Photosynthetic antenna proteins can be thought of as “programmed solvents”, which bind pigments at specific mutual orientations, thus tuning the overall energetic landscape and ensuring highly efficient light-harvesting. While positioning of chlorophyll cofactors is well understood and rationalized by the principle of an “energy funnel”, the carotenoids still pose many open questions. Particularly, their short excited state lifetime (<25 ps) renders them potential energy sinks able to compete with the reaction centers and drastically undermine light-harvesting efficiency. Exploration of the orientational phase-space revealed that the placement of central carotenoids minimizes their interaction with the nearest chlorophylls in the plant antenna complexes LHCII, CP26, CP29 and LHCI. At the same time we show that this interaction is highly sensitive to structural perturbations, which has a profound effect on the overall lifetime of the complex. This links the protein dynamics to the light-harvesting regulation in plants by the carotenoids.

The rapid, photoprotective down-regulation of plant light-harvesting in bright light proceeds via the non-photochemical quenching of chlorophyll excitation energy in the major photosystem II light-harvesting complex LHCII. However, there is currently no consensus regarding the precise mechanism by which excess energy is quenched. Current X-ray structures of this complex correspond to a dissipative conformation and therefore correct microscopic theoretical modelling should capture this property. Despite their accuracy in explaining the steady state spectroscopy of this complex, chlorophyll-only models (those that neglect the energetic role of carotenoids) do not explain the observed fluorescence quenching. To address this gap, we have used a combination of the semi-empirical MNDO-CAS-CI and the Transition Density Cube method to model all chlorophyll–carotenoid energy transfer pathways in the highly quenched LHCII X-ray structure. Our simulations reveal that the inclusion of carotenoids in this microscopic model results in profound excitation quenching, reducing the predicted excitation lifetime of the complex from 4 ns (chlorophyll-only) to 67 ps. The model indicates that energy dissipation proceeds via slow excitation transfer (>20 ps) from chlorophyll to the forbidden S₁ excited state of the centrally bound lutein molecules followed by the rapid (∼10 ps) radiationless decay to the ground state, with the latter being assumed from experimental measurements of carotenoid excited state lifetimes. Violaxanthin and neoxanthin do not contribute to this quenching. This work presents the first all-pigment microscopic model of LHCII and the first attempt to capture the dissipative character of the known structure.

In some molecular systems, such as nucleobases, polyenes or the active ingredients of sunscreens, substantial amounts of photo-excitation energy are dissipated on a sub-picosecond time scale, raising questions such as: where does this energy go or among which degrees of freedom it is being distributed at such early times? Here we use transient absorption spectroscopy to track excitation energy dispersing from the optically accessible vibronic subsystem into the remaining vibrational subsystem of the solute and solvent. Monitoring the flow of energy during vibrational redistribution enables quantification of local molecular heating. Subsequent heat dissipation away from the solute molecule is characterized by classical thermodynamics and molecular dynamics simulations. Hence, we present a holistic approach that tracks the internal temperature and vibronic distribution from the act of photo-excitation to the restoration of the global equilibrium. Within this framework internal vibrational redistribution and vibrational cooling are emergent phenomena. We demonstrate the validity of the framework by examining a highly controversial example, carotenoids. We show that correctly accounting for the local temperature unambiguously explains their energetically and temporally congested spectral dynamics without the ad hoc postulation of additional ‘dark’ states. An immediate further application of this approach would be to monitor the excitation and thermal dynamics of pigment–protein systems.

Plant light-harvesting is regulated by the Non-Photochemical Quenching (NPQ) mechanism involving the reversible formation of excitation quenching sites in the Photosystem II (PSII) antenna in response to high light. While the major antenna complex, LHCII, is known to be a site of NPQ, the precise mechanism of excitation quenching is not clearly understood. A preliminary model of the quenched crystal structure of LHCII implied that quenching arises from slow energy capture by Car pigments. It predicted a thoroughly quenched system but offered little insight into the defining aspects of this quenching. In this work, we present a thorough theoretical investigation of this quenching, addressing the factors defining the quenching pathway and possible mechanism for its (de)activation. We show that quenching in LHCII crystals is the result of slow energy transfer from chlorophyll to the centrally-bound lutein Cars, predominantly the Lut620 associated with the chlorophyll ‘terminal emitter’, one of the proposed in vivo pathways. We show that this quenching is rather independent of the particular species of Car and excitation ‘site’ energy. The defining parameter is the resonant coupling between the pigment co-factors. Lastly, we show that these interactions must be severely suppressed for a light-harvesting state to be recovered.

Carotenoids in photosynthetic proteins carry out the dual function of harvesting light and defending against photo-damage by quenching excess energy. The latter involves the low-lying, dark, excited state labelled S₁. Here “dark” means optically-forbidden, a property that is often attributed to molecular symmetry, which leads to speculation that its optical properties may be strongly-perturbed by structural distortions. This has been both explicitly and implicitly proposed as an important feature of photo-protective energy quenching. Here we present a theoretical analysis of the relationship between structural distortions and S₁ optical properties. We outline how S₁ is dark not because of overall geometric symmetry but because of a topological symmetry related to bond length alternation in the conjugated backbone. Taking the carotenoid echinenone as an example and using a combination of molecular dynamics, quantum chemistry, and the theory of spectral lineshapes, we show that distortions that break this symmetry are extremely stiff. They are therefore absent in solution and only marginally present in even a very highly-distorted protein binding pocket such as in the Orange Carotenoid Protein (OCP). S₁ remains resolutely optically-forbidden despite any breaking of bulk molecular symmetry by the protein environment. However, rotations of partially conjugated end-rings can result in fine tuning of the S₁ transition density which may exert some influence on interactions with neighbouring chromophores.