Figure 3.

Optimization of ion–ion and the ion–RNA interactions. (A) Activity derivative a_cc as a function of the MgCl₂ salt concentration with the optimized scaling factors for microMg and nanoMg (Table 1) and from experiments.⁸⁰ (B) Binding affinity ΔG_b⁰ in correlation with inverse of the Mg²⁺–phosphate oxygen distance 1/R_b. The experimental values (gray) are taken from refs (62, 63). (C) Free-energy profiles as a function of the distance between Mg²⁺ and the phosphate oxygen of DMP, r_MgOP, for different force fields. The Allnér–Villa and Panteva–York free-energy profiles were obtained from refs (16, 33) with permission. The insets show Mg²⁺ in the inner- and outer-sphere conformation.