Conformers

Do you have any plans to introduce a method for comparing two identical structures to see if they have the same conformation? Such a method would be extremely useful for certain purposes. For example, I would like to be able to distinguish methylcyclohexane with an axial or equatorial methyl group. I imagine some of your customers might like to be able to distinguish conformationally stable atropisomers such as (R)- and (S)-binaphthol.

Hi Bob,





Searching already works like that.





In 3D, the stereo configuration of an atom depend on the coordinates, so the R/S and even the double bond E/Z configurations are considered.





In the future we plan to introduce an option to also match the internal coordinates of the query and target. Therefore with this option you will only get hits when all rotomers, bond angles and bond lengths, etc. are all the same.





Best regards,





Szabolcs

Szabolcs wrote:

Searching already works like that. In 3D, the stereo configuration of an atom depend on the coordinates, so the R/S and even the double bond E/Z configurations are considered.

Yes, I know, but I doubt that's true for compounds like (R)- and (S)-binaphthol, which have no stereogenic atoms or E/Z double bonds. Their chirality is due solely to restricted rotation about a C-C single bond.

Quote:

In the future we plan to introduce an option to also match the internal coordinates of the query and target. Therefore with this option you will only get hits when all rotomers, bond angles and bond lengths, etc. are all the same.

That's what we need. Days, weeks, months?

bobgr wrote:

Yes, I know, but I doubt that's true for compounds like (R)- and (S)-binaphthol, which have no stereogenic atoms or E/Z double bonds. Their chirality is due solely to restricted rotation about a C-C single bond.

I'm with you now. You are right, this kind of stereo features are not handled currently.

bobgr wrote:

Quote: In the future we plan to introduce an option to also match the internal coordinates of the query and target. Therefore with this option you will only get hits when all rotomers, bond angles and bond lengths, etc. are all the same. That's what we need. Days, weeks, months?

It is scheduled for JChem 3.2, so I would say rather months.





All the best,


Szabolcs