is "Major Revision."
First, I must apologize for the length of time that this manuscript was under review. It was extremely difficult to find reviewers for this manuscript. Second, please ignore the reviewer's suggestion to submit to another journal. If properly revised, this work would be suitable for PLoSOne
We invite you to submit a revised version of the manuscript that addresses the points below:
1) the reviewer's comments mostly concern the clarity and motivation behind this work. Since PloSOne is not a technical computational journal, these comments must be addressed. Please provide the citations and explanations requested below.
2) the reviewer raises concerns as to whether or not the method actually works given the errors and numeric stability issues. Please provide further explanations as to the sources of these issues and in what context this could be considered a working code.
We encourage you to submit your revision within forty-five days of the date of this decision.
When your files are ready, please submit your revision by logging on to http://pone.edmgr.com/ and following the Submissions Needing Revision link. Do not submit a revised manuscript as a new submission. Before uploading, you should proofread your manuscript very closely for mistakes and grammatical errors. Should your manuscript be accepted for publication, you may not have another chance to make corrections as we do not offer pre-publication proofs.
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.
Please also include a rebuttal letter that responds to each point brought up by the academic editor and reviewer(s). This letter should be uploaded as a Response to Reviewers file.
In addition, please provide a marked-up copy of the changes made from the previous article file as a Manuscript with Tracked Changes file. This can be done using 'track changes' in programs such as MS Word and/or highlighting any changes in the new document.
If you choose not to submit a revision, please notify us.
Yours sincerely,
xxx
Academic Editor
PLOS ONE
Journal requirements:
When submitting your revision, we need you to address these additional
requirements.
1. Please include a copy of Supplementary Figure S1 which you refer to
in your text.
[Note: HTML markup is below. Please do not edit.]
Reviewers' comments:
Reviewer's Responses to Questions
Comments to the Author
1. Is the manuscript technically sound, and do the data support the conclusions?
The manuscript must describe a technically sound piece of scientific
research with data that supports the conclusions. Experiments must
have been conducted rigorously, with appropriate controls,
replication, and sample sizes. The conclusions must be drawn
appropriately based on the data presented.
Reviewer #2: Partly
________________________________
Please explain (optional).
Reviewer #2: The article describe the parallel implementation of a continuum-solvation scheme in combination with semi-empirical methods in a quantum-chemistry simulation package. The article is very clear, the results are reported rigorously and deficiencies of the methods have been clearly underlined. Nonetheless I would not recommend publication of this manuscript in PLOS one, as it appears to be not significantly novel with respect to other works in the literature: the
methods implemented are all standard in the quantum-chemistry literature, as well as their combination. The implementation is not deeply discussed in the text and, although showing reasonably good performances, does not appear as highly innovative, the solvation scheme considered (C-PCM) is already one of the simplest and fastest of its class. Moreover, results show deviations from a previous implementation of different authors (dating back to 1992) which are
not negligible: an error of almost 2 kcal/mol on solvation energies of the order of 60 kcal/mol is almost as big as the accuracy of the solvation model adopted. The authors suggest that numerical
differences in the implementation (cavity tessellation) are responsible for this deviation, suggesting also that their method is the one performing worse. It would have been more correct at this point to analyze the sources of such inaccuracy more in details. Similarly, some of the geometry optimizations and frequency calculations show numerical instabilities which are correctly pointed out, but not solved. Apart from the cases in which these deficiencies
only come out from the underlying algorithms in vacuum, the authors should at least have addressed more in details the numerical accuracy of the implemented method. Moreover, it is not clear to me why calculations performed with DIIS should be slower than the case with
no acceleration. Presenting convergence tests is tedious and not generally interesting to the public, but it is mandatory if the method only converges with very tight parameters and the article only deals with the timing, scalability and implementation issues of standard methods. As minor points, some of the formulas presented and the jargon adopted are not completely clear. In particular: it is not clear to me why there is a r_A in the denominator of equation (4); equation (14) is not usually addressed as the PCM solvation energy, as it lacks wavefunction and geometry relaxation effects (usual PCM solvation energy is defined as the difference between the free energy of the system optimized -nuclei and electrons- in solution and the one of the system optimized in vacuum); it is not clear to me what STO-3G calculations refer to (perhaps Hartree-Fock calculations with STO-3G basis set?); before equation (16) the authors refer to frequencies, without having introduced before what they are referring to (vibrational frequencies, computed from the diagonalization of the Hessian, as inferred from a following section); DIIS and SOSCF lack of a proper reference, if not of the full acronym explanation; a reference to GEPOL should be included, as all the other methods have been properly referenced.
________________________________
2. Has the statistical analysis been performed appropriately and rigorously?
Reviewer #2: Yes
________________________________
Please explain (optional).
Reviewer #2: (No Response)
________________________________
3. Does the manuscript adhere to standards in this field for data availability?
Authors must follow field-specific standards for data deposition in
publicly available resources and should include accession numbers in
the manuscript when relevant. The manuscript should explain what steps
have been taken to make data available, particularly in cases where
the data cannot be publicly deposited.
Reviewer #2: Yes
________________________________
Please explain (optional).
Reviewer #2: The authors use a locally modified version of an open
access quantum-chemistry code. The method of the authors is not
currently available for verification of the results, but it is
anticipated in the text that it will be available with the next code
release.
________________________________
4. Is the manuscript presented in an intelligible fashion and written
in standard English?
PLOS ONE does not copyedit accepted manuscripts, so the language in
submitted articles must be clear, correct, and unambiguous. Any
typographical or grammatical errors should be corrected at revision,
so please note any specific errors below.
Reviewer #2: Yes
________________________________
Please explain (optional).
Reviewer #2: Apart from a typo at the very beginning of the manuscript (page one, fourth line of the introduction "the" is repeated twice), the article is written in good comprehensible English. The jargon adopted and the acronyms are not always correctly addressed, as pointed out in the comments above. Moreover, I would avoid reporting explicitly the code keywords in the main text of the article, as is done in the computational details. As these details are important for the reproducibility of the results, I agree with the authors that they should be presented, but I would rather use the supplementary informations.
________________________________
5. Additional Comments to the Author (optional)
Please offer any additional comments here, including concerns about
dual publication or research or publication ethics.
Reviewer #2: In general, the manuscript appears to contain good work on a very technical issue. More details on the sources of numerical instabilities and deviations from previous results would be needed to complete the reported work. These further details, which I consider necessary, would make the work even more technical. As PLOS one is not focused on the implementation of computational methods, I would suggest submission to a more specific journal.
________________________________
6. If you would like your identity to be revealed to the authors,
please include your name here (optional).
Your name and review will not be published with the manuscript.
Reviewer #2: (No Response)
First of all it's a real pleasure to deal with an editor like this. Second:
Accuracy
Not quite sure yet how to address this yet. Some thoughts. I think Chudinov et al. might have implemented D-PCM, which is not guaranteed to get the same result as C-PCM I think. If we increase the number of tesserae do we get closer to Chudinov et al.? Also, what is the RMSD to experiment for our implementation? Any agreement with experiment must be considered fortuitous for both Chudinov et al. and us, since both studies only consider the electrostatic part of the solvation free energy.
Numerical stability
Add at the end of 2nd paragraph in conclusions: "We therefore consider the current implementation a working code for all practical purposes, but welcome feedback from readers who encounter numerical stability problems for large molecules."
It would also be interesting to see how MOPAC performs for these systems.
Clarifications/references
**"Moreover, it is not clear to me why calculations performed with DIIS should be slower than the case with no acceleration."
We should add a sentence saying "The increase in CPU time when using DIIS is due to the extra matrix operations associated with this method, which represent the computational bottleneck for sem-empirical methods."
**"Presenting convergence tests is tedious and not generally interesting to the public, but it is mandatory if the method only converges with very tight parameters and the article only deals with the timing, scalability and implementation issues of standard methods."
When using PCM the SCF converges with all three choices of convergence acceleration. We simply checked all three to see which one is the fastes.
**"As minor points, some of the formulas presented and the jargon adopted are not completely clear. In particular: it is not clear to me why there is a r_A in the denominator of equation (4)"
r_A is clearly defined immediately after equation (3)
**"equation (14) is not usually addressed as the PCM solvation energy, as it lacks wavefunction and geometry relaxation effects (usual PCM solvation energy is defined as the difference between the free energy of the system optimized -nuclei and electrons- in solution and the one of the system optimized in vacuum);"
We should replace "solvation energy" with "electrostatic interaction free energy"
**"it is not clear to me what STO-3G calculations refer to (perhaps Hartree-Fock calculations with STO-3G basis set?);"
We should replace "STO-3G" with "RHF/STO-3G" throughout
**"before equation (16) the authors refer to frequencies, without having introduced before what they are referring to (vibrational frequencies, computed from the diagonalization of the Hessian, as inferred from a following section);"
We should replace "frequencies" with "vibrational frequencies" right before Eq (16).
** "DIIS and SOSCF lack of a proper reference, if not of the full acronym explanation; a reference to GEPOL should be included, as all the other methods have been properly referenced."
Yes, define the acronyms and reference the methods.
----
From: PLOS ONE <plosone@plos.org>
Date: Fri, May 3, 2013 at 10:46 AM
Subject: PLOS ONE Decision: Revise [PONE-D-13-11686]
To: xxx
PONE-D-13-11686
Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program
PLOS ONE
Dear Dr Steinmann,
Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit, but is not suitable for publication as it currently stands. Therefore, my decision is "Major Revision."
First, I must apologize for the length of time that this manuscript was under review. It was extremely difficult to find reviewers for this manuscript. Second, please ignore the reviewer's suggestion to submit to another journal. If properly revised, this work would be suitable for PLoSOne
We invite you to submit a revised version of the manuscript that addresses the points below:
1) the reviewer's comments mostly concern the clarity and motivation behind this work. Since PloSOne is not a technical computational journal, these comments must be addressed. Please provide the citations and explanations requested below.
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Comments to the Author
1. Is the manuscript technically sound, and do the data support the conclusions?
The manuscript must describe a technically sound piece of scientific
research with data that supports the conclusions. Experiments must
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replication, and sample sizes. The conclusions must be drawn
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Reviewer #2: Partly
________________________________
Please explain (optional).
Reviewer #2: The article describe the parallel implementation of a continuum-solvation scheme in combination with semi-empirical methods in a quantum-chemistry simulation package. The article is very clear, the results are reported rigorously and deficiencies of the methods have been clearly underlined. Nonetheless I would not recommend publication of this manuscript in PLOS one, as it appears to be not significantly novel with respect to other works in the literature: the
methods implemented are all standard in the quantum-chemistry literature, as well as their combination. The implementation is not deeply discussed in the text and, although showing reasonably good performances, does not appear as highly innovative, the solvation scheme considered (C-PCM) is already one of the simplest and fastest of its class. Moreover, results show deviations from a previous implementation of different authors (dating back to 1992) which are
not negligible: an error of almost 2 kcal/mol on solvation energies of the order of 60 kcal/mol is almost as big as the accuracy of the solvation model adopted. The authors suggest that numerical
differences in the implementation (cavity tessellation) are responsible for this deviation, suggesting also that their method is the one performing worse. It would have been more correct at this point to analyze the sources of such inaccuracy more in details. Similarly, some of the geometry optimizations and frequency calculations show numerical instabilities which are correctly pointed out, but not solved. Apart from the cases in which these deficiencies
only come out from the underlying algorithms in vacuum, the authors should at least have addressed more in details the numerical accuracy of the implemented method. Moreover, it is not clear to me why calculations performed with DIIS should be slower than the case with
no acceleration. Presenting convergence tests is tedious and not generally interesting to the public, but it is mandatory if the method only converges with very tight parameters and the article only deals with the timing, scalability and implementation issues of standard methods. As minor points, some of the formulas presented and the jargon adopted are not completely clear. In particular: it is not clear to me why there is a r_A in the denominator of equation (4); equation (14) is not usually addressed as the PCM solvation energy, as it lacks wavefunction and geometry relaxation effects (usual PCM solvation energy is defined as the difference between the free energy of the system optimized -nuclei and electrons- in solution and the one of the system optimized in vacuum); it is not clear to me what STO-3G calculations refer to (perhaps Hartree-Fock calculations with STO-3G basis set?); before equation (16) the authors refer to frequencies, without having introduced before what they are referring to (vibrational frequencies, computed from the diagonalization of the Hessian, as inferred from a following section); DIIS and SOSCF lack of a proper reference, if not of the full acronym explanation; a reference to GEPOL should be included, as all the other methods have been properly referenced.
________________________________
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Reviewer #2: (No Response)
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Reviewer #2: The authors use a locally modified version of an open
access quantum-chemistry code. The method of the authors is not
currently available for verification of the results, but it is
anticipated in the text that it will be available with the next code
release.
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Reviewer #2: Apart from a typo at the very beginning of the manuscript (page one, fourth line of the introduction "the" is repeated twice), the article is written in good comprehensible English. The jargon adopted and the acronyms are not always correctly addressed, as pointed out in the comments above. Moreover, I would avoid reporting explicitly the code keywords in the main text of the article, as is done in the computational details. As these details are important for the reproducibility of the results, I agree with the authors that they should be presented, but I would rather use the supplementary informations.
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Please offer any additional comments here, including concerns about
dual publication or research or publication ethics.
Reviewer #2: In general, the manuscript appears to contain good work on a very technical issue. More details on the sources of numerical instabilities and deviations from previous results would be needed to complete the reported work. These further details, which I consider necessary, would make the work even more technical. As PLOS one is not focused on the implementation of computational methods, I would suggest submission to a more specific journal.
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Reviewer #2: (No Response)
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 (seeattached 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.
-----
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.
When submitting your revised manuscript through ACS Paragon Plus, please include a file or an entry in the text box that lets me know how you have revised your work.
To revise your manuscript, log into ACS Paragon Plus at https://acs.manuscriptcentral.com/acs and select "My Authoring Activity". There you will find your manuscript title listed under "Revisions and Resubmissions Requested by Editorial Office”. Your original files are available to you when you upload your revised manuscript. If you are replacing files, please remove the old version of the file from the manuscript before uploading the new file.
Prior to submitting the manuscript, please ensure that it is in compliance with the Journal’s author guidelines, which are available at http://pubs.acs.org/paragonplus/submission/jceda8/jceda8_authguide.pdf.
Revisions of JCE manuscripts should follow specific formatting guidelines, which are attached. Please review this document carefully before submitting, paying particular attention to the graphics submission instructions, which are very different from those of other ACS journals.
Journal Publishing Agreement: The Journal of Chemical Education offers an electronic Journal Publishing Agreement that can be completed from your Home page in ACS Paragon Plus. If you did not complete the Journal Publishing Agreement for the original version of your manuscript, you will receive a separate email with instructions on how to access and submit your electronic Journal Publishing Agreement.
I look forward to receiving your revised manuscript for publication in Journal of Chemical Education.
Sincerely yours,
xxx
*************************************************************
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
-----
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.
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
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.
-----
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.
When submitting your revised manuscript through ACS Paragon Plus, please include a file or an entry in the text box that lets me know how you have revised your work.
To revise your manuscript, log into ACS Paragon Plus at https://acs.manuscriptcentral.com/acs and select "My Authoring Activity". There you will find your manuscript title listed under "Revisions and Resubmissions Requested by Editorial Office”. Your original files are available to you when you upload your revised manuscript. If you are replacing files, please remove the old version of the file from the manuscript before uploading the new file.
Prior to submitting the manuscript, please ensure that it is in compliance with the Journal’s author guidelines, which are available at http://pubs.acs.org/paragonplus/submission/jceda8/jceda8_authguide.pdf.
Revisions of JCE manuscripts should follow specific formatting guidelines, which are attached. Please review this document carefully before submitting, paying particular attention to the graphics submission instructions, which are very different from those of other ACS journals.
Journal Publishing Agreement: The Journal of Chemical Education offers an electronic Journal Publishing Agreement that can be completed from your Home page in ACS Paragon Plus. If you did not complete the Journal Publishing Agreement for the original version of your manuscript, you will receive a separate email with instructions on how to access and submit your electronic Journal Publishing Agreement.
I look forward to receiving your revised manuscript for publication in Journal of Chemical Education.
Sincerely yours,
xxx
*************************************************************
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.
Thursday, May 2, 2013
Gold opportunity for open access?
I just found out that RSC has a limited offer for the publication of Open Access articles for free. The limitation is that each institution has a number of expandable tokens for a free publication equal to the number of subscribed RSC journals. It could be a good opportunity when funds are exausted and one run out of luck/excuses asking for fee waivers. The program is called "Gold for Gold" hence the title of the post. More information can be found at: http://www.rsc.org/Publishing/librarians/GoldforGold.asp
Does anybody know how many RSC journals are accessible through our library?
Does anybody know how many RSC journals are accessible through our library?
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