I've asked this several times now, and it is a step in a very long (16-20 steps) reaction mechanism that takes anywhere between 1 to 2 months to produce the end product.
Imagine halfway through the mechanism you have an arginine side chain in water that has undergone some modifications so it now has an imidazole ring as its functional part. One of these nitrogens is positively charged i.e., =N(+)H-
Do I:
1) Just remove the charge, disregarding how is became deprotonated. Use the new state as the next intermediate for the continuation of the mechanism.
2) Explicitly model every protonation and deprotonation event i.e., intermediate->TS->intermediate
I am attempting (2). I am trying to disassociate a proton from the protonated nitrogen by passing it into an explicit water solvent (about 12 molecules) i.e,. by finding the resultant transition state.
Sadly, for 3 months I have had zero success at removing the +1 charge from my system by attempt step (2).
So in short - should deprotonation/protonation events of amino acid functional groups in a water solution require explicit transition states? Or can you remove/add the charge and use that as the new thermodynamic state for the next step in the reaction mechanism?
Mr. Nash,
Could you write the equation, meaning the chemical reaction that you would like to study?
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