Simulations have been performed for the molecular dynamics of poly(l,4-frans-isoprene) and its monomer, isoprene, as inclusion complexes in the channel of crystalline perhydrotriphenylene. The system contains 90 molecules of perhydrotriphenylene and either 10 molecules of isoprene or a single methyl-terminated decamer of poly(l,4-frans-isoprene). The results are compared with previous simulations of the inclusion complex in which poly(l,4-trans-butadiene) is substituted for poly(l,4-frans-isoprene). Poly(l,4-frans-isoprene) interacts more strongly with the matrix of perhydrotriphenylene than does poly(l,4-trans-butadiene). Interaction between the methyl group and perhydrotriphenylene causes the poly(l,4-trans-isoprene) to distort the matrix so that the channel becomes elliptical in cross-section. The channel retained a circular crosssection in the inclusion complex with poly(l,4-trans-butadiene). Far from the ends of the chain, the conformation of the poly(l,4-trans-isoprene) in the inclusion complex is described by the repeating sequence TA*TAt, and the only motions on the nanosecond time scale are oscillations about these positions. Bonds near the ends of the chain are more mobile. They participate in coupled rotational isomeric state transitions represented by A±TAT = A^TA* and A±TA* TTT. Two types of motions are observed for the monomer, isoprene, on the nanosecond time scale. These motions are rotational diffusion of the monomer about the axis of the channel and translational diffusion of the monomer along this axis. No end-over-end flip by the monomer was observed on the time scale of the simulation.