Herein we report energy transfer studies in a series of Ru(II) and Os(II) linked coiled-coil peptides in which the supramolecular scaffold controls the functional properties of the assembly. A general and convergent method for the site-specific incorporation of bipyridyl Ru(II) and Os(II) complexes using solid-phase peptide synthesis and the copper-catalyzed azide-alkyne cycloaddition is reported. Supramolecular assembly positions the chromophores for energy transfer. Using time-resolved emission spectroscopy we measured position-dependent energy transfer that can be varied through changes in the sequence of the peptide scaffold. High level molecular dynamics simulations were used in conjunction with the spectroscopic techniques to gain molecular-level insight into the observed trends in energy transfer. The most efficient pair of Ru(II) and Os(II) linked peptides as predicted by molecular modeling also exhibited the fastest rate of energy transfer (with k(EnT) = 2.3 x 10(7) s(-1) (42 ns)). Additionally, the emission quenching for the Ru(II) and Os(II) peptides can be fit to binding models that agree with the dissociation constants determined for the peptides via chemical denaturation.