3d models of the chemicals in question that can be rotated look good (Java or VRML for this)
Rememebr that if you want to teach people things interactivity and resonsiveness are key, if people have to think rather than just read they learn better. With the age groups you are talking about remember that the average GCSE student has an attention span of about 12 milliseconds so try to keep 'em interested.
the more interaction that they can have the better, a mix of moving images, sounds and text will work best. I did a fully interactive tutorial website for 3D structural Biochemistry for my MSc project a few years ago so shout if you want any help. think about tests at the end of each section and a free form of navigation thorugh the site to avoid linear paths.
tbh designing how to best put across the information will take far longer than actually building the web site. Do you have the information to present in your head or are you going to be stealing from a text book?
HT