dearomatization when ambiguous H in aromatic ring

User a52f97d128

11-07-2006 13:01:37

Dear all,

I have a question related to the topic :

I have a big set of molecule having this issue :

since an implicit H is ambiguously defined in an aromatic ring (eg in COc1cc2nnnc2cc1C(=O)NCC3CCCN3CC=C) the dearomatization do not work on them (using jchem 3.1.5).

Since the structures in this set are pretty diverses, using the standardizer seem to be difficult. Would there be another way to dearomatize this kind of molecule ? (knowing that on which nitrogen the implicit hydrogen goes is not really important)

Thanks !


User 851ac690a0

12-07-2006 09:26:33


Dearomatization module has been improved.

Shortcoming of dearomatization about ambiguous “H” has been fixed.


ChemAxon d76e6e95eb

12-07-2006 12:07:28

Will be available soon in the new Marvin release.

User a52f97d128

12-07-2006 12:57:41

Sorry, this is a little unclear to me. You mean it has been fixed in the latest jchem release (3.1.7) or it has been fixed and will be included in the next jchem release ? If it's the latest option, do you know when it will be available ?



ChemAxon d76e6e95eb

12-07-2006 19:45:14

The issue just has been fixed. Dearomatization is part of the Marvin library, but JChem contains Marvin.

Marvin 4.1 will be released first hopefully this month, but no JChem release (containing Marvin 4.1) can be expected before the end of August, I am afraid.

User a52f97d128

01-08-2006 07:13:24

hello Gyuri,

any update on when this new marvin will be released ?


ChemAxon d76e6e95eb

01-08-2006 12:13:27

You can expect it this week.