Chlorophyll transition dipole moment orientations and pathways for flow of excitation energy among the chlorophylls of the major plant antenna, LHCII.

We have attempted in this work an assignment of the Qy dipole moment orientations for all the chlorophylls in the major plant antenna, light-harvesting complex II (LHCII). Information that has recently become available through a structural model of the LHCII, site-directed mutagenesis, and spectroscopy of both LHCII and CP29 has been evaluated to model the electronic excited state structure in the presence of chlorophyll-chlorophyll and chlorophyll-protein interactions. An assignment has been obtained which satisfactorily reproduces the polarized linear absorption characteristics. The assignment proposed has also been found to be adequate in reproducing the time scales of the energy transfer processes. The pathways for the flow of excitation energy among the chlorophylls of the complex have been suggested in the context of identity and orientation assignments.