For the hydrolysis di-peptide formation, there are two TS states. For the second TS where the water is eliminated from the peptide structure, the single point energy is calculated for which two structures? Water and rest of part of the peptide?
The distortion energy for the 2 TS is calculated with respect to intermedium state or initial ground state or final state? Please, give me a reply..
Are you trying to design an experiment to measure / determine the distortion or are you trying to calculate it on paper?
I wish to calculate distortion energy by theoretically. My questioned is that for the second TS, the distortion energy could be calculated with respect to intermedium state or initial state?
The short answer is that the distortion energy should be calculated relative to the intermediate state.
The longer more complete answer is that it depends on if you are trying to describe the energetics of just that step OR if you are trying to describe the OVERALL reaction.
If you are trying to describe ONLY the energy to form the second TS from the first intermediate, then you calculate the TS using the energy of the fist intermediate (which will likely be higher than ground state). If you are trying to describe the activation energy of the OVERALL reaction then you should use ground and the highest TS, whether the highest point is the first or second TS. I hope that's clear.
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