“DIY molecules” A web application to build your own 3D chemical structures

Angel Herráez

Dep. Bioquímica y Biología Molecular, Universidad de Alcalá, 28871 Alcalá de Henares (Madrid, Spain)

Perceiving molecules as three-dimensional entities is an essential ability to be acquired by students in chemistry and biochemistry. Plenty of tools exist to visualize 3D models of chemical structures; most of them rely, however, on the availability of files with molecular coordinates. It is hence interesting to have a tool that allows anyone to build on demand a model for any desired structure. Existing methods require separate software to draw the structure and to display the result, intermediate saving of files, or local installation of appropriate software, and learning how to use it.

The application here presented, “Do-It-Yourself Molecules”, runs within a web browser without the need for specific software, does not use a server and so can be used locally (even from a CD-ROM) as well as through the internet, under most operating systems. The interface integrates a panel for drawing the structure in 2D, a mechanism for generating an energy-optimized 3D conformation, and a panel where such 3D structure is displayed and may be interacted with.

Furthermore, the optimization of the flat structure towards a 3D conformation is displayed in real time, adding great pedagogical value, as the user sees the bonds stretching and wiggling until the model reaches a proper stereochemistry.

The model produced may be saved or directly submitted to an instructor for assessment.

All the software used is open source and cross-platform, and the application is offered under a Creative Commons licence.

21st Biennial Conference on Chemical Education. Denton, TX, USA, 1-5 August 2010.
Symposium S26: Web Based Applications in Chemistry Education (3 Aug., 2.00-5.00 pm)
Presentation P516 (3 Aug., 4.40-5.00 pm), pages 270-271 in Program Book.