I am modelling a nucleophilic addition of an amine onto the carbonyl group of an organic. This eventually results in an immine (schiff base) after the deprotonation of the bound amine and the removal of water. Subsequently I'm left with a R-N=CHR backbone.
Yet the first step requires a base to remove the hydrogen from the amine and an acid to protonate the carbonyl oxygen.
Then the second step a base to remove the second and final hydrogen from the nitrogen and an acid to disassociate the OH group from the central carbon, forming separate water.
My question:
I am using DFT (wb97xd) in Gaussian. What would be my best source of 'general acid' and 'general base'? I've tried linking two water molecules together as a means of proton transfer off the nitrogen and then onto the carbonyl region. But no success.
Would it be appropriate to attempt something as clear cut as H+ and OH- as my acid and base? I've never once seen this in DFT studies, it's always been a small linked arrangement of water molecules, so the reactants and the resulting intermediate/product has a whole water molecule rather than two sets of ions.
Thanks
Anthony
Dear Anthony,
In the last ten years I have published about 40-50 papers using DFT and ab initio methods for unraveling a number of intramolecular processes (enzyme models). I have used H3O+ as an acid and OH- bound to H2O as a base.
The calculation results were very good and were correlated nicely to experimental values. You can look over my publication in Researchgate (Rafik Karaman).
I should indicate that for the corresponding intermolecular processes I used acetate anion as a base and acetic acid as an acid in some cases.
Hoping this will be helpful,
Rafik
Dear Anthony,
In the last ten years I have published about 40-50 papers using DFT and ab initio methods for unraveling a number of intramolecular processes (enzyme models). I have used H3O+ as an acid and OH- bound to H2O as a base.
The calculation results were very good and were correlated nicely to experimental values. You can look over my publication in Researchgate (Rafik Karaman).
I should indicate that for the corresponding intermolecular processes I used acetate anion as a base and acetic acid as an acid in some cases.
Hoping this will be helpful,
Rafik
Hi Rafik,
Many thanks. I will take a look over your publications after the holidays. If there are anyones in particular that you have in mind which would be a great example of organic reaction mechanics, in particular for the elicidation of a schiff base, I would be very grateful.
Mr. Nash,
Please pay attention to the discussion below, it is exactly in the topic of the question. You should add only PCM for computation in solution or a solvent water molecule for micro-solvation approach if you would like to study a participation of a solvent water molecule in the H-transition process (eventually) between the acid and the base.
There is shown with examplex how to conduct the H-transfer (first example) an dthan how to optimize ion-pairs avoiding the back-H-transfer (resp. from the amine to the acid).
https://www.researchgate.net/post/Gaussian_OPT_for_ion_pair
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