Theoretically yes, but the method that is currently implemented (Hartree Fock) is notoriously inaccurate for molecular interactions. For example it does not predict the Van Der Waals force between water molecules.

I’m planning to add support for an alternative method called density functional theory which gives better results for molecular interaction.

In quantum chemistry, you decide where the bonds should be drawn. Internally, it's all an electron density field. So yes, you can model chemical reactions, for example by constraining the distance between two atoms, and letting everything else reach an equilibrium.