kekulize mol question

[tsn2027]

Hello all,

I am trying to make C=C1[CH]C=CC=C1 from c1ccccc1[CH2]

radical_smi = "c1ccccc1[CH2]"
mol = Chem.MolFromSmiles(radical_smi)
# mol = Chem.AddHs(mol) # unsure whether adding H would help.
products = AllChem.ReactionFromSmarts("[Cv3:0][c:1][cv4:2]>>[C:0]=[c:1][cv3:2]").RunReactants((mol,))

for i in range(len(products)):
    i1 = products[i][0]
    Chem.SanitizeMol(i1)
    display(Draw.MolToImage(i_1,size=(300,100)))

However, I received this error:

Can't kekulize mol.  Unkekulized atoms: 2 3 4 5 6
---------------------------------------------------------------------------
KekulizeException                         Traceback (most recent call last)
KekulizeException: Can't kekulize mol.  Unkekulized atoms: 2 3 4 5 6

If I don't kekulize mol, I got a weird ring connection, and a product does not look right either.

Does anyone know how to fix this problem or have an alternative approach? Thanks!

[dehaenw]

In my experience it is quite hard to work with radicals using the runreactants machinery.
Here is one approach that gives the intended output, the approach here is to use explicit Hs during the reaction, and then remove them afterwards. Another factor is that the entire benzene ring is factored in and explicitly dearomatized. See the below codeblock, which output the two expected structures

radical_smi = "c1cccc(Cl)c1[CH2]"
mol = Chem.MolFromSmiles(radical_smi)
mol = Chem.AddHs(mol) # unsure whether adding H would help.
products = AllChem.ReactionFromSmarts("[Cv3:0]-[c:1]1[c:2][c:3][c:4][c:5][c:6]1>>[C:0]=[C:1]1-[Cv3:2]=[C:3]-[C:4]=[C:5]-[C:6]1").RunReactants((mol,))

for i in range(len(products)):
    i1 = products[i][0]
    i1 = Chem.RemoveAllHs(i1)
    display(Draw.MolToImage(i1,size=(300,100)))

[tsn2027]

Thank you! This is what I want to get!