The light-harvesting antenna systems collect sunlight and transfer excitation energy rapidly to the photosynthetic reaction centers, where the energy is trapped in an electron-transfer reaction. To obtain an idea on mechanisms and functions of the photosynthetic apparatus, knowledge on energy levels of the participating pigment molecule and their complex structures are needed. Experimental spectroscopic results combined with known X-ray structures have made possible theoretical studies to explain spectroscopic and energy transfer properties of single light-harvesting antenna structures. In this project we are focusing on theoretical aspects of energy transfer and light harvesting processes in self-aggregated supramolecular pigment protein structures. The main focuses are in the dark electronic and vibration states of pigments of light-harvesting antenna and reaction center complexes. Modern quantum chemical methods are combined with near atomic-resolution X-ray structures of the complexes to construct vibronic Hamiltonians for different electronic states of the pigments in the protein complexes and in full photosynthetic units. The so obtained vibrational and electronic wave functions are used to calculate vibrational overlap integrals (Franck-Condon factors) that modulate magnitudes of the electronic transition dipole vectors. Finally, we will simulate optical spectra of different light-harvesting antenna complexes and photosynthetic units and study energy transfer processes within the units that for the first time fully account for effects of dark electronic states and vibration states in the ground and excited electronic states. We expect to show that the dark vibronic states may have important role in intra- and inter-antenna energy transfer processes, by increasing spectral overlap/density between initial and final states. No former optical spectroscopic studies of large organic molecules with quantum chemically constructed vibronic Hamiltonians are known.