Table 1.
MP2(full)/6-311G** Calculated A-Form RNA Hydrogen Bonding, Intra-Strand Base-Stacking, and Inter-Strand Base-Stacking Energies (kcal/mol).a
| Hydrogen-Bonding Energies (kcal/mol)
| |||||
|---|---|---|---|---|---|
| Bases | Ebind,H | Ebind,Me | Bases | Ebind,H | Ebind,Me |
| A–U | −9.78 | −11.46 | C–G | −25.97 | −25.86 |
| (−11.36) | (−12.29) | (−19.35) | (−20.61) | ||
|
| |||||
|
Intra-Strand Base-Stacking Energies (kcal/mol)
| |||||
| Bases | Ebind,H | Ebind,Me | Bases | Ebind,H | Ebind,Me |
|
|
|
||||
| 5’A | −0.14 | −3.69 | 5’G | −5.88 | −6.35 |
| 3’A | (−5.23) | (−8.87) | 3’A | (−8.79) | (−9.59) |
| 5’A | −1.95 | −2.56 | 5’G | −8.80 | −9.24 |
| 3’C | (−7.81) | (−8.49) | 3’C | (−9.19) | (−10.09) |
| 5’A | −5.48 | −4.71 | 5’G | −0.12 | −0.56 |
| 3’G | (−9.93) | (−8.02) | 3’G | (−7.71) | (−8.52) |
| 5’A | −2.06 | −3.81 | 5’G | −0.36 | −2.03 |
| 3’U | (−6.70) | (−7.56) | 3’U | (−7.32) | (−8.36) |
|
|
|
||||
| 5’C | −1.83 | −2.38 | 5’U | +0.38 | −3.49 |
| 3’A | (−4.46) | (−5.11) | 3’A | (−1.83) | (−4.65) |
| 5’C | −0.46 | −1.07 | 5’U | +1.51 | −3.23 |
| 3’C | (−5.66) | (−6.24) | 3’C | (−2.06) | (−5.96) |
| 5’C | −3.17 | −3.70 | 5’U | +0.04 | −1.90 |
| 3’G | (−3.69) | (−4.39) | 3’G | (−3.13) | (−4.69) |
| 5’C | −2.85 | −4.52 | 5’U | +2.20 | −0.65 |
| 3’U | (−4.61) | (−5.49) | 3’U | (−3.08) | (−4.14) |
|
| |||||
|
Inter-Strand Base-Stacking Energies (kcal/mol)
| |||||
| Bases | Ebind,H | Ebind,Me | Bases | Ebind,H | Ebind,Me |
|
|
|
||||
| 5’A_3’ | −0.24 | −0.27 | 5’_A3’ | +1.14 | +1.08 |
| 3’_A5’ | (−1.12) | (−1.02) | 3’A_5’ | (−3.50) | (−3.55) |
| 5’A_3’ | +0.42 | +0.42 | 5’_A3’ | 0.00 | −0.14 |
| 3’_C5’ | (−0.38) | (−0.24) | 3’C_5’ | (−3.18) | (−3.22) |
| 5’A_3’ | −2.44 | −2.39 | 5’_A3’ | −2.95 | −3.06 |
| 3’_G5’ | (−1.19) | (−4.45) | 3’G_5’ | (−4.33) | (−4.45) |
| 5’A_3’ | +1.06 | −0.54 | 5’_A3’ | −1.01 | −2.70 |
| 3’_U5’ | (+0.55) | (−0.26) | 3’U_5’ | (−2.11) | (−3.03) |
|
|
|
||||
| 5’C_3’ | +1.14 | +0.94 | 5’_C3’ | +7.80 | +0.93 |
| 3’_C5’ | (−0.11) | (−0.11) | 3’C_5’ | (+4.29) | (−0.10) |
| 5’C_3’ | −2.29 | −3.00 | 5’_C3’ | −3.37 | −3.53 |
| 3’_G5’ | (+0.04) | (−0.44) | 3’G_5’ | (−3.26) | (−3.45) |
| 5’C_3’ | +1.09 | −0.57 | 5’_C3’ | −0.49 | −2.27 |
| 3’_U5’ | (+0.72) | (−0.13) | 3’U_5’ | (−0.46) | (−1.37) |
|
|
|
||||
| 5’G_3’ | +2.79 | +15.28 | 5’_G3’ | −0.48 | −0.64 |
| 3’_G5’ | (−1.06) | (−4.45) | 3’G_5’ | (−3.95) | (−4.22) |
| 5’G_3’ | +2.05 | +0.52 | 5’_G3’ | +2.68 | +1.12 |
| 3’_U5’ | (+0.68) | (−0.19) | 3’U_5’ | (−1.37) | (−2.35) |
| 5’U_3’ | +3.11 | +0.75 | 5’_U3’ | +3.56 | +0.74 |
| 3’_U5’ | (−2.43) | (+0.67) | 3’U_5’ | (+0.91) | (−0.18) |
a
Non-solvated Ebind,H and Ebind,Me values on top and not in parentheses. Solvated Ebind,H and Ebind,Me values on bottom and in parentheses. Solvation accounted for via the PCM method.