Standardizing Mechanisms: Diers-Alder Reaction of Bicyclic Compounds in SMILES

From our last Diers-Alder we did a regular formation of a cyclohexene ring. So let’s try this out where we you do one mechanism with me and one to take home.

The five membered ring, cyclopenta, with two double bonds, diene, where the the C1 and C1 denote a ring connection where the molecule connects. We give the two carbons the same number to say that everything in between is in this ring.

So the SMILES of the starting reaction is:

starting_material = 'C1C=CC=C1'
reactant_one = 'C=C'

So we know our first step is the virtual bond creation and the ring forms.

Which then we can write our SMILES (without stereochemistry) this is to make it easier to see the ring conjunctions. to be:

first_step_mechanism = 'C12~CC~C(C2)C~C1'

And our final product:

final_product = 'C12C=CC(C2)CC1'

We can write then this full mechanism as:

diers_alder_bicyclo = {
    'reactants': ['C1C=CC=C1', 'C=C']
    'step_1': ['C12~CC~C(C2)C~C1'],
    'step_2': ['C12C=CC(C2)CC1']
}

Try doing the cyclohexadiene one for practice.