Program that simulates basic reactions in organic chemistry
As you mentioned, there've been quite some attempts on CAOS (Computer-Assisted Organic Synthesis), such as


WODCA from the Gasteiger group 
CHIRON from the Hanessian group 
LHASA from the Corey group


I might be awfully wrong, but I think they were/are all closed source.

But you might want to have a look at OSET, an open source Java project on which Ivan Tubert-Brohman worked some ten years ago.