Table 3.
Calculated and estimated experimental activation free energies ΔG≠ (kcal/mol) for RNA transesterification model reactions with different leaving groups (Scheme 1). Experimental estimates were obtained from reaction rate constants using the Eyring equation.77
| Calc. ΔG≠ |
Expt.a ΔG≠ |
|||||||
|---|---|---|---|---|---|---|---|---|
| UFF |
UAKS |
PRPpOR |
UpOR |
UpOR |
GpOR |
|||
| Leaving Group | 25°C | 80°C | 25°C | 80°C | 80°C | 25°C | 65°C | 35°C |
| (CH3)2CHO– | 25.96 | 26.36 | 23.82 | 24.15 | 30.76 | 26.01 | - | - |
| CH3CH2CH2O– | 24.26 | 24.52 | 22.73 | 23.00 | - | - | - | - |
| CH3CH2O– | 25.84 | 26.37 | 23.17 | 23.56 | 28.55 | 23.37 | 25.30 | - |
| CH3O– | 24.43 | 24.75 | 22.36 | 22.67 | 27.09 | - | - | - |
| HOCH2CH2O– | 19.64 | 20.10 | 22.99 | 23.52 | 26.66 | - | - | - |
| ClCH2CH2O– | 18.55 | 18.92 | 20.08 | 20.67 | - | 20.64 | - | - |
| FCH2CH2O– | 20.11 | 20.51 | 21.08 | 21.75 | - | - | - | - |
| CHCCH2O– | 17.75 | 18.23 | 17.66 | 18.11 | - | - | - | - |
| CF3CH2O– | 15.87 | 16.37 | 16.62 | 17.14 | - | - | - | - |
| CH3CH2S– | 14.42 | 14.64 | 16.17 | 16.46 | - | - | - | - |
| CH3S– | 14.94 | 15.32 | 15.67 | 15.94 | - | - | - | - |
| PhO– | 14.76 | 15.14 | 15.70 | 16.24 | 22.62 | 15.98 | - | 24.22 |
| 3-CNPhO– | 13.87 | 14.42 | 14.05 | 14.53 | - | - | - | - |
| 4-CNPhO– | 12.62 | 13.03 | 13.96 | 14.55 | - | - | - | - |
| p-NO2PhO– | 11.99 | 12.41 | 13.80 | 14.50 | 20.12 | 13.46 | - | 22.81 |
| 2,3,5,6-F4PhO– | 10.96 | 11.38 | 10.97 | 11.39 | - | - | - | |
| CH3COO– | 11.91 | 12.31 | 11.22 | 11.58 | - | - | - | - |
a
Experimental model systems are for the cyclization reaction of 2-hydroxypropyl phosphate (PRP-pOR),58 uridine 3′-phosphate (UpOR)33,56,75 and guanosine 3′-phosphate (GpOR).76