Molecular dynamics simulations have been performed to study the intramolecular interactions of biphenyl ({B}) and cholesterol ({C}) substituents on linear oligomeric siloxanes. These interactions are of interest due to the liquid crystalline behaviour of these materials. Molecules with alternating diblock and triblock substituent arrangements were examined, as were unmixed substituents. The orientational behaviour of the mesogens and the stability of {B}-{B}, {C}-{C}, and {B}-{C} interactions were characterized by an order parameter for the mesogens as a function of simulation time. Results indicate that the {C}-{C} interaction is the strongest, with the {B}-{B} and {B}-{C} interactions being weaker. However, the arrangement of {B} and {C} mesogens in the different molecules strongly influenced the level of mesogen ordering. The flexibilities of the siloxane backbone and the spacer groups used to attach the mesogens give the mesogens a wide range of motion, allowing them to and energetically favourable arrangements and moderate to high order parameters.