. Author manuscript; available in PMC: 2012 Dec 1.

Published in final edited form as: J Phys Chem B. 2011 Nov 8;115(47):13911–13924. doi: 10.1021/jp206963g

Table 2.

List of the specific reaction mechanisms studied here (the mechanisms containing thio-substitutions formally correspond to the pro-R_P/pro-R_P/G8/A38H⁺ path and are summarized separately in Table 4).

Name	General base	General acid	G8 form	A38 form
G/A⁺/G8^-/A38H⁺	G8^-	A38H⁺	G8^-	A38H⁺
pro-R_P/pro-R_P/G8/A38H⁺	G+1(pro-R_P)	G+1(pro-R_P)	G8	A38H⁺
pro-R_P/pro-R_P/G8t/A38H⁺	G+1(pro-R_P)	G+1(pro-R_P)	G8t	A38H⁺
pro-R_P/pro-R_P/G8/A38	G+1(pro-R_P)	G+1(pro-R_P)	G8	A38
pro-R_P/A⁺/G8/A38H⁺	G+1(pro-R_P)	A38H⁺	G8	A38H⁺
pro-S_P/pro-S_P/G8/A38H⁺	G+1(pro-S_P)	G+1(pro-S_P)	G8	A38H⁺
pro-S_P/pro-S_P/G8t/A38H⁺	G+1(pro-S_P)	G+1(pro-S_P)	G8t	A38H⁺
pro-S_P/pro-S_P/G8/A38	G+1(pro-S_P)	G+1(pro-S_P)	G8	A38

The identifying names of each QM/MM scan are composed of four indicators separated by “/”: i) the groups acting as general base, ii) general acid, iii) the protonation state of the G8 and iv) A38 in precursor state at the beginning of the cleavage reaction. Details of protonation states of G8, A38 and phosphate/phosphorane/cyclic phosphate in all R, IN/TS, and P states are listed in Table S2 in Supporting Information.