Sunday, March 20, 2011

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.

Sunday, March 13, 2011

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).

Saturday, March 5, 2011

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