Standardizing Mechanisms: Diers-Alder Reaction in SMILES

Diers-Alder reaction is a common reaction to teach organic chemistry students for ring formations.

The reaction is really simple, where the diene reactions with ethylene to form cyclohexene:

So let’s continue our way of writing reactions:

starting_material = 'C=CC=C'
reactant_one = 'C=C'

So what happens that this mechanisms happens all at once to form the ring. Each arrow could be perceived as a virtual bond until it becomes one.

So we can write this in the SMILES like so

first_step_mechanism = 'C1~CC~CC~C1'

The final product is then the cyclohexene, which we can copy/paste into ChemDraw:

final_product = 'C1=CCCCC1'

We can write then this full mechanism as:

diers_alder = {
    'reactants': ['C=CC=C', 'C=C']
    'step_1': 'C1~CC~CC~C1',
    'step_2': ['C1=CCCCC1']
}