Using Gaussian - DFT, wb97xd/6-31+g* default water solvent - I am really struggling finding the TS from an unstable carbinoamine (R-HC(OH)NH-R) to a schiff base (R-N=CHR).
I believe there are two reaction pathways, one via an acid and the other a base. The acid results in the nucleophilic attack on the acid by the -OH leaving group. This forces the lone pair on the nitrogen to fulfil the four bonds on a carbon making nitrogen charged. The second, using a base, the hydrogen comes off the nitrogen meanwhile the OH comes off as above.
Here's a good picture:
http://employees.csbsju.edu/hjakubowski/classes/ch331/catalysis/schiffbase.gif
Unfortunately I am really struggling trying to find either transition state (I have spent more time using water a base rather than down the acid route). I am essentially using two water molecules to remove the proton from the nitrogen by moving a single proton between the two oxygens and finally to the OH group in order to disassociate the OH group and encourage a double N=C bond e.g.,
Proton shift and OH leaving group are in brackets.
R-N-(H)--->HO-(H)--->HO-(H)--->(OH)-C-R
Any suggestions on how to best model a TS state where the product is a schiff base? I sometime think I've found a TS but IRC is telling me otherwise.
Thanks
Dear Anthony,
A possibility is to run a QTS2 and, in addition, run a small scan of the transfer. Maybe in this way you can find a good guess for the TS.
Also, one day, I localized a TS for the formation of a Schiff base. In few days I will be able to search and send it to you.
Hi Joaquim, I've been struggling with this particular TS for about three months. I've tried, TS, QST2, QST3 and dozen of Scan searches.
I think at one stage I may have found it, however, I wasn't able to isolate either a reactant or product using IRC.
I'm now considering H3O+, OH-, H+ variations, even though I've seen a similar publication using HOH proton transfers.
Thanks for your help Joaquim, any data you are willing to share is very appreciated.
Dear Anthony,
I think that maybe could be useful to try to find the TS at gas phase, and then, if you found it go to water solvation. The TS should not be different, but sometime, the addition of solvent in OPT calculation can imply some problems, i.e in convergence.
Agreed. I am currently using an implicit water model. Thanks for the idea, I'll rerun some of them and see what happens.
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