The photophysics of a series of peptides carrying naphthalene and protoporphyrin IX, covalently bound to epsilon-amino groups of lysine residues were investigated in methanol solution by steady-state and time-resolved fluorescence experiments, as well as by transient absorption spectra. The general formula of the series is Boc-Leu-Leu-Lys-(Ala)(n)-Leu-Leu-Lys-OtBu, where Leu = L-leucine, Lys = L-lysine, Ala = L-alanine, and n = 0-4. Quenching of excited naphthalene takes place by electronic energy transfer and proceeds on a time scale of 3-8 ns. A minor and slower (approximate to 45 ns) fluorescence decay was also measured, which was ascribed to exciplex quenching since it does not depend on the interchromophoric distances. IR spectra in methanol solution indicate that intramolecularly H-bonded conformations form, and circular dichroism data in both methanol and water-methanol mixtures suggest the presence of variable amounts of alpha-helix structure, depending on the chain length. The probability distribution of center-to-center distances of chain-linked donor-acceptor pairs was calculated by a rotational isomeric states model, in which rotation around each bond in the chromophore linkages is restricted to a few highly populated, low-energy isomeric states. By using the calculated distributions and applying a Forster type mechanism, the kinetics of the energy transfer were satisfactorily reproduced for all the compounds investigated only when the mutual orientations of the chromophores were also taken into account because interconversion among conformational substates of probe linkages is slow on the time scale of the transfer process.