User 870ab5b546
04-03-2009 23:30:01
From what I can tell, JChem cannot distinguish allenes with different configurations. Is that correct? For example, 2,3-pentadiene can exist in two enantiomeric forms, and 3,4-hexadien-2-ol has four isomers (two pairs of diastereomers).
ChemAxon a3d59b832c
05-03-2009 10:24:54
Yes, that is correct. Allene stereochemistry is not supported at the moment. Neither the tetrahedral-like one you mention (for even number of consecutive double bonds), nor the cis-trans type of stereochemistry (for odd number of double bonds). E.g. hexa-2,3,4-triene.
Do you want to use it in the context of searching?
Best regards,
Szabolcs
User 870ab5b546
05-03-2009 13:50:33
We want it in the context of matching two molecules (MolSearch), but we don't need it for database searching.
I also find that minimizing the structure of an allene with Clean3D doesn't work properly (even with the latest version, Marvin 5.1.5). Minimization of 2,3-pentadiene puts the C-CH3 bonds coplanar.
ChemAxon a3d59b832c
09-03-2009 08:04:07
Hi Bob,
We will discuss what is needed to support this, and will get back here with a time estimation.
Regarding 3D clean, it seems to me that Marvin 5.1.5 generates non-coplanar coordinates, see attached image.
Best regards,
Szabolcs