Table 2.

QM/MM energies (kcal/mol) and key distances (Å) along the self-cleavage reaction path, i.e., for the pre-cleavage (R), transition (TS), and post-cleavage (P) states. The experimental reaction barrier is shown in the TS state column for comparison.

	R	TS	P
EQM/MMa	3.6	24.9±5.0	15.1±4.6
ΔG‡exp	-	17.2–22.6b	-
A-1(O2’)…G1(P)	3.1	2.0	1.7
G1(P)…G1(O5’)	1.6	1.9	2.9
A-1(O2’)…H	1.0	1.8	2.6
H…G40(N1)	1.8	1.0	1.0
GlcN6P(N)…H	1.0	1.3	1.8
H…G1(O5’)	1.8	1.2	1.0

^aThe energies of all states were corrected for the 3.6 kcal/mol thermodynamic penalty due to the rare protonation form of the reactive state. The TS energy was averaged over five calculations starting from different structures (see Table S2 in Supporting Information). The TS energy was further corrected by −4.6 kcal/mol to account for the inaccurate QM-MM coupling in the calculations using the minimal QM region. See Supporting Information for explanation of the error estimates.

^bThe range stands for the different rate constants reported for different conditions, namely in the presence of concentrations of 3 mM MgCl₂⁶⁶ and 30 mM MgCl₂²⁶.