Light harvesting in higher plants involves a complex multi-dimensional problem the solution of which encompasses contributions from various fields of research involving experiments and theoretical modelling. The intricate relation between the structure and spectral properties of such complexes lies at the core of its diverse functionality and had been brought to light many times in the past, both experimentally and theoretically. A broader understanding of the interplay between the EET and ET process which make up the complex energy landscape of such complexes becomes crucial when attempting to elucidate such relationships. A proper combination of the QM or QM/MM method(s) with structures generated from a long classically simulated MD trajectory provides an efficient strategy of including dynamical effects of the protein-pigment complex on the computed quantities of interest. Such incorporation of long time scale conformational changes is essential when elucidating the structure-property relation of the complexes. The additional spectral changes that accompany such conformational changes and which were oblivious in the original work are reported in chapters 3 and 4. In particular, we observed two prominent spectral changes that are discussed in chapters 3 and 4 respectively – 1) A drop in the oscillator strength of the chlorophyll dimer which resulted from an increase in the charge transfer contribution of the total oscillator strength, and 2) An accompanying red-shift of the lowest excitonic state on account of mixing with charge transfer states which drops in energy for the equilibrated structure of the two chlorophylls towards the end of the MD trajectory. In chapter 5 we presented a generalized approach wherein molecular fragment orbitals could be used as a reference basis to generate a set of localized occupied and valence virtual orbitals (denoted as ILMOs). Since the original localization scheme of obtaining ILMOs as described in chapter 2 retained only a minimal description of the virtual valence space, we further explored a pragmatic approach for localizing higher-lying hard virtual orbitals using a similar procedure as done for the occupied orbitals. The ILMOs, by themselves, are an interesting set of molecular orbitals which upon visualization can already provide a qualitative understanding of the nature of chemical bonding and antibonding orbitals as demonstrated. Since they represent an orthogonal set of orbitals, it can also be directly used in subsequent embedding calculations without the need for the construction of any projection operators. In this regard, we presented a simple one-step embedding approach for generating a set of re-canonicalized ILMOs (RILMOs) for each subsystem starting from a set of CMOs. In contrast to the ILMOs, these orbitals are delocalized over individual subsystem and retain the intrinsic Ï€ and π∗ character corresponding to bonding and antibonding orbitals as encountered in isolated conjugated systems. These orbitals are comparable to a set of polarized orthonormal orbitals arising from a top-down projection based embedding procedure. Moreover, in this chapter, we outlined a strategy for obtaining LE and CT approximate diabatic states from TDDFT including their corresponding electronic couplings in the basis of these orbitals. We also investigated the effect of different levels of truncation (truncation in the number of hard virtuals kept in the localization procedure versus truncation in the number of diabatic states used to reproduce the exact supersystem results) on the energies of the final adiabatic states. Such truncations are in the best interest of studying excited state processes in medium to large-sized molecules where working with matrices of reduced dimension can be computationally beneficial. Overall, our framework is general and can be easily extended to any other excited state methods which is envisaged as part of future work.