A peer-reviewed article of this Preprint also exists.
Some quick comments
1.The charge and spin state of each model should be defined.
2. Constraining CA atoms is pretty standard in such studies, but I haven’t seen CB atoms constrained. My initial reaction is that this seems pretty constrained.
3. Given these constraints did you need to do anything special with the TS search in Firefly
4. I would have colored S yellow and Hg green
5. Generally these kinds of studies focus on Kcat and start from the enzyme-substrate complex. I would therefore use Int1 as the reference and forget about the binding.
6. When comparing CH3S- and CH3SH reactions paths you should take energy required to deprotonate at pH 7 into account RTln(10)(pH-pKa) (DOI 10.1007/s002490050236) where pKa of CH3SH is 10.4
7. Where did you get DeltaG = -RT ln 10^-pH from?
8. No PCM in the optimization will make the H3O+ structure very dependent on the number and position of water molecules. How well did you investigate this?
9. Line 48 reads funny
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