Table 1.

Relative free energy (kcal/mol) and reaction coordinate (Δbond) values (Å) computed for stationary points along the coordinate of the native and thio-substituted RNA phosphate transesterification reaction models shown in Scheme 1.[^[a]]

Reaction	TS1		Int.		TS2
	Δ G ‡	Δbond	Δ G	Δbond	Δ G ‡	Δbond
Nat QM/MM	18.8[[b]]	−0.43	17.7[[b]]	−0.12	24.1[[b],[c]]	0.67
Nat0 PCM	17.3	−0.36	17.0	−0.12	21.0[[b],[c]]	0.54
Nat PCM	18.6	−0.36	18.3	−0.12	21.0[[b]]	0.54
S3′ PCM	16.9	−0.55	16.0	−0.04	17.8	0.54
S5′ PCM	16.6	−0.02	n.a.[[d]]	n.a.[[d]]	n.a.[[d]]	n.a.[[d]]

^[a]Δbond (Å) is defined as the difference of the bond distance between the breaking bond P—X5′ and the forming bond P—O2′. ΔG values are in kcal/mol. Nat₀ is PCM energy (Fig. 1) shifted by the thermal corrections at TS₂. Boldface type indicates the rate controlling transition state suggested by comparison with experimental KIE measurements.

^[b]Statistical uncertainties are 1.1, 0.8, 1.4 kcal/mol for TS₁, Int., TS₂, respectively.

^[c]Experimental estimated barrier for UpG transphosphorylation is 19.9 kcal/mol.^[12]

^[d]Not applicable as Int. and TS₂ cannot be found.