User 81a38f9467
09-12-2010 22:06:44
I am using Standardizer 5.4.0.0. The tautomerize action in some cases introduces wavy bonds, even though the input stereochemistry is well defined.. It is my expectation that the Tautomerize action will generate a canonical tautomer; I do not expect (or want) the Tautomerize action to make decisions about whether or not particular double bonds are configurational stable. Given that the stereochemistry of the input structure is clearly defined, is there a way to have the structure canonicalized without introducing wavy bonds?
ChemAxon e08c317633
15-12-2010 14:30:22
We will check this issue. Thanks for the report.
Zsolt
User 851ac690a0
10-01-2011 15:00:40
Hi,
..is there a way to have the structure canonicalized without introducing wavy bonds?
There is no way to change the normal behaviour of the canonical tautomer generation, the "wavy bond" automatically adjusted.
The "wavy bond" in the canonical tauotmer represents two stereoisomers as shown on the attached figure.
Jozsi
User 81a38f9467
13-01-2011 18:56:47
The "wavy bond" in the canonical tautomer represents two stereoisomers
This is precisely why I don't want the wavy bond to be introduced.
Perhaps a second example will better illustrate my point. In this example, two structures differ in the depiction of the pyrazole ring; only one stereoisomer is present in each of these structures. Canonical tautomerization (using Standardizer 5.4.0.1) produces the same ouput structure for both input structures, with the pyrazole ring now drawn exactly the same for both structures. Unfortunately, canonical tautomerization currently also introduces wavy bonds into both structures, implying that two stereoisomers are present. Since only one stereoisomer is present, the introduction of the wavy bonds is wrong.
The tautomerization process should not make decisions about the number of stereoisomers present.
User 851ac690a0
13-01-2011 20:50:15
Hi,
Yes, your request is right. We introduced a tautomerization option for this purpose. It is called : "Protect double bond stereo" . The "wavy bond" will not be adjusted if this option is "Switched on"!
Your first example (bouble bond between rings) have been "too difficult" for the "Protect double bond stereo" option. There is a bug in that case. We fix it asap.
Thanks!
Jozsi
User 81a38f9467
17-01-2011 21:45:17
We introduced a tautomerization option for this purpose. It is called : "Protect double bond stereo" . The "wavy bond" will not be adjusted if this option is "Switched on"!
The "protect double bond stereo" option would be helpful to me if it were available in the standalone version of the Standardizer. While this tautomerization option appears in the standardizer accessed through MarvinSketch, the current version of the standalone Standardizer (5.4.0.1) does not have any configuration options for the Tautomerize action. Will you be adding these configuration options to a future release of the standalone Standardizer?
ChemAxon e08c317633
20-01-2011 09:39:30
tparrott wrote: |
The "protect double bond stereo" option would be helpful to me if it were available in the standalone version of the Standardizer. While this tautomerization option appears in the standardizer accessed through MarvinSketch, the current version of the standalone Standardizer (5.4.0.1) does not have any configuration options for the Tautomerize action. Will you be adding these configuration options to a future release of the standalone Standardizer?
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Yes, we will add protect options to the "tautomerize" action in the future.
Zsolt