Table 8.
Kinetic isotope effects on the (A) native, (B) S3′, and (C) S5′ simplest models of RNA transphosphorylation in solution. All values are computed from the Bigeleisen equation. “--” denotes the molecular structure of that particular state could not be determined.
| Native (37°C) | Kinetic Isotope Effects in Solution (ratio of isotopic reaction rates) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Electronic Struct. Theory | ETS
|
LTS
|
||||||||
| 18kNuc | 18kLea | 18kO3′ | 18kO1P | 18kO2P | 18kNuc | 18kLea | 18kO3′ | 18kO1P | 18kO2P | |
|
|
|
|
||||||||
| HF/3-21+G* | 1.0105 | 1.0063 | 1.0022 | 1.0037 | 1.0046 | 0.9515 | 1.0805 | 1.0022 | 1.0038 | 1.0035 |
| B3LYP/6-31+G(d) | 1.0169 | 1.0064 | 1.0051 | 1.0041 | 1.0039 | 0.9673 | 1.0607 | 1.0051 | 1.0049 | 1.0026 |
| M06-2X/6-31+G(d) | 1.0239 | 1.0060 | 1.0040 | 1.0031 | 1.0023 | 0.9630 | 1.0716 | 1.0050 | 1.0039 | 1.0027 |
| B3LYP/6-311+G(d,p) | 1.0117[a] | 1.0078[a] | 1.0064[a] | 1.0049[a] | 1.0046[a] | 0.9677 | 1.0602 | 1.0057 | 1.0050 | 1.0024 |
| M06-2X/6-311+G(d,p) | 1.0229 | 1.0064 | 1.0043 | 1.0035 | 1.0026 | 0.9635 | 1.0719 | 1.0054 | 1.0042 | 1.0024 |
| MP2/6-311+G(d,p) | 1.0190 | 1.0075 | 1.0046 | 1.0047 | 1.0045 | 0.9665 | 1.0683 | 1.0043 | 1.0039 | 1.0029 |
|
| ||||||||||
| (A) | ||||||||||
| S3′ (37°C) | Kinetic Isotope Effects in Solution (ratio of isotopic reaction rates) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Electronic Struct. Theory | ETS
|
LTS
|
||||||||
| 18kNuc | 18kLea | 34kS3′ | 18kO1P | 18kO2P | 18kNuc | 18kLea | 34kS3′ | 18kO1P | 18kO2P | |
|
|
|
|
||||||||
| HF/3-21+G* | 1.0209 | 1.0076 | 1.0007 | 1.0024 | 1.0023 | 0.9510 | 1.0697 | 1.0008 | 1.0019 | 1.0013 |
| B3LYP/6-31+G(d) | 1.0250 | 1.0086 | 1.0010 | 1.0033 | 1.0038 | 0.9709 | 1.0575 | 1.0014 | 1.0017 | 1.0026 |
| M06-2X/6-31+G(d) | 1.0276 | 1.0075 | 1.0010 | 1.0016 | 1.0024 | 0.9646 | 1.0714 | 1.0009 | 1.0007 | 1.0013 |
| B3LYP/6-311+G(d,p) | 1.0242 | 1.0092 | 1.0010 | 1.0034 | 1.0038 | 0.9713 | 1.0557 | 1.0015 | 1.0014 | 1.0021 |
| M06-2X/6-311+G(d,p) | 1.0277[b] | 1.0076[b] | 1.0011[b] | 1.0021[b] | 1.0021[b] | 0.9641[b] | 1.0723[b] | 1.0010[b] | 1.0007[b] | 1.0011[b] |
| MP2/6-311+G(d,p) | 1.0264 | 1.0088 | 1.0011 | 1.0035 | 1.0030 | 0.9659 | 1.0666 | 1.0013 | 1.0020 | 1.0024 |
|
| ||||||||||
| (B) | ||||||||||
| S5′ (37°C) | Kinetic Isotope Effects in Solution (ratio of isotopic reaction rates) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Electronic Struct. Theory | ETS
|
LTS
|
||||||||
| 18kNuc | 34kLea | 18kO3′ | 18kO1P | 18kO2P | 18kNuc | 34kLea | 18kO3′ | 18kO1P | 18kO2P | |
|
|
|
|
||||||||
| HF/3-21+G* | 1.0150 | 1.0022 | 1.0036 | 1.0025 | 1.0033 | -- | -- | -- | -- | -- |
| B3LYP/6-31+G(d) | 1.0198 | 1.0021 | 1.0051 | 1.0037 | 1.0037 | -- | -- | -- | -- | -- |
| M06-2X/6-31+G(d) | 1.0203 | 1.0022 | 1.0027 | 1.0030 | 1.0016 | -- | -- | -- | -- | -- |
| B3LYP/6-311+G(d,p) | 1.0187 | 1.0020 | 1.0056 | 1.0039 | 1.0039 | -- | -- | -- | -- | -- |
| M06-2X/6-311+G(d,p) | 1.0196 | 1.0019 | 1.0035 | 1.0027 | 1.0018 | -- | -- | -- | -- | -- |
| MP2/6-311+G(d,p) | 1.0211 | 1.0019 | 1.0064 | 1.0037 | 1.0040 | -- | -- | -- | -- | -- |
|
| ||||||||||
| (C) | ||||||||||