Molecular alignment of rigid rods in nonrigid spherical pores

We have investigated the orientation ordering of two shish-kebab chains confined by spherically harmonic potentials through Monte Carlo simulations and asymptotic analysis. The rigid rod is modeled as shish-kebab chains consisting of tangent hard spheres aligned in the same axis, and the harmonic potential is chosen to model nonrigid cavities. We first show that the interactions between a rod and the spherically harmonic potential are independent of chain orientation, indicating that the alignment of two confined rods arises from the excluded volume interactions alone. In the strong fields, the order parameter of two confined rods converges to different values, depending on the parity of chain length. From asymptotic order parameters, we find that the rods of odd-number beads rotate more freely even under the limiting strong confinement. However, the two rods of even-number beads are essentially trapped in a configuration of perpendicular alignment through intercalation of their central grooves. We attribute the dependence of the parity of chain length to the different locations of the center-of-mass in a rod for these two cases. Furthermore, we compare the shish-kebab chains with different rod models in the simulations, and utilize these models to explore the effect of the local rod smoothness on molecular alignment. Our findings suggest that increasing local rod smoothness enhances the rotational degree of freedom for confined rods, and the effect of local rod roughness emerges under strong enough applied potentials.