Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers

Abstract We quantify the excitonic coupling in the homodimer of the dimeric Venus fluorescent protein using a quantum-classical hybrid workflow. Because the anionic chromophore carries appreciable double-excitation character, we obtain its site energy from domain-based local-pair-natural-orbital similarity-transformed equation-of-motion coupled-cluster theory (DLPNO-STEOM-CCSD), which places the in-protein bright ππ* state at 523.90 nm, in good agreement with the experimental absorption maximum near 515 nm and validated against an explicit triples-corrected EOM-CCSD(fT) benchmark; single-excitation time-dependent density functional theory (TDDFT) blueshifts this state. Applying a transition-density coupling (TDC) formalism to the STEOM transition density and simulating the VenusA206 tandem-dimer construct (two β-barrels covalently joined by an inter-domain linker), the covalent tether holds the A206 interface docked throughout 1 ns of room-temperature dynamics. We obtain a thermally averaged coupling of J = 32.8 ± 1.6 cm–1 across the 1000-frame trajectory (Davydov splitting 2|J| = 65.6 ± 3.1 cm–1), representing a 19% near-field enhancement over the ensemble point-dipole estimate (JPDA = 27.6 ± 1.3 cm–1) at the 24.69 ± 0.32 Å chromophore centroid separation. Furthermore, we argue that a separation of time scales resolves the apparent theoretical tension between intermediate experimental excitonic couplings and the highly decoherent biological environment. While it has been hypothesized that the fluorescent protein β-barrel scaffold sustains coupling by shielding the chromophore from thermal fluctuations, we emphasize that the separation of time scales applies irrespective of the exact degree of environmental decoherence and dissipation. Collective photoexcitation imprints the Davydov splitting under optical-limit dielectric screening upon absorption, preceding bulk solvent relaxation and sub-picosecond environmental dephasing. To characterize the subsequent post-absorption evolution, we employ stochastic wavefunction simulations to model the transition from a delocalized exciton superposition to incoherent hopping between localized chromophore states.