Semiempirical configuration interaction calculations in biochemical environments: Parametrization and application to γD-crystallin, an eye-lense protein

We approach the problem of optical excitations in molecular aggregates in complex biochemical environments from a computational, all-atom perspective. The system is divided into a π orbital part described by a Pariser-Parr-Pople model with configuration interaction using singly excited Slater determinants (PPP-CIS). It is coupled to the protein and water charges of a classical force field. Strategies for a high-accuracy reparameterization and an efficient computational solution are presented. For γD-crystallin, a band edge consisting of charge-transfer states emerges for a coupled molecular aggregate compared to the uncoupled residues. The energies of some charge-transfer states strongly depend on the dielectric properties of the model, giving a first insight into the potential temporal evolution of these excitations. Possible biochemical implications are discussed.

Graphical AbstractResearch Highlights►Protein optical excitations are computed using π electron models. ►A system-specific reparametrization is imperative. ►Aromatic amino acid aggregates show a charge transfer absorption edge. ►Excitations can be traced following dielectric relaxation.