Do-It-Yourself Molecules: Preparation of Molecular Models from the Drawn Formula

Abstract

Perception of molecules as three-dimensional entities is an essential ability in Chemistry and Biology. Many suitable computerized tools depend on the availability of coordinate files. It is, hence, interesting to have a tool that allows anyone to build a model at will for any desired molecule. The application here presented, “Brico-moléculas” (or Do-It-Yourself Molecules), runs within a web browser without any special software and may be used both locally (e.g. from a CD-ROM) and via the internet. The interface integrates a panel for sketching the chemical structure, a mechanism for generating an optimised conformation and another interactive panel where the latter is displayed three-dimensionally. In addition, optimisation in real time of the initially flat structure towards a three-dimensional conformation adds a great pedagogical value, since the user sees the bonds stretch and wiggle until the model reaches a correct stereochemistry. The generated model may be saved or sent to the instructor for assessment