Tautomer distribution prediction fails on phthalocyanine

User 7d1702e205

25-06-2012 19:46:06



Attempts to predict tautomer distribution fails with the following SMILES string (phthalocyanine):


No distribution is calculated either via GUI or cxcalc.


Any assistance would greatly appreciated. :)

User 25d107bd42

28-06-2012 11:30:06


testing these problems I found the following results, see screenshots.

1) Pasting the SMILES into MarvinSketch produces the attached formula. There are several wrong double bonds, and what is the meaning of the wedge bonds ?

2) Calculating tautomers here produces 26 formulas. But no % distribution is shown.

Something goes wrong here.

Best regards, Hans-Ulrich

User 7d1702e205

28-06-2012 20:54:26

Hi Hans-Ulrich,

So I'm not quite sure about the incorrect bonds you speak of - they all appear to be correct from what I can tell.  I don't think there are any wedge bonds in this SMILES string from what I can see?

Thank you for all of your help,

Kind regards,


User 25d107bd42

29-06-2012 06:20:47

Hi Trevor,

I mean the three "zig-zag"-bonds in the attached screenshot image "Pasting SMILES to MarvinSketch".

What is the meaning of these bonds I have called "wedge bonds" ?

And two rings are in wrong positions, too.

Kind regards, Hans-Ulrich

User 851ac690a0

29-06-2012 12:59:00


There are  many bugs  with this structure. The Wedge bond , the graphic representation of the  rings, and the  tautomer generation.


The tautomer generation problem will be fixed in the upcoming release of 5.10.1.

I attached 2 figures to show the "way"  for generating the right structures.

Thank you for dealing with this problem.


ChemAxon 60613ab728

08-07-2013 13:15:09

We have registered the 2D clean issue as a bug.

The tautomer generation issue is fixed.


User 677b9c22ff

29-08-2013 17:19:40


I usually clean 3D first and then 2D that also solves issues, and 4 tautomers are created. No Problem.