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major microspecies vs major tautomer
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Sébastien

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Link to postPosted: Wed Mar 16, 2016 9:22 amPost subject: major microspecies vs major tautomer Reply with quote

Hi

for particular pH and temperature what are in JChem the differences between "major microspecies" and "major tautomer" ?

 

Regards

Sébastien

Daniel
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Link to postPosted: Wed Mar 16, 2016 2:38 pmPost subject: Reply with quote

Hi, 

The major microspecies is the microspecies found in the greatest amount at a given pH. A microspecies is a form of an ionizable molecule that lost one/more of its ionizable Hs. This is closely related to the pKa value of that site.

The major tautomer is the tautomer form found in the greatest amount at a given pH, that is the most relevant tautomer for at a given pH. Tautomeric forms are forms of the same molecule that we get by changing the places of double bonds and Hs within the molecule.

I hope this helps, 

Daniel

Sébastien

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Link to postPosted: Wed Mar 16, 2016 2:56 pmPost subject: Reply with quote

Hi

 

much clearer now.

But is "major microspecies" a subset of "major tautomer" in JChem.

I mean every time we ask for the major tautomer, is the major microspecies automatically done internally?

 

Regards

Sébastien

Daniel
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Link to postPosted: Fri Mar 18, 2016 3:43 pmPost subject: Reply with quote

Hi, 

No, the major microspecies is not a "subset" of the major tautomers. In fact, the reverse is true. I mean that when you calculate the major micros. for an input structure, you can select optionally to take into consideration the tautomerization. In this case the major micros. will be calculated for the major tautomer form. But this is not default behaviour. 

However, you can take into account the pH effect when you calculate the major tautomer form for a molecule. It means that first you calculate the major tautomer form, and then take its major micro form at the given pH.

I hope this helps.

Daniel

 

 

Sébastien

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Link to postPosted: Fri Mar 18, 2016 4:44 pmPost subject: Reply with quote

Thanks for your explanations.

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