Table 5.
Single-level Wiberg bond order (bond index) 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 | Gas (Å)
|
Solution (Å)
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Electronic Struct. Theory | ETS | Int | LTS | ETS | Int | LTS | ||||||
| BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | |
|
|
|
|
|
|
|
|
||||||
| HF/3-21+G* | -- | -- | -- | -- | 0.11 | 0.47 | 0.52 | 0.28 | 0.48 | 0.41 | 0.18 | 0.53 |
| B3LYP/6-31+G(d) | -- | -- | -- | -- | 0.15 | 0.44 | 0.50 | 0.29 | 0.47 | 0.40 | 0.21 | 0.52 |
| M06-2X/6-31+G(d) | -- | -- | -- | -- | 0.12 | 0.46 | 0.53 | 0.20 | 0.46 | 0.42 | 0.16 | 0.53 |
| B3LYP/6-311+G(d,p) | -- | -- | -- | -- | 0.14 | 0.45 | 0.51[b] | 0.33[b] | --[c] | --[c] | 0.20 | 0.54 |
| M06-2X/6-311+G(d,p) | -- | -- | -- | -- | 0.10 | 0.48 | 0.55 | 0.21 | 0.49 | 0.42 | 0.14 | 0.56 |
| MP2/6-311+G(d,p) | -- | -- | -- | -- | 0.09 | 0.46 | 0.52 | 0.24 | 0.47 | 0.39 | 0.14 | 0.53 |
|
| ||||||||||||
| (A) | ||||||||||||
| S3′ | Gas (Å)
|
Solution (Å)
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Electronic Struct. Theory | ETS | Int | LTS | ETS | Int | LTS | ||||||
| BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | BOO5′ | BOO2′ | |
|
|
|
|
|
|
|
|
||||||
| HF/3-21+G* | 0.49 | 0.15 | --[c] | --[c] | 0.14 | 0.49 | 0.54 | 0.19 | 0.45 | 0.45 | 0.18 | 0.54 |
| B3LYP/6-31+G(d) | 0.47 | 0.23 | 0.43 | 0.43 | 0.19 | 0.47 | 0.52 | 0.22 | 0.44 | 0.43 | 0.20 | 0.53 |
| M06-2X/6-31+G(d) | 0.49 | 0.15 | 0.44 | 0.44 | 0.11 | 0.49 | 0.53 | 0.16 | 0.44 | 0.44 | 0.14 | 0.54 |
| B3LYP/6-311+G(d,p) | 0.47 | 0.23 | 0.43 | 0.42 | 0.19 | 0.48 | 0.53 | 0.22 | 0.45 | 0.43 | 0.20 | 0.54 |
| M06-2X/6-311+G(d,p) | 0.51 | 0.13 | 0.44 | 0.45 | 0.10 | 0.51 | 0.56 | 0.15 | 0.46 | 0.45 | 0.13 | 0.57 |
| MP2/6-311+G(d,p) | 0.48 | 0.14 | 0.42 | 0.42 | 0.12 | 0.47 | 0.53 | 0.14 | 0.44 | 0.43 | 0.14 | 0.53 |
|
| ||||||||||||
| (B) | ||||||||||||
| S5′ | Gas (Å)
|
Solution (Å)
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Electronic Struct. Theory | ETS | Int | LTS | ETS | Int | LTS | ||||||
| BOS5′ | BOO2′ | BOS5′ | BOO2′ | BOS5′ | BOO2′ | BOS5′ | BOO2′ | BOS5′ | BOO2′ | BOS5′ | BOO2′ | |
|
|
|
|
|
|
|
|
||||||
| HF/3-21+G* | 0.48 | 0.16 | -- | -- | -- | -- | 0.72 | 0.20 | -- | -- | -- | -- |
| B3LYP/6-31+G(d) | 0.41 | 0.18 | -- | -- | -- | -- | 0.66 | 0.22 | -- | -- | -- | -- |
| M06-2X/6-31+G(d) | 0.50 | 0.16 | -- | -- | -- | -- | 0.68 | 0.18 | -- | -- | -- | -- |
| B3LYP/6-311+G(d,p) | 0.39 | 0.17 | -- | -- | -- | -- | 0.65 | 0.22 | -- | -- | -- | -- |
| M06-2X/6-311+G(d,p) | 0.49 | 0.15 | -- | -- | -- | -- | 0.67 | 0.18 | -- | -- | -- | -- |
| MP2/6-311+G(d,p) | 0.45 | 0.16 | -- | -- | -- | -- | 0.71 | 0.16 | -- | -- | -- | -- |
|
| ||||||||||||
| (C) | ||||||||||||
[a]
BOO5′ is the bond order between O5′ and P, BOO2′ is the bond order between O2′ and P, BOS5′ is the bond order between S5′ and P. “--” 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.