Theoretically, you should be

Theoretically, you should be able to use the Molecules custom URL scheme molecules://[location of molecule] to point to a particular molecular structure somewhere on the Web. I'm not sure if iBooks respects this, and even if it did you'd need to have Molecules installed on the device for this to work.

As an alternative to this, there may be ebooks coming out soon that embed some of Molecules' code within them to do in-book visualization.

Sunset Lake Software - Comments for "Integrating Molecules with epub format ebooks"

Theoretically, you should be