Chemistry - Program that simulates basic reactions in organic chemistry

Solution 1:

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.

Solution 2:

A few more links to those listed above:

  • Peter Ertl's synthetic accessibility score (SAscore)
  • ArChem - also called Route Designer

There was also a lot of hype a few years ago about an effort called Chematica, but I have not seen an actual shipping product (commercial or otherwise).