Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation

Abstract

Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

“…This "tuning" is mainly realized through electrostatic and polarization effects of the protein residues which can significantly affect both site energies and exciton couplings. [94][95][96] For such complexes, but also for other types of excitonic systems, combining a Frenkel exciton model with a polarizable embedding is a very effective strategy. This combination has been developed and implemented by our group in collaboration with Dr. C. Curutchet in Barcelona using the IPD formulation of the polarizable embedding.…”

Molecular dynamics simulations in photosynthesis

“…The interested reader is referred to the following reviews which provide a more detailed overview of the combination of MD simulations with quantum chemical calculations applied to photosynthetic pigment-protein complexes (Buda 2009;Neugebauer 2009;Segatta et al 2019;Cupellini et al 2019). For more general reviews on QM/MM methods, we refer the reader to Wanko et al (2006) and Senn and Thiel (2009).…”

Charge transfer from the carotenoid can quench chlorophyll excitation in antenna complexes of plants

“…Due to the difficulty in revealing the quenching mechanisms through a direct observation, computational simulations can really represent a fundamental tool, which can not only support experimental evidence, but also integrate it with a molecular-level description of the quenching processes 22,23 . In the literature, the examples of studies focusing on the possible quenching mechanisms are still limited, and almost exclusively focused on the EET mechanism 9,10,24,25 .…”