Bond lengths, Avogadro, Google Docs, and gamification

Recently a colleague of mine, Henrik, lamented that at a recent oral exam many first year students had no clue what a typical bond length in a molecule is.  I am not a big fan of memorizing something that can be easily Googled, but we're talking order of magnitude here, not the last decimal place.

This is a place where molecular modeling tools such as Avogadro can help, but how to do this exactly?  Knowing an approximate bond length by heart comes from looking at many, many molecular structures, and imagining a worksheet with dozens of fill-in-the-blank bond lengths already puts me to sleep.

But how about something like: use Avogadro to build a molecule with the longest CC single bond possible.  This sounds a bit more fun and I bet a few strategies are already popping into your mind. 

Based on my recent excellent experience with Google Docs, I would then have student collect answers on a common Google spreadsheet.  Students could either collect their work on a single sheet or one sheet per student/team. This allows students to learn different design principles from each other and adds an element of competition (gamification) since you can now compare results.

Would this actually work?  I challenge you to find out!
By work I mean: engage students enough to build a large number of molecules and think about bond lengths?  I don't know, but how about testing it out here?  I have started a spreadsheet with a few entries.  If you can do better, feel free to add your entries.

Some ground rules: 
1. The bond length must come from the lowest energy conformation
2. To beat a current entry the CC bond length must be longer by 0.005 Å
3. You must use the MMFFs force field (which will limit the number of elements at your disposal).
4. For now I'll leave the maximum number of atoms open, but the fewer atoms you use, the more impressed I will be.

You might have the students figure these issues out by themselves. Explaining why they are important could be very teachable moments.

Practical tips
1. As the molecules get more complicated, naming them becomes difficult.  In that case I suggest using SMILES, which you can generate with this GUI.  It would be nice if Avogadro has a "Copy SMILES" option.
2. You can build your molecule using SMILES.

Using Google Docs spreadsheets when teaching molecular modeling

Every year I teach DFT in the Computational Chemistry course here at the University of Copenhagen, where I give a 2 hour lecture one day, and give them an assignment to complete another day in the computer lab across the hall from my office.

I typically start them off around 10 am and they typically finish around 2 or 3 pm, when I then lead them through a discussion of the data.  In past years this has been pretty chaotic: computed energies are missing or wrong, and relative energies had to be converted to kcal/mol on the fly.

This year, inspired by Luca De Vico, I set up a Google spreadsheet where they could collect their data (they work in pairs) on separate sheets.  This worked great:

The students where able to see each others data, and they quickly discovered when they made mistakes (which I then helped them fix).

A "best practice" with respect to organization and presentation of the data was quickly adopted.

Discussion of the data was made much easier since I could just show the spreadsheet on the projector.

Finally, I could follow their progress from my computer and figure out when most people had finished, so we could start discussion.

Highly recommended!

Molecular Modeling Basics Reviewed in ChemPhysChem

A very nice review of the book (and mention of the blog) by Ralf Tonner in ChemPhysChem.  Much appreciated. 

Reinventing Discovery: Practical steps toward open science

What can you do if you're a scientist?

I recently finished reading Michael Nielsen's book Reinventing Discovery.  This is not another review of the book (there are many: Google it).  I'll just say it is a well written book on a very important topic, so go buy it now.

Towards the end of the book there is a section entitled "Practical steps toward open science" and one subsection is about what you can do if you're a scientist.  There are some good suggestions, some of which I'd like to expand on here, and I'd like to add some new suggestions as well.  The suggestions are roughly ordered in increasing effort (though not necessarily impact!), together with my own examples (where applicable).

Read the rest of the post over at Proteins and Wave Functions

"Missing" MOPAC parameters

A long, long time ago in a land far, far away I implemented MNDO, AM1, and PM3 in GAMESS.  This was done by taking chunks of code from MOPAC that contained contained the parameters, integral code, and Fock matrix builder.  In doing so, I never noticed that the parameter file contained more parameters than where published in the papers describing the method.  This conundrum came back to haunt us recently as we're trying to implement PM6.

Read the rest of the post over at Proteins and Wave Functions

Meanwhile, in another part of the blogosphere

From Henry Rzepa's blog
Computers 1967 - 1985
Computers 1985 - 1989
Computers 1990 - 1994
Moore's Law and molecules
Related: Steve Jobs and chemistry: a personal recollection

Video lectures by Luca De Vico on Proteins and Wave Functions
Basis sets
Optimization techniques - part 1
Optimization techniques - part 2

Peer instruction questions: internal energy

Peer instruction questions: internal energy

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These slides show questions I used when teaching internal energy using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

The slide use a Molecular Workbench simulation you can access here (or download here once you have MW installed), and is further described in this blog post.

I start and carefully explain the simulation on the left, then ask what we will see when we start the simulation on the right.  Then vote, and explain answer.  Then finally run the simulation on the right.  

Related blog posts
See all posts related to peer instruction here.
Internal energy and molecular motion
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Chemistry of the future: 3D and augmented reality

Way cool! 'Nough said.

I have a cold: a molecular perspective

Correction to Eq 2.45

Astute reader James McNeely found an error in Eq 2.45.  Here is the correct version.  Thanks James!

I have started a separate page listing known errors here.  If you find mistakes in the book please leave a comment on that page (or send me an email).

Rotating molecules in Powerpoint - part 2

Animation in Powerpoint
One of the most accessed posts on this blog is Rotating molecules in Powerpoint.  I wrote the post more than a year ago, and had I written the post today it would be different thanks to a great free program called Screencast-o-matic.

The screencast above shows how to use Screencast-o-matic to make short movies of rotating molecules and other molecular animation and include them in Powerpoint presentations.

Jmol in Powerpoint
A lot of people end up on this blog by searching for "Jmol in in Powerpoint" or some similar term.  As far as I know it is not possible to embed Jmol in Powerpoint slides.  It is possible in Beamer, as discussed in this post by Janus Eriksen.

Using Screencast-o-matic you of course record any sequence of Jmol animations, but it will not be interactive.  Personally, I make a web page with my Jmol model, with buttons to control what I want to do and simply switch between Powerpoint and a browser.  I give a short example using this Jmol model in the screencast below.

Blurring the boundary between linear scaling QM, QM/MM and polarizable force fields Part 2

My talk at WATOC 2011.  Slides can be found here

Here's how I made the video: I recorded my talk using the Voice Memo app on my iPhone.  Then I replayed the talk on my Mac using iTunes as I went through my slides on Powerpoint.  I recorded the screencast + audio using Screenflow.

Thanks to Anders Christensen for recording the video.

Summarizing a paper using Prezi and Screencast-o-matic

In a previous post I summarized a paper using two programs: Prezi and Screencast-o-matic.  Both are free and easy to use.  The screencast above shows how I did it. Anyone can do this.

I did this on a mac, so I used the earphones/microphone that came with my iPhone.  The sound is not the greatest, but good enough I think.

The screencast is 9 minutes long, which might be too long.  It's hard to strike a balance between detail and the big picture.  Hopefully, I will improve with time.  Feedback is very welcome.

Update: be sure to check out the comments below

New paper: Ring current effects in proteins

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

Anders S. Christensen*, Stephan P. A. Sauer, and Jan H. Jensen*

Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark

J. Chem. Theory Comput., 2011, 7 (7), pp 2078–2084

DOI: 10.1021/ct2002607

Abstract (the paper is summarized in the video at the end of the post)
The ring current effect on chemical shifts of amide protons (Δδ_RC) is computed at the B3LYP/6-311++G(d,p)//B3LYP/aug-cc-pVTZ level of theory for 932 geometries of dimers of N-methylacetamide and aromatic amino acid side chains extracted from 21 different proteins. These Δδ_RC values are scaled by 1.074, based on MP2/cc-pVQZ//B3LYP/aug-cc-pVTZ chemical shift calculations on four representative formamide/benzene dimers, and are judged to be accurate to within 0.1 ppm based on CCSD(T)/CBS//B3LYP/aug-cc-pVTZ calculations on formamide. The 932 scaled Δδ_RC values are used to benchmark three empirical ring current models, including the Haigh–Mallion model used in the SPARTA, SHIFTX, and SHIFTS chemical shift prediction codes. Though the RMSDs for these three models are below 0.1 ppm, deviations up to 0.29 ppm are found, but these can be decreased to below 0.1 ppm by changing a single parameter. The simple point-dipole model is found to perform just as well as the more complicated Haigh–Mallion and Johnson–Bovey models.

The paper Instructions on how I made the video will appear in a future post. In the mean time, enjoy!

Blurring the boundary between linear scaling QM, QM/MM and polarizable force fields

Jan Jensen's presentation at WATOC 2011

View more presentations from molmodbasics

Thursday morning, room B

Update: a recording of the talk can be found here

Peer instruction: mixing

Peer instruction questions: mixing

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These slides show questions I used when teaching mixing functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slides 1-3 show results from a Molecular Workbench simulation, which you access here.  It is a variation on the simulation I used to illustrate entropy.  If you understand why the gas expands in that example, you also understand why the gasses mix.

Slides 4-10 show results from a Molecular Workbench simulation, which you access here.

Slides 4-5: after two votes there was no clear consensus, but most students likes A "no interactions between molecules".  The second vote came at the end of the first of three back-to-back lectures, so we had a third vote after the break.  There really was intense discussion of this during the break, when most finally settled on B "equal interactions between molecules".   I think A was popular because "ideal solution" conjures up an analogy to "ideal gas", but how can you have a liquid if there are no intermolecular attractions?

Slide 7-8: here is alternated between the simulation and the question a few times.  A better approach would have been to include the question on the web site with the simulation.

Related blog posts
See all posts related to peer instruction here.
Illustrating mixing
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Peer instruction: radial distribution functions

Peer instruction questions for radial distribution functions

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These slides show questions I used when teaching radial distribution functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slide 8: The hint is given after the first vote.

Slides 11-18 show results from two Molecular Workbench exercises, which you can download here and here, once you have installed Molecular Workbench on your computer.

Slide 11: First I run the solid simulation, then pose the question and have a couple of votes, then click on the "show pair correlation function" in the MW simulation.  Note that you have to run for at least 100,000 fs to get good statistics (i.e. relatively smooth curves).  Then I explain the answer (slides 12 and 13)

Slide 14: Same procedure as slide 11, but for the liquid.

Slide 16: No vote, since the answer is pretty obvious, but I do ask where the peak at r = ~1.5 Å comes from.  Of course it comes from the attractive part of the Lennard-Jones potential, and you can clearly see some particles sticking together in the gas simulation.  To check, I change the depth of the well from 0.1 eV to 0.001 eV (simply double-click on any of the particles, and you will see what to do), re-run the simulation, and show the radial distribution function (summarized in slide 17).

See all posts related to peer instruction here.

Peer instruction: entropy

Peer instructions questions on entropy

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These slides show questions I used when teaching entropy using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

The slides refer to two Molecular Workbench simulations, which you can access here and here, and read more about here and here.

Specific comments to the slides
Slides 1-5: Here I start the simulation without removing the separator.  Then pose the question, two rounds of votes (usually not needed for the first simulation with 100 particles, as more than 80 % submit the correct answer), then remove the separator and explain.

Slides 10-15: Here I run the first simulation (small volume, low temperature) and carefully explain what the recorded times mean and how they correlate with probability.  Then I pose the first question (slide 10), two rounds of votes, then run the double volume simulation, then summarize the right answer (slide 11), and explain it (slide 12).  Same process for doubling the temperature.

See all posts related to peer instruction here.

Related blog posts
Illustrating entropy
Entropy, volume, and temperature
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Peer instruction: force fields and energy minimization

Peer instruction questions on force fields and energy minimization

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These slides show questions I used when teaching force fields (slides 1-4) and energy minimization (slides 5-8) using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate.  Many of the equations are discussed in Sections 1.5 and 2.1 of Molecular Modeling Basics.

I also use the Avogadro program when teaching force fields.  See for example this post.

I have made a Jmol model to illustrate energy minimization, as discussed in this post.


See all posts related to peer instruction here.

Molecular modeling and peer instruction

Last Tuesday I had my first go at using peer instruction.  Peer instruction is a fancy term for a relatively simple process:

1. Put up a multiple choice question
2. Ask the students to come up with an answer without talking to each other. Give them 2-3 minutes.
3. Have a vote (more on how below)
4. If 80 % or more get the right answer, show the right answer, give a short explanation, and move on.
5. If less than 80 % get the right answer, ask the students to discuss it with their neighbor. Give them 3-5 minutes.
6. Have another vote.
7. Give them the right answer and explain it.

Voting using Polleverywhere.com

The screencast (best viewed in full-screen mode) shows how I use the website Polleverywhere.com for the voting.  It requires the students to have access to a browser, so I ask them to bring a smartphone or a laptop to class.  It is also possible to submit votes by SMS, but Polleverywhere only provides a British phone number for Europe, so this gets pricey in Denmark.

The free version of Polleverywhere.com can register up to 30 votes.  For larger classes your department needs to buy a six or 12 month subscription, the latter is about $900.  You just create an account on the site, create your poll, and you are ready to go. 

All my questions have four options labelled A, B, C, and D, so I just create one poll per course.  The example in the screencast is used in a course called KemiF1, so the codes for the options are kemif1A - kemif1D.  You do need to create completely unique codes.  The site assigns you numerical codes by default, so you can also just use those.  The website with the question is here.  Option D is "don't know".  It is important to have that option so that everyone casts a vote every time.

I thought it would be cool for the students to see the votes coming in live, but they felt it biased their vote too much, so it is better to leave the question up as they vote, and show the results when the vote is done.  You can monitor the progress on the vote on another device such as a smartphone or iPad.

Why use peer instruction?
Much has been written about peer instruction (just google it), but I find the two videos posted here especially informative.  And think about this: if you lecture on organic chemistry and less than 80 % of your students understand what you mean when you draw a hexagon, is there really any point in going on to more complicated material?


Peer instruction and molecular modeling
The real challenge when using peer instruction is to come up with good questions and I think molecular modeling and visualization can contribute a lot here.  For example, the spinning models in the example  reinforces the fact that cyclohexane is not planar.  Note that the students can go to the page and interact with each model as they mull their options.

I will show more examples of using molecular modeling and peer instruction in future posts.

Interactive chemistry ebooks: interactive figures

Here is version 2 of my ebook mockup page (see here for a description of version 1).  Actually there are two versions: one using Jmol and one for the iPad.

The Jmol version is how I would like the page to look.  The static figures are replaced with interactive Jmol versions embedded right in the page, and the figure captions contain links (denoted by ">>") to larger version of the figures on a separate page, that also contain extra features such as animations (Figure 3.1) or overlays (Figure 3.2).  An alternative design would have been to keep the static images, but insert links to the larger figures.  I think I like the current look better.  But for pages with more figures loading-time could become an issue with Jmol.

The iPad version is what is currently possible for the iPad with ChemDoodle Web Components.  We are waiting for two things to happen: 1) WebGL in Mobile Safari, which will allow real 3D representations of the molecules, and 2) Implementation of contours and surface maps in ChemDoodle Web Components.

For the iPad version I generated the necessary ChemDoodle Web Component HTML code using the ChemDoodle software package, as I show in this screencast.  The mol2 file I start with is generated with Avogadro.

ChemDoodle costs $60, and normally I restrict this blog to free software, but I am making an exception here because I think iChemlabs deserves to be supported since they made ChemDoodle Web Components open source.  Furthermore, since I have access to the source code I could probably figure out the format for the HTML code, if I wasn't so lazy.

Related blog-posts:
Interactive chemistry ebooks: highlight and annotate
Interactive chemistry ebooks: let us start now!
ChemDoodling: now in 3D, but not (yet) on the iPad
ChemDoodling on the iPad and the future of interactive chemistry text books
iPad: even 3D molecules that can be viewed from any angle

Interactive chemistry ebooks: highlight and annotate

In a previous post I argued that the best way to get started on making interactive chemistry ebooks is to do it on the web with straight HTML, rather than wait for the epub technology to catch up.  But how would one highlight text and scribble notes in such a book?

One solution is to use Diigo, which is a free add-on to your browser as well as a free iPad app.  The picture above show a screenshot of annotation I added to the web page mock-up I talked about earlier.  Notice the "Web Highlighter" in the bookmarks bar, which, when clicked, gives you the blue tool bar you see.  The highlights and annotations are stored in the cloud, so they can be seen and modified from any browser where you have installed Diigo.  It also appears possible, though I haven't tried it myself, to share your notes with a group of people you define, which sounds like a very interesting study tool.

The computer version of the Diigo browser plug-in also has a "read it later" option, where the web page is saved and can be read in the Diigo app off-line.  For some reason this option is not there when using the iPad browser.  It also not possible to annotate in the Diigo app.  But I wouldn't be surprised if both options would appear in future releases.

Related blog-posts:
Interactive chemistry ebooks: interactive figures
Interactive chemistry ebooks: let us start now!

Interactive chemistry ebooks: let us start now!

The problem
Henry Rzepa writes thought-provoking blogposts and his latest, entitled What is the future of books?, is no exception.  He describes the current state-of-the-art in science e-publishing and the very limited options and steep learning curves facing aspiring authors in this area.

Currently, there is only one publisher of interactive science e-texbooks: Inkling.  As a result, Inkling has their hands full and is unlikely to be interested in anything but the biggest best sellers in this area.

This means we chemists have to go at it alone, but there a is a big practical hurtle: there a no tools available to us.  The ePub 3 format that will allow interactivity will be released this month.  But when will tools to create and read ePub 3 files become available?

My first, and so far only, attempt at creating an ePub document taught me that the e-editors and e-readers are completely geared towards fiction.  Looking at Chapter 3 of Inklings Biology textbook on the iPad, which is available for free, is very educational.  Their design looks nothing like the traditional book that current e-readers such as Stanza and iBooks try to emulate with page swipes and similar layout considerations.  So we are not really waiting for these apps to become ePub 3 compatible; we are waiting for a science e-book reading app.  Who will write this and when?

One solution
But do we need all this stuff?  Broadly speaking, ePub is HTML in a zip file and ePub readers are hacked web browsers, and both are aimed at letting you read HTML off-line.   If we assume internet access, the need for ePub is mostly gone and this allows us to get started now by doing what we already know how to do: make interactive web pages.  Even if you think off-line access is essential, I hope you'll agree that "web-books" allow to test some design ideas for science e-books in ePub 3 format or book apps.

To kick things off, I have made a web page mock-up of how the section on electron density from my book Molecular Modeling Basics might look in the hands of the Inkling people, using an iPad-friendly template kindly made available by Matthew James Taylor. 

This is version 1, quite bare bones, and with a few blemishes.  For example, the top bar moves on the iPad (and on Chrome) because Mobile Safari does not respect position:fixed, and the Table of Content menu at the top doesn't work.  I would very much appreciate tips and suggestions from HTML experts on how to improve such things. You are very welcome to copy the HTML and the associated css, and experiment with this yourself.  (I am quite confident that a skilled HTML programmer could make a web page that is essentially indistinguishable from a page in Inkling's Biology book.)

Basic design considerations
Basic layout: The page can be read in both landscape and portrait mode.  The layout ensures that the main window is the same width in each mode, so that the formatting stays the same.  Portrait mode gives you reading without the clutter, landscape mode gives you access to options on the side.  Should the sidebar be on the left?  Should the sidebar scroll independently, and how do I do that?  When publishing Our Choice, Pushpoppress decided on landscape mode only, with a novel navigation, but I not sure this would look good for a real textbook. 

Continuous pages:  The section is not divided up in pages.  This avoids problems like figure captions spreading over 2 pages, but I think I would prefer this layout for fiction books as well: scrolling down on the iPad is a more natural gesture then side-swipe in my opinion.  I don't think I'll change that.

Table of content: Navigating a science textbook is very important.  The menu I have on the top left, will become too big, if I include the entire TOC.  Perhaps a nested drop down menu like this?  Could this be made to appear on a right-click?  Alternatively, I should I simply include a link to a separate page that holds the entire TOC, like iBooks?  Inkling's Biology book has a cool side-swipe feature where the TOC appears, but I have no idea how to do that.

Reading progress: Almost all readers have some indication of far along your are in the book or chapter, usually with dots.  Much of this is a legacy from novels.  In a textbook, you don't really care how much of the book you have read.  Perhaps it's important for a chapter?  Certainly in a section the position of the scroll bar is indication enough?  I don't think this has high priority.

Future plans
My plan for version 2 is to add interactive figures (should they be embedded or in separate pages?), and in subsequent versions I plan to add additional items to the right side-bar.  What should these items be?  Movies? Quizzes?  Again, suggestions are very welcome, as are links to similar mock-ups.

Now is the time to decide what interactive chemistry e-books should look like.  What do you think?

Related blogposts:
Interactive chemistry ebooks: interactive figures
Interactive chemistry ebooks: highligt and annotate
iPad: even 3D molecules that can be viewed from any angle
The Molecular Modeling Basics Electronic Color Supplement

Discussion page for Section 3.1 The electron density

The purpose of this post is to provide a forum for discussion of Section 3.1 The electron density of Molecular Modeling Basics.  Please post your questions an comments about electron density below.

A Jmol atom picker

On this page you can find a simple example of how to identify atoms in a Jmol molecule.  My idea is to use it to create interactive practice problems for identifying chiral centers and things like that.  But I haven't really had time to pursue it, and for a while I even forgot the link to the page. So, I'll throw it up here so I know where it is, and perhaps someone else can make use of it too. 

You can see the whole code on the page (right-click, "view page source", but the main new thing here is the

jmolGetPropertyAsArray

function. The code is basically and extract of this page, written by Angel Herraez (thanks, Angel, for pointing me to that page).

Building molecules: What's in a name?

In the discussion of a previous blog post Geoff Hutchison and Marcus Hanwell made me aware of a really cool building feature in Avogadro: building by naming.  I demonstrate this feature on the screencast above. All the hours spend learning organic nomenclature is finally coming in useful!

Notice that, just like in MolGrabber, you get 2D coordinates, so it is important to energy minimize the structure.

ChemDoodle Web Components: 2D to 3D and MolGrabber

Kevin Theisen and his colleagues over at iChemLabs have made a very useful web page that is both a great builder and a great educational tool.  I have written about "2D to 3D building" before, but what makes this site special is the integration with MolGrabber combined with Chemical Indentifier Resolver by Markus Sitzmann, which generates 3D coordinates.

First, I can't think of an easier way* to build (i.e. generate the coordinates of), say, aspirin, than typing "aspirin".  And of course you can modify the structure further, using aspirin as a starting point.  In the screencast I show how to save the file and load it into Avogadro for minimization and GAMESS input file generation.  UPDATE: Kevin has informed me that the coordinates you get are the 2D coordinates from the sketcher.  *Also, there is actually an easier way as explained in the comments.

Second, the site is a great tool for showing/learning the connection been nomenclature and structure (what's the difference between 1-butene and 2-butene?), as well as the connection between 2D and 3D structure (cyclohexane is not flat like benzene!). 

Currently, in order to see the 3D model you need to use the Chrome or Firefox 4 browser.  Also, it is a lot of fun to draw the 2D molecules on the iPad!  But the 3D model does not work in mobile Safari yet.

Lastly, iChemLabs has also made another very useful site where you can go directly from the name to the 3D structure (though here you don't have access to the coordinates).

The Molecular Modeling Basics Electronic Color Supplement

Figure 3.5. (a) RHF/6-31G(d) 0.002 au isodensity surface with superimposed electrostatic potential for (a) cis-HO(H)C=C(H)OH and (b) cis-CH₃(H)C=C(H)CH₃ and. In both cases, the maximum potential value is 0.05 au. 

From page 79 of Molecular Modeling Basics: "Figure 3.5 shows such plots for cis-CH₃(H)C=C(H)CH₃ and cis-HO(H)C=C(H)OH and clearly shows the difference in polarity between hydroxyl and methyl groups."

Not really.

As I wrote on the blog: "A big part of the motivation for my blog came from writing a book called Molecular Modeling Basics that was published in May, 2010 by CRC Press. While writing the applications sections it was frustrating to turn the beautifully colored figures into black-and-white versions in order to keep the cost of the book reasonable. But it was also apparent that even colored figures in a book would be a somewhat poor substitute for the interactive versions they are based on. Especially, when turning them around to find just the right orientation for the figure. Wouldn't it be much better to have the reader decide for him/herself?

This is all a long winded way of explaining why there'll be a lot of posts with (color) figures that look like they came out of a book (they'll have figure captions below them). You can click on them for a bigger version. In many of the posts there'll also be a screencast showing how I made them, and an interactive Jmol version. They'll all be labelled "color figures from the book" so they should be easy find."

I have now made an electronic color supplement in epub format (dowload here), which is an edited compilation of these blog posts. I see it as the next step in the evolution of Molecular Modeling Basics, and it is my first experiment with the epub format. I used the (open source!) Sigil software, as suggested by Henry Rzepa whose ebooks and wiki how-to served as an inspiration.

ePub standards are far from universally accepted, so this color supplement can look very different in different readers.  On my Mac it looks OK in the Firefox epub reader plugin but not in Adobe Digital Editions or Stanza, while on my iPad it looks OK on both Stanza and iBook.  I would be interested to hear about problems or successes with these and similar platforms and software.

Almost all figures link to web pages with interactive Jmol versions of the figures.  None of the interactive models will work on the iPad, due to its lacks of Java support. In the not too distant future, Mobile Safari will support WebGL, and my plan is to slowly convert the interactive figures from Jmol to ChemDoodle Web Components, as the capabilities of the latter software increases.

Right now, accessing the interactive figures and videos switches you from the reader to a browser.
When the new epub format, epub3, matures (along with the readers) I hope it will become possible to view and interact with these interactive features directly within the reader.

In fact I hope to use this color supplement as a "laboratory" to experiment with these new capabilities as they become available, and make this color supplement a prototype for the next generation of scientific book publishing. Wish me luck ...

Related blog posts:
ChemDoodling: now in 3D, but not (yet) on the iPad
ChemDoodling on the iPad and the future of interactive chemistry text books
iPad: even 3D molecules that can be viewed from any angle

ChemDoodling: now in 3D, but not (yet) on the iPad

 

You need Google Chrome or Firefox 4 to view the molecule.

In a previous post I wrote "The 3D version of ChemDoodle Web Components requires something called WebGL, which is not available in standard browsers yet, but should be soon.  You can get access to it now by downloading Google Chrome (BETA)."

Now you just need Google Chrome or Firefox, i.e. if you view this post in the Google Chrome or Firefox 4 browser you should be able to interact with the molecule.  Other browsers should include WebGL soon, and when it reaches Mobile Safari, it should work on the iPad.

This means ChemDoodle Web Components is ready for use in research and education.  It's quite easy to use: see here for installation instructions and here for a simple html example.  Furthermore, "Over the next couple years, we intend to match all functionality in JMol" according to Kevin Theisen.

I note that the ChemDoodle Web Components are open source, so feel free to pitch in!

Course: QM/MM modeling of enzymatic reactions

source

I am teaching a graduate course QM/MM modeling of enzymatic reactions.  Though this is about as non-basic as you can get in molecular modeling it may be of interest to some readers of this blog.

In addition to the course website, which includes a list of papers and lectures slides updated weekly, I also hope to make blog posts summarizing the in-class discussion.  This will happen over at Proteins and Wave Functions, a new group blog I have started to facilitate group communication - both within the group and with the scientific community at large (constructive comments from anyone are greatly appreciated).

Jean-Claude Bradley's links to e-resources for organic chemistry

An interesting e-resource page for undergraduate organic chemistry compiled by open science pioneer Jean-Claude Bradley.

I haven't gone through all the links yet, but my favorite so far is the chirality relationships exercise (number 10 on the list), where Jmol is used to ask chirality-related questions (NB: I could get this to load properly in Safari, but not Firefox or Chrome). 

I think this mirrors the "mental rotations", that experienced organic chemists do to answer such questions, quite accurately.  I'm not an experienced organic chemist, so I hope I didn't make too many mistakes in the screencast.