Table 3.
Dual-level CCSD(T) relative free energy calculated for stationary points along the intrinsic reaction coordinate of the (A) native, (B) S3′, and (C) S5′ simplest models of RNA transphosphorylation in both gas and solution phases.[a]
| Native (37°C) | Gas (kcal/mol)
|
Solution (kcal/mol)
|
||||
|---|---|---|---|---|---|---|
| Electronic Struct. Theory CCSD(T)/6-311+G(d,p) // | ΔG‡ETS | ΔGInt | ΔG‡LTS | ΔG‡ETS | ΔGInt | ΔG‡LTS |
|
|
|
|
||||
| HF/3-21+G* | -- | -- | 40.8 | 17.5 | 17.5 | 20.2 |
| B3LYP/6-31+G(d) | -- | -- | 41.3 | 17.4 | 17.0 | 20.3 |
| M06-2X/6-31+G(d) | -- | -- | 41.0 | 17.1 | 17.3 | 20.1 |
| B3LYP/6-311+G(d,p) | -- | -- | 41.5 | 17.2[b] | --[c] | 20.2 |
| M06-2X/6-311+G(d,p) | -- | -- | 41.4 | 17.2 | 17.1 | 20.2 |
| MP2/6-311+G(d,p) | -- | -- | 41.1 | 17.6 | 17.5 | 20.5 |
|
| ||||||
| (A) | ||||||
| S3′ (37°C) | Gas (kcal/mol)
|
Solution (kcal/mol)
|
||||
|---|---|---|---|---|---|---|
| Electronic Struct. Theory CCSD(T)/6-311+G(d,p) // | ΔG‡ETS | ΔGInt | ΔG‡LTS | ΔG‡ETS | ΔGInt | ΔG‡LTS |
|
|
|
|
||||
| HF/3-21+G* | 32.2 | --[c] | 33.5 | 16.0 | 14.7 | 16.2 |
| B3LYP/6-31+G(d) | 32.3 | 31.4 | 33.5 | 15.0 | 13.5 | 15.7 |
| M06-2X/6-31+G(d) | 32.8 | 32.6 | 33.5 | 14.9 | 13.6 | 15.1 |
| B3LYP/6-311+G(d,p) | 32.3 | 31.5 | 33.8 | 15.0 | 13.6 | 15.9 |
| M06-2X/6-311+G(d,p) | 32.2 | 32.0 | 33.2 | 14.4[d] | 13.1[d] | 14.7[d] |
| MP2/6-311+G(d,p) | 32.2 | 31.6 | 33.0 | 15.5 | 14.2 | 16.2 |
|
| ||||||
| (B) | ||||||
| S5′ (37°C) | Gas (kcal/mol)
|
Solution (kcal/mol)
|
||||
|---|---|---|---|---|---|---|
| Electronic Struct. Theory CCSD(T)/6-311+G(d,p) // | ΔG‡ETS | ΔGInt | ΔG‡LTS | ΔG‡ETS | ΔGInt | ΔG‡LTS |
|
|
|
|
||||
| HF/3-21+G* | 25.9 | -- | -- | 15.6 | -- | -- |
| B3LYP/6-31+G(d) | 26.5 | -- | -- | 16.3 | -- | -- |
| M06-2X/6-31+G(d) | 27.1 | -- | -- | 15.5 | -- | -- |
| B3LYP/6-311+G(d,p) | 26.7 | -- | -- | 16.5 | -- | -- |
| M06-2X/6-311+G(d,p) | 26.7 | -- | -- | 15.8 | -- | -- |
| MP2/6-311+G(d,p) | 26.8 | -- | -- | 15.7 | -- | -- |
|
| ||||||
| (C) | ||||||
[a]
CCSD(T) is not included in the thermal corrections. “--” denotes the molecular structure of that particular state could not be determined.
[b]
As in Table 2, the ETS is determined but along with very small value of non-reactive imaginary frequency.
[c]
As in Table 2, no intermediate could be determined by us that satisfies all default criteria in Gaussian 09.[41]
[d]
As in Table 2, the reactant is determined but along with very small value of non-reactive imaginary frequency.