I recently came across this report on inkling.com, a new company aimed at bringing interactive textbooks to the iPad. Interactive molecular models was mentioned two times and clearly left an impression on the author (italics are mine):
"Inkling’s software turns textbooks into interactive content, with video, hyperlinks between text and images, notes that can be shared between students and teachers, and even 3-D molecules that can be viewed from any angle."
"MacInnis – who worked at Apple for eight years, including a stint in the company’s educational division — says that the iPad is the perfect device for the kind of interactivity that Inkling provides because it has the ability to produce high-end graphics, such as the 3-D spinning molecule that is a feature of the company’s biology textbook."
This feature is also shown in inklings promotion video, excerpt below:
Update: MacInChemBlog keeps a list of science related iPhone/iPad apps.