The molecular structure of the light-harvesting complex peridinin-chlorophyll-protein from the dinoflagellate Amphidinium carterae (A-PCP) provides the positions and orientations of the eight peridinin (Per) and two chlorophyll a (Chl) molecules in the complex whose apoprotein is 32 kD. We made structure-based calculations of the distinctive optical properties (absorption and CD spectral of A-PCP and of the complex containing a ratio of four peridinin and one chlorophyll per complex (apoprotein similar to 15 kD) obtained from the related species Heterocapsa pygmaea (H-PCP). The latter structure has not been determined but can be inferred from that of A-PCP. A point-monopole approximation was used to represent the low-energy transition of peridinin in the blue region of the spectrum and that of chlorophyll in the Soret region. Vibronic interactions are taken into account for peridinin because of the strong vibrational progression exhibited by the spectrum of the latter. From the calculations, we are able to simulate the absorption and CD spectra for H-PCP and A-PCP by using, in addition to the atomic coordinates taken from the A-PCP structure, one and only one set of parameters, adjusted for the small unit of four Per and one Chi common to both systems. In particular, the four peridinin site energies were assigned values in the range 18 500-19 500 cm(-1), and those for the B-x and B-y transitions of chlorophyll a were given the common value 23 100 cm(-1). The transition moments for peridinin were in the range 10.6-12.4 D, and those of the chlorophyll B-x and B-y transitions were 9.0 and 1.0 D, respectively. Each resolved vibronic transition was given the same Gaussian line width of 550 cm(-1) Excitonic coupling among the different chromophores of the small cluster unit of the complex is not sufficient to describe the A-PCP optical properties. Intercluster interactions are necessary in order to reproduce the CD spectrum. The H-PCP spectrum, being practically identical to the former, is reproduced only if such interactions are maintained, meaning that the solution unit is a dimer of the monomeric polypeptide as previously inferred from the biochemical properties.