 Solution

The rigid naphthalene core fixes the separation and directions of the two arm attachment points. In A they point from more separated regions of the core, so closure requires the flexible arms to span the core and adopt less favorable torsional arrangements. In B the closer, more convergent attachment geometry permits the UPy ends to meet with less conformational strain and better preorganization.

Both rings gain similar local UPy hydrogen-bonding interactions, but A pays a larger deformation cost in its linkers and overall geometry. That can rationalize its higher calculated total energy and its greater tendency to open into intermolecular chains.

The quoted $50\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$ is large compared with $RT\simeq 2.48\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$. Nevertheless a total-energy difference is not automatically a solution Gibbs free-energy difference: solvent and entropy contributions would be needed before converting it into an equilibrium population ratio.