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Amide-Imide protonation problem
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Leandro

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Link to postPosted: Mon Feb 02, 2015 3:12 pmPost subject: Amide-Imide protonation problem Reply with quote

We are having a problem with some molecules which are generated as imines or imidic acid instead of amines. 
This happens with all inputs in the local Java API but is reproducible with Chemicalize.org with the InChI string. Note: the InChI string is generated from the Smiles by chemicalize. Using the corrected one (having fixed hydrogens) the error dissapears but the displayed InChI string is trunctated to the previous one. 
Smiles
[H]C(N(C(=O)C(N)CC1=CNC=N1)C1=CC=C(Br)C=C1C)C(=O)NCCCC(N)=O
InChI original
InChI=1/C19H25BrN6O3/c1-12-7-13(20)4-5-16(12)26(10-18(28)24-6-2-3-17(22)27)19(29)15(21)8-14-9-23-11-25-14/h4-5,7,9,11,15H,2-3,6,8,10,21H2,1H3,(H2,22,27)(H,23,25)(H,24,28)
InChI with fixed hydrogens
InChI=1/C19H25BrN6O3/c1-12-7-13(20)4-5-16(12)26(10-18(28)24-6-2-3-17(22)27)19(29)15(21)8-14-9-23-11-25-14/h4-5,7,9,11,15H,2-3,6,8,10,21H2,1H3,(H2,22,27)(H,23,25)(H,24,28)/f/h23-24H,22H2
It happens when we, by example call to run() method in StereoIsomer plugin, of Tautomerization plugin, or Pka plugin.
Regards!
Janos
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Link to postPosted: Tue Feb 03, 2015 1:32 pmPost subject: Reply with quote

I moved this to the approapriate forum, someone will respond soon.

Daniel
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Link to postPosted: Thu Feb 05, 2015 4:12 pmPost subject: Re: Amide-Imide protonation problem Reply with quote

leandro.radusky wrote:
We are having a problem with some molecules which are generated as imines or imidic acid instead of amines. 
This happens with all inputs in the local Java API but is reproducible with Chemicalize.org with the InChI string. Note: the InChI string is generated from the Smiles by chemicalize. Using the corrected one (having fixed hydrogens) the error dissapears but the displayed InChI string is trunctated to the previous one. 
Smiles
[H]C(N(C(=O)C(N)CC1=CNC=N1)C1=CC=C(Br)C=C1C)C(=O)NCCCC(N)=O
InChI original
InChI=1/C19H25BrN6O3/c1-12-7-13(20)4-5-16(12)26(10-18(28)24-6-2-3-17(22)27)19(29)15(21)8-14-9-23-11-25-14/h4-5,7,9,11,15H,2-3,6,8,10,21H2,1H3,(H2,22,27)(H,23,25)(H,24,28)
InChI with fixed hydrogens
InChI=1/C19H25BrN6O3/c1-12-7-13(20)4-5-16(12)26(10-18(28)24-6-2-3-17(22)27)19(29)15(21)8-14-9-23-11-25-14/h4-5,7,9,11,15H,2-3,6,8,10,21H2,1H3,(H2,22,27)(H,23,25)(H,24,28)/f/h23-24H,22H2
It happens when we, by example call to run() method in StereoIsomer plugin, of Tautomerization plugin, or Pka plugin.
Regards!

Dear Leandro, 

We have managed to reproduce the problem and we will fix it soon.

Best regards, 

Daniel

 

Leandro

Joined: 22 Apr 2014
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Link to postPosted: Thu Mar 12, 2015 9:36 pmPost subject: Reply with quote

hello,

 

no news about this?

 

Regards, Leandro

Daniel
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Link to postPosted: Wed Mar 25, 2015 5:07 pmPost subject: Reply with quote

Dear Leandro,

Sorry for the late answer, but we needed time to discuss this issue. 

Chemicalize.org is not under development at the moment, therefore we are not going to put out new features for the calculations. The options of the calculations on chemicalize.org are just some of the all available ones, and we recommend you to try MarvinSketch, if you want all.

Please apply for an evaluation license for MarvinSketch.

Daniel 

Leandro

Joined: 22 Apr 2014
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Link to postPosted: Wed Mar 25, 2015 5:13 pmPost subject: Reply with quote

Our problem is that, in our opinion, the results in chemicalize are ok and the api results are wrong, but we can not reproduce de chemicalize results in the api.

We are wrong?

Regards,

Leandro

Daniel
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Link to postPosted: Wed Apr 01, 2015 3:16 pmPost subject: Reply with quote

Dear Leandro, 

We can't really understand your problem based on the description. Can you please give us a detailed description of your use case? What did you calculate? What was your input? What do you want as an output? What was the problem?

Daniel

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