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).
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