Molecular models for PSI, PSII, and the BRC were extracted from crystal structures of Synechococcus elongatus (PDB entry 1JB0), Thermococcus vulcanus (PDB en-try 3WU2), and Rhodobacter sphaeroides (PDB entry 1M3X), respectively, obtained from the Protein Data Bank . Missing hydrogen atoms of photosynthetic co-factors were added with the Reduce program , whereas the hydrogen atoms of the protein environment were added using CHARMM22 topology files . To saturate cut protein bonds, neutral groups -C(O)CH 3 and -NH 2 were applied as N-and C-termini, respectively. In these capping groups, bond distances were initially set to experimentally determined average values characteristic for small organic compounds . Two types of models were considered in this work: i) models, in which the long hydrocarbon tails R of Chl molecules (see Fig. ) were left unchanged and ii) models with the tail R truncated and replaced by a -CH 3 group. In case of dimeric molecular models such as the inner pair, sets of modified molecular structures with different orientations of the fragments were created. Thus, the initial crystal structures were adjusted by making mutual vertical and horizontal shifts of chlorophyll molecules. For this purpose, coordinates of truncated chlorophyll rings (without hydrogens and substituents at aromatic cycles) were fitted by a pair of parallel planes minimizing vertical distances to the atoms. Then, vectors of perpendicular and parallel shifts were determined. For the latter case, we chose vectors lying within the parallel planes and oriented along the Mg→C-5 directions of the corresponding molecules. In the following, we denote distances between these parallel planes as R ⊥ , while vertical and horizontal shifts are referred to as ∆R ⊥ and ∆R , respectively. Note that in case of horizontal shifts ∆R , coordinates of both aromatic macro-cycles are modified simultaneously by the corresponsing translation vectors of lengths ∆R . Binding pocket models of PSI, PSII, and BRC considered in Sec. 5.3 were created by specifying radii of 4.0 Å around each atom of the inner pair. All surrounding co-factors, water molecules, and amino acid residues with at least one atom within these radii were included explicitly into the models. Addition of missing hydrogens and cut bond saturation were conducted in a similar fashion as for smaller models considered in this work (see above). Amino acid residues were considered to be neutral and protonated in the created binding pocket models. Chl a BChl a To distinguish the created inner pair models with and without phytyl tails, we introduce label "t" for truncation. For example, [tP D1 • • • tP D2 ] +• should be understood as the truncated complex of P D1 and P D2 , while its non-truncated counterpart is denoted as Created molecular structures for neutral dimeric models in vacuum were optimized in two subsequent steps using the Orca program package. At first, the positions of hydrogens were relaxed keeping all other atomic coordinates fixed. Secondly, the structure optimization was carried out for the set of intramolecular bond distances. Two atoms A and B were considered as bound if the distance between them is in the interval of r(A)+r(B)±t, where r(A) and r(B) are covalent radii of the corresponding atoms and t = 0.5 Å is a tolerance parameter. This procedure ensured that structural parameters are partly optimized, while the relative orientation of fragments is still very close to that in the original crystal structure. Note that the second step does not imply any explicit constraints to bond and dihedral angles. In fact, they can slightly change during the optimization procedure. In both steps, the BP86 XC functional and the def2-TZVP basis set were applied. To reduce the computational cost, the resolution-ofthe-identity approximation in conjunction with the auxiliary Coulomb-fitting def2-TZV/J basis was enabled. Dispersion interactions were taken into account with the D3BJ correction with Becke-Johnson damping . "Loose" convergence criteria were applied for inner pair models. These optimized molecular structures of neutral complexes were then used in subsequent single-point calculations of the corresponding radicals.