D vs. 2H in SMILES

When I write a SMILES string as:

  [2H]C([2H])(O)C\C=C\C

it is correctly shown using molconvert or when pasted into MarvinSketch (5.12.1)

However, when I write the chemically identical SMILES string as:

  [D]C([D])(O)C\C=C\C

both molconvert and MarvinSketch seem to interpret that as a substitution pattern (SMARTS? using "A" labels) rather than proper SMILES.

When I export the structure with the correct "D" atoms, it gives me the
second SMILES string. When I immediately re-import it, I get the
structure with the A & D1 labels...

Students ought to know that 2H = D, but that is not always apparent when talking about deuterated reactants and products. Is there a way to use SMILES and still render them correctly as D? Is this a bug?

Thanks.

   Michiel

Hi  Michiel,

We don't support the import of D (and neither T) from SMILES as Hydrogen isotopes. The Daylight definition has no mention of D or T and I couldn't find any information about them in SMILES.
Exporting such SMILES is a bug, but unfortunately we can't reproduce the export of "[D]C([D])(O)C\C=C\C" from Marvin. Please send us a code example or a video demonstration how you managed to export that (with exact Marvin version).

Best regards,
Peter

Hi Peter,

I think I may be mixing things up here: I'm working with a customer who is interested in converting from JME to MarvinJS. (They want to get rid of Java altogether.)

I can reproduce the [D] format in JME but I can't in Marvin (at least right now; I have no recollection what exact sequence I used before I wrote in).

The short of it is; if I can't import JME content to Marvin, what method could I use to convert it to Marvin so I don't have to tell the customer that existing work needs to be rewritten? Any ideas?

Thanks,

   Michiel

Hi Michiel,

Thank you for the correction, I thought you could somehow generate the smiles with [D]-s in it from Marvin.

I think replacing [D] to [2H] in the string before giving it to Marvin should work fine as [D] (or [T]) is not a valid thing in SMILES. It shold work in the other way too, the [2H] in the SMILES generated by Marvin can be replaced to [D] as well.

Regards,

Peter