I think there was some confusion between left and right in the original
message, but RDKit prefers the representation that preserves the octet at
the expense of having more formal charges:
In [9]: mol = Chem.MolFromSmiles('O=I(=O)([O-])')
In [10]: Chem.MolToSmiles(mol)
Out[10]: '[O-][I+2]([O-])[O-]'
I don't think there's right and wrong here; it's just a matter of a toolkit
picking a canonical convention.
Carboxylates are different in that the popular representation (C(=O)[O-])
doesn't break the octet rule. But another interesting case is nitro groups:
In [11]: mol = Chem.MolFromSmiles('CN(=O)=O')
In [12]: Chem.MolToSmiles(mol)
Out[12]: 'C[N+](=O)[O-]'
Ivan
On Thu, Jan 21, 2021 at 9:06 PM Peter S. Shenkin <shen...@gmail.com> wrote:
> It seems to me offhand RDKit's choice is analogous the way carboxylates
> are generally notated:
>
> R-C(=O)O- rather than R-C+(O-)O- .
>
> Both are legitimate and in fact equivalent upon application of
> chemical knowledge, but do you prefer the second representation for
> carboxylates?
>
> -P.
>
>
>
>
>
> On Thu, Jan 21, 2021 at 2:06 PM Jason Biggs <jasondbi...@gmail.com> wrote:
>
>> The RDKit will always convert iodate from the form on the left, with an
>> expanded octet on iodine and a single negative charge, into the form on the
>> right with all single bonds and a charge on every atom (image here
>> https://i.stack.imgur.com/hq3St.png). This happens no matter how I
>> import the molecule, from SMILES or from a file. The only way to avoid it
>> is to skip sanitization, which I'd rather avoid.
>>
>> Is this the desired behavior?
>>
>> Thanks
>> Jason
>>
>> [image: image.png]
>>
>>
>>
>>
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>>
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