Hi,
I am struggling understand a mechanism, part of the amadori product rearrangement just after a Schiff base. As can be seen in the attachment, using DFT I'm trying to optimise both reactants and products, and thus no good chance of running QST3 without either. The circled H transfers to a neighbouring water, which transfers a proton to the neighbouring water, which in turn finally protonates the nitrogen. This results in the switch in double bond between N-C to C-C down the backbone.
However, when I try and optimise the reactants using wb97xd/6-31+g* in Gaussian (vacuum, no implicit water), I can't get the oxygen on the water to 'associate' with the hydrogen of the carbon, ready for the proton transfer. But given that water is polar, and C-H probably doesn't have much of a dipole, the system eventually convergences to a minimum without this important association.
Any help is much appreciated. Thanks.
This was part of a pathway from a publication. I, however, believe there might be at least two steps in between, (1) turning the OH to a carbonyl whilst removing the carbon's hydrogen (giving the carbon a delta+). (2) the nitrogen retrieving a proton from the environment whilst relinquishing the double bond to form a C=C instead.
Dear Anthony,
The process should involve two steps:
1-Protonation of the imine nitrogen by a water molecule and then
2-Deprotonation of the hydrogen alpha to the imine by the hydroxyl anion left from step 1.
The rate limiting step will be step 2. Therefore, locate TS of step 2 and make your rate calculations based on the this step activation energy.
Hoping this will be helpful,
Rafik
Many thanks Rafik. I suspected this was the case, but I am very pleased that you (with more experience than I) could confirm this. Thanks again.
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