Modelling biological processes is challenging for contemporary computational methods, requiring accurate characterization of chemical properties within complex environments. This thesis aims to establish an atomistic and electronic level understanding of biomolecular systems using multiscale quantum mechanics/molecular mechanics (QM/MM) approaches, integrating accurate QM methods with classical molecular dynamics (MD) simulations.

First, we illustrate a multilayer approach using the domain-based pair natural orbital implementation of coupled cluster theory (DLPNO-CCSDT) on simple QM cluster models. This method is employed to estimate redox potentials and solvation free energies of hydrated transition metal ions at the coupled-cluster level, maintaining high-level treatment of the metal complex and explicitly coordinated waters. This protocol represents a promising route for applying accurate QM methods to complex open-shell systems. The core of the thesis explores mechanisms relevant to excitation energy transfer (EET), primary charge separation and photoprotection in natural photosynthesis. The initial processes involve intricate mechanisms of light harvesting and charge separation in Photosystem II (PSII). We describe the complete low-energy excitation spectrum of PSII, including singlet-triplet excitations and charge transfer (CT) states, using long-range corrected time-dependent density functional theory (TD-DFT) and QM/MM, calculate electron paramagnetic resonance (EPR) properties of chlorophyll triplet states and describe the electrostatic modulation of excited state energetics of RC pigments by specific redox-active cofactors. Furthermore, we investigate how three genetic variants of a crucial RC protein differentially tune the optical and redox properties of the pigments involved in the primary processes of photosynthesis, identifying residues responsible for specific matrix-induced adjustments of CT properties. Finally, we investigate the low-energy excitation manifold of the CP43 core antenna, utilizing TD-DFT/MM combined with large-scale perturbed matrix method (PMM) calculations which provides a refined basis for interpreting spectroscopic observations and understanding EET within PSII. Overall, the work in this thesis highlights: (i) methodological aspects for QM based multiscale modelling of proteins, and (ii) the role of solvation and protein environment in obtaining biologically relevant properties.