Figure 2.

Reaction coordinates utilized to build the 2D PMF surfaces for RNA 1×1 UU base pairs. In A, the torsional angle highlighted in red is χ (O4′–C1′–N1–C2) responsible for the syn ↔ anti transformation. In order to investigate the base stacking ↔ unstacking, pseudodihedral angles, θ₁ and θ₂, defined by the center-of-masses (COMs) of four atom groups in B were chosen as reaction coordinates.