The programmed assembly of p-octiphenyl rods carrying six complementary tripeptide strands was studied in the presence of bilayer membranes using circular dichroism (CD) spectroscopy. Thermal CD experiments demonstrated programmed assembly of anionic and cationic rods into supramolecules at low temperature that irreversibly transform into more stable supramolecules at intermediate and high temperature. Higher activation energies for programmed assembly with rods containing multiple guanidinium rather than ammonium cations was consistent with stabilization by guanidinium-anion complexes. Qualitative thermal inversion of supramolecular chirality during programmed assembly was detected continuously. Inversion of supramolecular chirality occurred with decreasing solvent polarity as well.