Table 5. Results for Ion–RNA Properties for the Optimized Parameters in Direct Comparison with Experimental Binding Affinity Towards the Phosphate Oxygen of DMP, ΔGb0, and Mg2+–Phosphate Oxygen Distance in Inner-Sphere Conformation, Rba.
| ΔGb0 [kBT] | Rb [nm] | ΔF* [kBT] | |
|---|---|---|---|
| microMg(TIP3P)26 | –0.633 ± 0.6 | 0.207 ± 0.004 | 17.2 |
| nanoMg(TIP3P)26 | –0.375 ± 0.1 | 0.207 ± 0.004 | 13.6 |
| microMg(SPC/E) | –1.26 ± 0.62 | 0.209 ± 0.004 | 16.5 |
| nanoMg(SPC/E) | –1.19 ± 0.50 | 0.208 ± 0.004 | 13.5 |
| microMg(TIP3P-fb) | –1.13 ± 0.90 | 0.208 ± 0.004 | 17.6 |
| nanoMg(TIP3P-fb) | –1.15 ± 0.24 | 0.208 ± 0.004 | 16.5 |
| microMg(TIP4P/2005) | –0.97 ± 0.24 | 0.208 ± 0.004 | 15.5 |
| nanoMg(TIP4P/2005) | –0.88 ± 0.48 | 0.207 ± 0.004 | 14.5 |
| microMg(TIP4P-Ew) | –0.95 ± 0.46 | 0.208 ± 0.004 | 15.3 |
| nanoMg(TIP4P-Ew) | –0.91 ± 0.32 | 0.208 ± 0.004 | 13.7 |
| microMg(TIP4P-D) | –1.02 ± 0.27 | 0.207 ± 0.004 | 16.4 |
| nanoMg(TIP4P-D) | –1.15 ± 0.23 | 0.207 ± 0.004 | 15.6 |
| exp. | –1.03677 | 0.206–0.20878 | n.a. |
a
ΔGb0 is derived from the log stability constant of the DMP (log K = 0.45) given in ref (77). Barrier heights ΔF* of microMg and nanoMg separate the first and second minima of the free energy profile along the distance between one of the nonbridging phosphate oxygens of the DMP and Mg2+. ΔF* is the free energy difference between the top and the first minimum (Figure 6B,C). Values for usage in TIP3P are taken from ref (26).