Bioexcitons by Design: How Do We Get There?

Abstract

Biological pigment−protein complexes (PPCs) exhibit a remarkable ability to tune the optical properties of biological excitons (bioexcitons) through specific pigment−protein interactions. While such fine-tuning allows natural systems (e.g., photosynthetic proteins) to carry out their native functions with near-optimal performance, native function itself is often suboptimal for applications such as biofuel production or quantum technology development. This perspective offers a look at nearterm prospects for the rational reoptimization of PPC bioexcitons for new functions using site-directed mutagenesis. The primary focus is on the "structure−spectrum" challenge of understanding the relationships between structural features and spectroscopic properties. While recent examples demonstrate that site-directed mutagenesis can be used to tune nearly all key bioexciton parameters (e.g., site energies, interpigment couplings, and electronic−vibrational interactions), critical challenges remain before we achieve truly rational design of bioexciton properties.

De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs

“…The stronger coupling of SP2 relative to SP1 may re ect the closer spacing of the ZnPPaM molecules in SP2, whereas the stronger coupling of the purple bacterial special pair is due to the stronger Q y transition dipole moment of bacteriochlorins as compared to chlorins (Knox & Spring, 2003). Prediction of the spectroscopic properties of a Chl dimer in a protein is complicated by the fact that Chl-Chl coupling energies are typically similar in magnitude to the available thermal energy, Frank-Condon active vibrational and phonon reorganization energies, and local Chl vibrational frequencies (Reppert, 2023). Accurate optical predictions require benchmarking of theoretical methods using robust model systems.…”

“…To control these degrees of freedom, we sought to design homodimers with perfect two-fold cyclic (C 2 ) symmetry, which bind a C 2 -symmetric Chl pair such that the C 2 symmetry axes of the protein and chromophore are coincident, similar to native reaction centers, which can have true C 2 symmetry (Chen et al, 2020; Gisriel et al, 2017) or pseudo-C 2 symmetry (Figure 1a). C 2 symmetry ensures that the two bound Chl molecules will have near-degenerate site energies, improving the resonance between pigment transitions necessary to create delocalized states (Reppert, 2023). For Chl dimer protein scaffolds, we chose hyperstable C 2 -symmetric repeat protein dimers containing symmetric pockets with tunable sizes and geometries (Brunette et al, 2015(Brunette et al, , 2020Doyle et al, 2015;Fallas et al, 2017;Hicks et al, 2022).…”

Large language models as tax attorneys: a case study in legal capabilities emergence

“…Reppert et al . [ 26 ] develop iterated decomposition, a human-in-the-loop workflow for developing and refining compositional LLM programs that improves performance on real-world science question and answer tasks.…”

Detangling Solvatochromic Effects by the Effective Fragment Potential Method

“…In recent years, several computational tools for decomposing the total system energy into pairwise contributions have been developed, including pairwise interaction energy decomposition analysis (PIEDA) extension of the fragment molecular orbital (FMO) method, and functional symmetry-adapted perturbation theory (F-SAPT). − Similar questions about structure–function relations in extended photochemically active systems might be even more acute. For example, while mutagenesis is an established technique for elucidating details of light-induced processes in photosynthetic pigment–protein complexes and proteins of the GFP family, theoretical tools for the analysis of mutagenesis’s effects on proteins’ photochemistry still need to be developed. − Additionally, as electronically excited states are often delocalized, the results of mutagenesis on the photochemical processes might be more convoluted and less linear than in the case of the ground state. In this article, we address the question of structure–function relations in extended photoactive systems by introducing a new computational technique for the pairwise decomposition analysis of solvatochromic shifts in embedded electronically excited chromophores.…”