Table 2.
H-bonds detected by AIM analysis to stabilize platform base pairs. The entries correspond to the most stable example of each type of base pair (in terms of interaction energy). The distances between heavy atoms are given in Å, the hydrogen-bonding A-H…B (A/B = O, N, C) angles are given in degrees, and the charge density along with its second derivatives in a.u. The major stabilizing H-bonds are highlighted in boldface. Note that the spurious C9Met(A)…N7(A) interaction of the AA-1hr2-3 pair is not relevant to real RNA systems.
| Base pair | Acceptor | Donor | Distance | Angle | Density (ρ) | Density Laplacian (▽2ρ) |
|---|---|---|---|---|---|---|
| GU-2qus-1 | O4(U) | N2(G) | 2.9 | 164.1 | 0.033 | 0.024 |
| N3(G) | C5(U) | 3.6 | 160.5 | 0.009 | 0.007 | |
| AA-1hr2-3 | N3(A) | N6(A) | 3.0 | 150.8 | 0.022 | 0.017 |
| N7(A) | C9Met(A) | 3.5 | 150.1 | 0.009 | 0.007 | |
| UC-1drz-1 | O2(U) | N4(C) | 3.0 | 157.8 | 0.019 | 0.020 |
| O2(U) | C5(C) | 3.3 | 129.4 | 0.009 | 0.009 |