Temperature Dependence of Excitation Transfer in LH2 of Rhodobacter sphaeroides

Simulation of the Pump-Probe Spectra and Excitation Energy Relaxation of the B850 Band of the LH2 Complex in Purple Bacteria

Ultrafast spectroscopic techniques have been vital in studying excitation energy transfer (EET) in photosynthetic light harvesting complexes. In this paper, we simulate the pump-probe spectra of the B850 band of the light harvesting complex 2 (LH2) of purple bacteria, by using the hierarchical equation of motion method and the optical response function approach. The ground state bleach, stimulated emission, and excited state absorption components of the pump-probe spectra are analyzed in detail. The laser pulse-induced population dynamics are also simulated to help understand the main features of the pump-probe spectra and the EET process. It is shown that the excitation energy relaxation is an ultrafast process with multiple time scales. The first 40 fs of the pump-probe spectra is dominated by the relaxation of the k = ±1 states to both the k = 0 and higher energy states. Dynamics on a longer time scale around 200 fs reflects the relaxation of higher energy states to the k = 0 state.

Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes

Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.

Carotenoid-Mediated Long-Range Energy Transfer in the Light Harvesting-Reaction Center Complex from Photosynthetic Bacterium Roseiflexus castenholzii

The light harvesting-reaction center complex (LH-RC) of Roseiflexus castenholzii binds bacteriochlorophylls a (BChls a), B800 and B880, absorbing around 800 and 880 nm, respectively. We comparatively investigated the interband excitation energy transfer (EET) dynamics of the wild-type LH-RC (wt-LH-RC) of Rfl. castenholzii and its carotenoid (Car)-less mutant (m-LH-RC) and found that Car can boost the B800 → B880 EET rate from (2.43 ps)-1 to (1.75 ps)-1, accounting for 38% acceleration of the EET process. Interestingly, photoexcitation of wt-LH-RC at 800 nm induced pronounced excitation dynamics of Car despite the insufficient photon energy for direct Car excitation, a phenomenon which is attributed to the BChl-Car exciplex 1[B800(↑↑)···Car(↓↓)]*. Such an exciplex is suggested to play an essential role in promoting the B800 → B880 EET process, as corroborated by the recently reported cryo-EM structures of wt-LH-RC and m-LH-RC. The mechanism of Car-mediated EET will be helpful to deepen the understanding of the role of Car in bacterial photosynthesis.

Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria

In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.

Optical cavity-mediated exciton dynamics in photosynthetic light harvesting 2 complexes

Strong light-matter interaction leads to the formation of hybrid polariton states and alters the photophysical dynamics of organic materials and biological systems without modifying their chemical structure. Here, we experimentally investigated a well-known photosynthetic protein, light harvesting 2 complexes (LH2) from purple bacteria under strong coupling with the light mode of a Fabry-Perot optical microcavity. Using femtosecond pump probe spectroscopy, we analyzed the polariton dynamics of the strongly coupled system and observed a significant prolongation of the excited state lifetime compared with the bare exciton, which can be explained in terms of the exciton reservoir model. Our findings indicate the potential of tuning the dynamic of the whole photosynthetic unit, which contains several light harvesting complexes and reaction centers, with the help of strong exciton-photon coupling, and opening the discussion about possible design strategies of artificial photosynthetic devices.

Structures of a phycobilisome in light-harvesting and photoprotected states

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae^1,2. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching^3-6. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties⁷, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

Energy funnelling within multichromophore architectures monitored with subnanometre resolution

The funnelling of energy within multichromophoric assemblies is at the heart of the efficient conversion of solar energy by plants. The detailed mechanisms of this process are still actively debated as they rely on complex interactions between a large number of chromophores and their environment. Here we used luminescence induced by scanning tunnelling microscopy to probe model multichromophoric structures assembled on a surface. Mimicking strategies developed by photosynthetic systems, individual molecules were used as ancillary, passive or blocking elements to promote and direct resonant energy transfer between distant donor and acceptor units. As it relies on organic chromophores as the elementary components, this approach constitutes a powerful model to address fundamental physical processes at play in natural light-harvesting complexes.

Energy Transfer Dynamics in Light-Harvesting Complex 2 Variants Containing Oxidized B800 Bacteriochlorophyll a

Excitation energy transfer (EET) in light-harvesting proteins is vital for photosynthetic activities. The pigment compositions and their organizations in these proteins are responsible for the EET functions. Thus, changing the pigment compositions in light-harvesting proteins contributes to a better understanding of EET mechanisms. In this study, we investigated the EET dynamics of two light-harvesting complex 2 (LH2) variants, in which nine B800 bacteriochlorophyll (BChl) a pigments were entirely or half converted to 3-acetyl chlorophyll (AcChl) a. The AcChl a pigments showed a Q_y band, which was blue-shifted by 107 nm from B800 BChl a in the two variants. EET from AcChl a to B850 BChl a was observed in both fully oxidized and half-oxidized LH2 variants, but the EET rates were lower than that from B800 to B850 BChl a. EET from AcChl a to the co-present B800 was barely detected in the half-oxidized LH2. The preferential EET from AcChl a to B850 instead of B800 was rationalized by little spectral overlap of AcChl a with B800 BChl a and the pigment geometry in the protein. The EET rate from B800 to B850 BChl a in the half-oxidized LH2 was analogous to that in native LH2, indicating that partial oxidation of B800 did not disturb the EET channel from the residual B800 to B850.

Excitation Energy Transfer from Bacteriochlorophyll b in the B800 Site to B850 Bacteriochlorophyll a in Light-Harvesting Complex 2

Control of the spectral overlap between energy donors and acceptors provides insight into excitation energy transfer (EET) mechanisms in photosynthetic light-harvesting proteins. Substitution of energy-donating B800 bacteriochlorophyll (BChl) a with other pigments in the light-harvesting complex 2 (LH2) of purple photosynthetic bacteria has been extensively performed; however, most studies on the B800 substitution have focused on the decrease in the spectral overlap integral with energy-accepting B850 BChl a by reconstitution of chlorophylls into the B800 site. Here, we reconstitute BChl b into the B800 site of the LH2 protein from Rhodoblastus acidophilus to increase the spectral overlap with B850 BChl a. BChl b in the B800 site had essentially the same hydrogen-bonding pattern as B800 BChl a, whereas it showed a red-shifted Q_y absorption band at 831 nm. The EET rate from BChl b to B850 BChl a in the reconstituted LH2 was similar to that of native LH2 despite the red shift of the Q_y band of the energy donor. These results demonstrate the importance of the contribution of the density of excitation states of the B850 circular assembly, which incorporates higher lying optically forbidden states, to intracomplex EET in LH2.

Universal quenching of common fluorescent probes by water and alcohols

Although biological imaging is mostly performed in aqueous media, it is hardly ever considered that water acts as a classic fluorescence quencher for organic fluorophores. By investigating the fluorescence properties of 42 common organic fluorophores recommended for biological labelling, we demonstrate that H2O reduces their fluorescence quantum yield and lifetime by up to threefold and uncover the underlying fluorescence quenching mechanism. We show that the quenching efficiency is significantly larger for red-emitting probes and follows an energy gap law. The fluorescence quenching finds its origin in high-energy vibrations of the solvent (OH groups), as methanol and other linear alcohols are also found to quench the emission, whereas it is restored in deuterated solvents. Our observations are consistent with a mechanism by which the electronic excitation of the fluorophore is resonantly transferred to overtones and combination transitions of high-frequency vibrational stretching modes of the solvent through space and not through hydrogen bonds. Insight into this solvent-assisted quenching mechanism opens the door to the rational design of brighter fluorescent probes by offering a justification for protecting organic fluorophores from the solvent via encapsulation.

Comparison of the Energy-Transfer Rates in Structural and Spectral Variants of the B800-850 Complex from Purple Bacteria

Photosynthetic light harvesting can occur with a remarkable near-unity quantum efficiency. The B800-850 complex, also known as light-harvesting complex 2 (LH2), is the primary light-harvesting complex in purple bacteria and has been extensively studied as a model system. The bacteriochlorophylls of the B800-850 complex are organized into two concentric rings, known as the B800 and B850 rings. However, depending on the species and growth conditions, the number of constituent subunits, the pigment geometry, and the absorption energies vary. While the dynamics of some B800-850 variants have been exhaustively characterized, others have not been measured. Furthermore, a direct and simultaneous comparison of how both structural and spectral differences between variants affect these dynamics has not been performed. In this work, we utilize ultrafast transient absorption measurements to compare the B800 to B850 energy-transfer rates in the B800-850 complex as a function of the number of subunits, geometry, and absorption energies. The nonameric B800-850 complex from Rhodobacter (Rb.) sphaeroides is 40% faster than the octameric B800-850 complex from Rhodospirillum (Rs.) molischianum, consistent with structure-based predictions. In contrast, the blue-shifted B800-820 complex from Rs. molischianum is only 20% faster than the B800-850 complex from Rs. molischianum despite an increase in the spectral overlap between the rings that would be expected to produce a larger increase in the energy-transfer rate. These measurements support current models that contain dark, higher-lying excitonic states to bridge the energy gap between rings, thereby maintaining similar energy-transfer dynamics. Overall, these results demonstrate that energy-transfer dynamics in the B800-850 complex are robust to the spectral and structural variations between species used to optimize energy capture and flow in purple bacteria.

Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials

Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically, simulations must go beyond the Born-Oppenheimer approximation to account for non-adiabatic coupling between excited states. Indeed, non-adiabatic dynamics is commonly associated with exciton dynamics and photophysics involving charge and energy transfer, as well as exciton dissociation and charge recombination. Understanding the photoinduced dynamics in such materials is vital to providing an accurate description of exciton formation, evolution, and decay. This interdisciplinary field has matured significantly over the past decades. Formulation of new theoretical frameworks, development of more efficient and accurate computational algorithms, and evolution of high-performance computer hardware has extended these simulations to very large molecular systems with hundreds of atoms, including numerous studies of organic semiconductors and biomolecules. In this Review, we will describe recent theoretical advances including treatment of electronic decoherence in surface-hopping methods, the role of solvent effects, trivial unavoided crossings, analysis of data based on transition densities, and efficient computational implementations of these numerical methods. We also emphasize newly developed semiclassical approaches, based on the Gaussian approximation, which retain phase and width information to account for significant decoherence and interference effects while maintaining the high efficiency of surface-hopping approaches. The above developments have been employed to successfully describe photophysics in a variety of molecular materials.

Before Förster. Initial excitation in photosynthetic light harvesting

Electronic 2D spectroscopy allows nontrivial quantum effects to be explored in unprecedented detail. Here, we apply recently developed fluorescence detected coherent 2D spectroscopy to study the light harvesting antenna 2 (LH2) of photosynthetic purple bacteria. We report double quantum coherence 2D spectra which show clear cross peaks indicating correlated excitations. Similar results are found for rephasing and nonrephasing signals. Analysis of signal generating quantum pathways leads to the conclusion that, contrary to the currently prevailing physical picture, the two weakly coupled pigment rings of LH2 share the initial electronic excitation leading to quantum mechanical correlation between the two clearly separate absorption bands. These results are general and have consequences for the interpretation of initially created excited states not only in photosynthesis but in all light absorbing systems composed of weakly interacting pigments where the excitation transfer is commonly described by using Förster theory. Being able to spectrally resolve the nonequilibrium dynamics immediately following photoabsorption may provide a glimpse to the systems' transition into the Förster regime.

How Well Does the Hole-Burning Action Spectrum Represent the Site-Distribution Function of the Lowest-Energy State in Photosynthetic Pigment-Protein Complexes?

For the first time, we combined Monte Carlo and nonphotochemical hole burning (NPHB) master equation approaches to allow for ultrahigh-resolution (<0.005 cm^-1, smaller than the typical homogeneous line widths at 5 K) simulations of the NPHB spectra of dimers and trimers of interacting pigments. These simulations reveal significant differences between the zero-phonon hole (ZPH) action spectrum and the site-distribution function (SDF) of the lowest-energy state. The NPHB of the lowest-energy pigment, following the excitation energy transfer (EET) from the higher-energy pigments which are excited directly, results in the shifts of all excited states. These shifts affect the ZPH action spectra and EET times derived from the widths of the spectral holes burned in the donor-dominated regions. The effect is present for a broad variety of realistic antihole functions, and it is maximal at relatively low values of interpigment coupling (V ≤ 5 cm^-1) where the use of the Förster approximation is justified. These findings need to be considered in interpreting various optical spectra of photosynthetic pigment-protein complexes for which SDFs (describing the inhomogeneous broadening) are often obtained directly from the ZPH action spectra. Water-soluble chlorophyll-binding protein (WSCP) was considered as an example.

Simulating Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of Multichromophoric Systems

We present a theory for modeling fluorescence-detected two-dimensional electronic spectroscopy of multichromophoric systems. The theory is tested by comparison of the predicted spectra of the light-harvesting complex LH2 with experimental data. A qualitative explanation of the strong cross-peaks as compared to conventional two-dimensional electronic spectra is given. The strong cross-peaks are attributed to the clean ground-state signal that is revealed when the annihilation of exciton pairs created on the same LH2 complex cancels oppositely signed signals from the doubly excited state. This annihilation process occurs much faster than the nonradiative relaxation. Furthermore, the line shape difference is attributed to slow dynamics, exciton delocalization within the bands, and intraband exciton-exciton annihilation. This is in line with existing theories presented for model systems. We further propose the use of time-resolved fluorescence-detected two-dimensional spectroscopy to study state-resolved exciton-exciton annihilation.

Theory of Excitonic Delocalization for Robust Vibronic Dynamics in LH2

Nonlinear spectroscopy has revealed long-lasting oscillations in the optical response of a variety of photosynthetic complexes. Different theoretical models that involve the coherent coupling of electronic (excitonic) or electronic-vibrational (vibronic) degrees of freedom have been put forward to explain these observations. The ensuing debate concerning the relevance of either mechanism may have obscured their complementarity. To illustrate this balance, we quantify how the excitonic delocalization in the LH2 unit of Rhodopseudomonas acidophila purple bacterium leads to correlations of excitonic energy fluctuations, relevant coherent vibronic coupling, and importantly, a decrease in the excitonic dephasing rates. Combining these effects, we identify a feasible origin for the long-lasting oscillations observed in fluorescent traces from time-delayed two-pulse single-molecule experiments performed on this photosynthetic complex and use this approach to discuss the role of this complementarity in other photosynthetic systems.

New Insights into the Mechanism of Uphill Excitation Energy Transfer from Core Antenna to Reaction Center in Purple Photosynthetic Bacteria

The uphill excitation energy transfer (EET) from the core antenna (LH1) to the reaction center (RC) of purple photosynthetic bacteria was investigated at room temperature by comparing the native LH1-RC from Thermochromatium ( Tch.) tepidum with the hybrid LH1-RC from a mutant strain of Rhodobacter ( Rba.) sphaeroides. The latter protein with chimeric Tch-LH1 and Rba-RC exhibits a substantially larger RC-to-LH1 energy difference (Δ E = 630 cm^-1) of 3-fold thermal energy (3 k_B T). The spectroscopic and kinetics results are discussed on the basis of the newly reported high-resolution structures of Tch. tepidum LH1-RC, which allow us to propose the existence of a passage formed by LH1 BChls that facilitates the LH1 → RC EET. The semilogarithmic plot of the EET rate against Δ E was found to be linear over a broad range of Δ E, which consolidates the mechanism of thermal activation as promoted by the spectral overlap between the LH1 fluorescence and the special pair absorption of RC.

Computational Modeling of Exciton-Bath Hamiltonians for Light Harvesting 2 and Light Harvesting 3 Complexes of Purple Photosynthetic Bacteria at Room Temperature

Light harvesting 2 (LH2) complex is the primary component of the photosynthetic unit of purple bacteria that is responsible for harvesting and relaying excitons. The electronic absorption line shape of LH2 contains two major bands at 800 and 850 nm wavelength regions. Under low light conditions, some species of purple bacteria replace LH2 with light harvesting 3 (LH3), a variant form with almost the same structure as the former but with distinctively different spectral features. The major difference between the absorption line shapes of LH2 and LH3 is the shift of the 850 nm band of the former to a new 820 nm region. The microscopic origin of this difference has been the subject of some theoretical/computational investigations. However, the genuine molecular level source of such a difference is not clearly understood yet. This work reports a comprehensive computational study of LH2 and LH3 complexes so as to clarify different molecular level features of LH2 and LH3 complexes and to construct simple exciton-bath models with a common form. All-atomistic molecular dynamics simulations of both LH2 and LH3 complexes provide detailed molecular level structural differences of bacteriochlorophylls (BChls) in the two complexes, in particular, in their patterns of hydrogen bonding (HB) and torsional angles of the acetyl group. Time-dependent density functional theory calculation of the excitation energies of BChls for structures sampled from the MD simulations suggests that the observed differences in the HB and torsional angles cannot fully account for the experimentally observed spectral shift of LH3. Potential sources that can explain the actual spectral shift of LH3 are discussed, and their magnitudes are assessed through fitting of experimental line shapes. These results demonstrate the feasibility of developing simple exciton-bath models for both LH2 and LH3, which can be employed for large-scale exciton quantum dynamics in their aggregates.

Origin of the Two Bands in the B800 Ring and Their Involvement in the Energy Transfer Network of Allochromatium vinosum

Bacterial photosynthesis features robust and adaptable energy-harvesting processes in which light-harvesting proteins play a crucial role. The peripheral light-harvesting complex of the purple bacterium Allochromatium vinosum is particularly distinct, featuring a double peak structure in its B800 absorption band. Two hypotheses-not necessarily mutually exclusive-concerning the origin of this splitting have been proposed; either two distinct B800 bacteriochlorophyll site energies are involved, or an excitonic dimerization of bacteriochlorophylls within the B800 ring takes place. Through the use of two-dimensional electronic spectroscopy, we present unambiguous evidence that excitonic interaction shapes the split band. We further identify and characterize all of the energy transfer pathways within this complex by using a global kinetic fitting procedure. Our approach demonstrates how the combination of two-dimensional spectral resolution and self-consistent fitting allows for extraction of information on light-harvesting processes, which would otherwise be inaccessible due to signal congestion.

Energy transfer and charge separation dynamics in photoexcited pyrene-bodipy molecular dyads

The photophysical properties of two pyrene-bodipy molecular dyads, composed of a phenyl-pyrene (Py-Ph) linked to the meso position of a bodipy (BD) molecule with either H-atoms (BD1) or ethyl groups (BD2) at the 2,6 positions, are investigated by stationary, nanosecond and femtosecond spectroscopy. The properties of these dyads (Py-Ph-BD1 and Py-Ph-BD2) are compared to those of their constituent chromophores in two solvents namely 1,2-dichloroethane (DCE) and acetonitrile (ACN). Stationary spectroscopy reveals a weak coupling among the subunits in both dyads. Excitation of the pyrene (Py) subunit leads to emission that is totally governed by the BD subunits in both dyads pointing to excitation energy transfer (EET) from the Py to BD chromophore. Femtosecond fluorescence and transient absorption spectroscopy reveal that EET takes place within 0.3-0.5 ps and is mostly independent of the solvent and the type of the BD subunit. The EET lifetime is in reasonable agreement with that predicted by Förster theory. After EET has taken place, Py-Ph-BD1 in DCE and Py-Ph-BD2 in both solvents decay mainly radiatively to the ground state with 3.5-5.0 ns lifetimes which are similar to those of the individual BD chromophores. However, the excited state of Py-Ph-BD1 in ACN is quenched having a lifetime of 1 ns. This points to the opening of an additional non-radiative channel of the excited state of Py-Ph-BD1 in this solvent, most probably charge separation (CS). Target analysis of the TA spectra has shown that the CS follows inverted kinetics and is substantially slower than the recombination of the charge-separated state. Occurrence of CS with Py-Ph-BD1 in ACN is also supported by energetic considerations. The above results indicate that only a small change in the structure of the BD units incorporated in the dyads significantly affects the excited state dynamics leading either to a dyad with long lifetime and high fluorescence quantum yield or to a dyad with ability to undergo CS.

Simple Quantum Dynamics with Thermalization

In this paper, we introduce two simple quantum dynamics methods. One is based on the popular surface-hopping method, and the other is based on rescaling of the propagation on the bath ground-state potential surface. The first method is special, as it avoids specific feedback from the simulated quantum system to the bath and can be applied for precalculated classical trajectories. It is based on the equipartition theorem to determine if hops between different potential energy surfaces are allowed. By comparing with the formally exact Hierarchical Equations Of Motion approach for four model systems we find that the method generally approximates the quantum dynamics toward thermal equilibrium very well. The second method is based on rescaling of the nonadiabatic coupling and also neglect the effect of the state of the quantum system on the bath. By the nature of the approximations, they cannot reproduce the effect of bath relaxation following excitation. However, the methods are both computationally more tractable than the conventional fewest switches surface hopping, and we foresee that the methods will be powerful for simulations of quantum dynamics in systems with complex bath dynamics, where the system-bath coupling is not too strong compared to the thermal energy.

Ultrafast Non-Förster Intramolecular Donor-Acceptor Excitation Energy Transfer

Ultrafast intramolecular electronic energy transfer in a conjugated donor-acceptor system is simulated using nonadiabatic excited-state molecular dynamics. After initial site-selective photoexcitation of the donor, transition density localization is monitored throughout the S₂ → S₁ internal conversion process, revealing an efficient unidirectional donor → acceptor energy-transfer process. Detailed analysis of the excited-state trajectories uncovers several salient features of the energy-transfer dynamics. While a weak temperature dependence is observed during the entire electronic energy relaxation, an ultrafast initially temperature-independent process allows the molecular system to approach the S₂-S₁ potential energy crossing seam within the first ten femtoseconds. Efficient energy transfer occurs in the absence of spectral overlap between the donor and acceptor units and is assisted by a transient delocalization phenomenon of the excited-state wave function acquiring Frenkel-exciton character at the moment of quantum transition.

New insights into the photochemistry of carotenoid spheroidenone in light-harvesting complex 2 from the purple bacterium Rhodobacter sphaeroides

Light-harvesting complex 2 (LH2) from the semi-aerobically grown purple phototrophic bacterium Rhodobacter sphaeroides was studied using optical (static and time-resolved) and resonance Raman spectroscopies. This antenna complex comprises bacteriochlorophyll (BChl) a and the carotenoid spheroidenone, a ketolated derivative of spheroidene. The results indicate that the spheroidenone-LH2 complex contains two spectral forms of the carotenoid: (1) a minor, "blue" form with an S₂ (1¹B _u⁺ ) spectral origin band at 522 nm, shifted from the position in organic media simply by the high polarizability of the binding site, and (2) the major, "red" form with the origin band at 562 nm that is associated with a pool of pigments that more strongly interact with protein residues, most likely via hydrogen bonding. Application of targeted modeling of excited-state decay pathways after carotenoid excitation suggests that the high (92%) carotenoid-to-BChl energy transfer efficiency in this LH2 system, relative to LH2 complexes binding carotenoids with comparable double-bond conjugation lengths, derives mainly from resonance energy transfer from spheroidenone S₂ (1¹B _u⁺ ) state to BChl a via the Q_x state of the latter, accounting for 60% of the total transfer. The elevated S₂ (1¹B _u⁺ ) → Q_x transfer efficiency is apparently associated with substantially decreased energy gap (increased spectral overlap) between the virtual S₂ (1¹B _u⁺ ) → S₀ (1¹A _g^- ) carotenoid emission and Q_x absorption of BChl a. This reduced energetic gap is the ultimate consequence of strong carotenoid-protein interactions, including the inferred hydrogen bonding.

Femtosecond to nanosecond studies of octupolar molecules and their quadrupolar and dipolar analogues

The fs–ps anisotropy dynamics of octupolar, quadrupolar and dipolar molecules with different π-bridges.

Protein Configuration Landscape Fluctuations Revealed by Exciton Transition Polarizations in Single Light Harvesting Complexes

Protein is a flexible material with broad distribution of conformations forming an energy landscape of quasi-stationary states. Disentangling the system dynamics along this landscape is the key for understanding the functioning of the protein. Here we studied a photosynthetic antenna pigment-protein complex LH2 with single molecule two-dimensional polarization imaging. Modeling based on the Redfield relaxation theory well describes the observed polarization properties of LH2 fluorescence and fluorescence excitation, strongly suggesting that at 77 K the conformational subspace of the LH2 is limited to about three configurations with relatively frequent switching among each other. At room temperature the next level of fluctuations determines the conformational dynamics. The results support the multitier model of the energy landscape of proteins and demonstrate the potential of the method for the studies of structural dynamics in proteins.

Structure-Based Modeling of Fluorescence Kinetics of Photosystem II: Relation between Its Dimeric Form and Photoregulation

A photosystem II-enriched membrane (PSII-em) consists of the PSII core complex (PSII-cc) which is surrounded by peripheral antenna complexes. PSII-cc consists of two core antenna (CP43 and CP47) and the reaction center (RC) complex. Time-resolved fluorescence spectra of a PSII-em were measured at 77 K. The data were globally analyzed with a new compartment model, which has a minimum number of compartments and is consistent with the structure of PSII-cc. The reliability of the model was investigated by fitting the data of different experimental conditions. From the analysis, the energy-transfer time constants from the peripheral antenna to CP47 and CP43 were estimated to be 20 and 35 ps, respectively. With an exponential time constant of 320 ps, the excitation energy was estimated to accumulate in the reddest chlorophyll (Red Chl), giving a 692 nm fluorescence peak. The excited state on the Red Chl was confirmed to be quenched upon the addition of an oxidant, as reported previously. The calculations based on the Förster theory predicted that the excitation energy on Chl29 is quenched by ChlZD1(+), which is a redox active but not involved in the electron-transfer chain, located in the D1 subunit of RC, in the other monomer with an exponential time constant of 75 ps. This quenching pathway is consistent with our structure-based simulation of PSII-cc, which assigned Chl29 as the Red Chl. On the other hand, the alternative interpretation assigning Chl26 as the Red Chl was not excluded. The excited Chl26 was predicted to be quenched by another redox active ChlZD2(+) in the D2 subunit of RC in the same monomer unit with an exponential time constant of 88 ps.

Dependence of Spurious Charge-Transfer Excited States on Orbital Exchange in TDDFT: Large Molecules and Clusters

Time-dependent density functional theory (TDDFT) is a powerful tool allowing for accurate description of excited states in many nanoscale molecular systems; however, its application to large molecules may be plagued with difficulties that are not immediately obvious from previous experiences of applying TDDFT to small molecules. In TDDFT, the appearance of spurious charge-transfer states below the first optical excited state is shown to have significant effects on the predicted absorption and emission spectra of several donor-acceptor substituted molecules. The same problem affects the predictions of electronic spectra of molecular aggregates formed from weakly interacting chromophores. For selected benchmark cases, we show that today's popular density functionals, such as purely local (Local Density Approximation, LDA) and semilocal (Generalized Gradient Approximation, GGA) models, are qualitatively wrong. Nonlocal hybrid approximations including both semiempirical (B3LYP) and ab initio (PBE1PBE) containing a small fraction (20-25%) of Fock-like orbital exchange are also susceptible to such problems. Functionals that contain a larger fraction (50%) of orbital exchange like the early hybrid (BHandHLYP) are shown to exhibit far fewer spurious charge-transfer (CT) states at the expense of accuracy. Based on the trends observed in this study and our previous experience we formulate several practical approaches to overcome these difficulties providing a reliable description of electronic excitations in nanosystems.

Fluorescence polarization measures energy funneling in single light-harvesting antennas--LH2 vs conjugated polymers

Numerous approaches have been proposed to mimic natural photosynthesis using artificial antenna systems, such as conjugated polymers (CPs), dendrimers, and J-aggregates. As a result, there is a need to characterize and compare the excitation energy transfer (EET) properties of various natural and artificial antennas. Here we experimentally show that EET in single antennas can be characterized by 2D polarization imaging using the single funnel approximation. This methodology addresses the ability of an individual antenna to transfer its absorbed energy towards a single pool of emissive states, using a single parameter called energy funneling efficiency (ε). We studied individual peripheral antennas of purple bacteria (LH2) and single CP chains of 20 nm length. As expected from a perfect antenna, LH2s showed funneling efficiencies close to unity. In contrast, CPs showed lower average funneling efficiencies, greatly varying from molecule to molecule. Cyclodextrin insulation of the conjugated backbone improves EET, increasing the fraction of CPs possessing ε = 1. Comparison between LH2s and CPs shows the importance of the protection systems and the protein scaffold of LH2, which keep the chromophores in functional form and at such geometrical arrangement that ensures excellent EET.

Effects of Different Quantum Coherence on the Pump-Probe Polarization Anisotropy of Photosynthetic Light-Harvesting Complexes: A Computational Study

Observations of oscillatory features in the 2D spectra of several photosynthetic complexes have led to diverged opinions on their origins, including electronic coherence, vibrational coherence, and vibronic coherence. In this work, effects of these different types of quantum coherence on ultrafast pump-probe polarization anisotropy are investigated and distinguished. We first simulate the isotropic pump-probe signal and anisotropy decay of the Fenna-Matthews-Olson (FMO) complex using a model with only electronic coherence at low temperature and obtain the same coherence time as in the previous experiment. Then, three model dimer systems with different prespecified quantum coherence are simulated, and the results show that their different spectral characteristics can be used to determine the type of coherence during the spectral process. Finally, we simulate model systems with different electronic-vibrational couplings and reveal the condition in which long time vibronic coherence can be observed in systems like the FMO complex.

Probing energy transfer events in the light harvesting complex 2 (LH2) of Rhodobacter sphaeroides with two-dimensional spectroscopy

Excitation energy transfer events in the photosynthetic light harvesting complex 2 (LH2) of Rhodobacter sphaeroides are investigated with polarization controlled two-dimensional electronic spectroscopy. A spectrally broadened pulse allows simultaneous measurement of the energy transfer within and between the two absorption bands at 800 nm and 850 nm. The phased all-parallel polarization two-dimensional spectra resolve the initial events of energy transfer by separating the intra-band and inter-band relaxation processes across the two-dimensional map. The internal dynamics of the 800 nm region of the spectra are resolved as a cross peak that grows in on an ultrafast time scale, reflecting energy transfer between higher lying excitations of the B850 chromophores into the B800 states. We utilize a polarization sequence designed to highlight the initial excited state dynamics which uncovers an ultrafast transfer component between the two bands that was not observed in the all-parallel polarization data. We attribute the ultrafast transfer component to energy transfer from higher energy exciton states to lower energy states of the strongly coupled B850 chromophores. Connecting the spectroscopic signature to the molecular structure, we reveal multiple relaxation pathways including a cyclic transfer of energy between the two rings of the complex.

Quantum coherent energy transfer over varying pathways in single light-harvesting complexes

The initial steps of photosynthesis comprise the absorption of sunlight by pigment-protein antenna complexes followed by rapid and highly efficient funneling of excitation energy to a reaction center. In these transport processes, signatures of unexpectedly long-lived coherences have emerged in two-dimensional ensemble spectra of various light-harvesting complexes. Here, we demonstrate ultrafast quantum coherent energy transfer within individual antenna complexes of a purple bacterium under physiological conditions. We find that quantum coherences between electronically coupled energy eigenstates persist at least 400 femtoseconds and that distinct energy-transfer pathways that change with time can be identified in each complex. Our data suggest that long-lived quantum coherence renders energy transfer in photosynthetic systems robust in the presence of disorder, which is a prerequisite for efficient light harvesting.

Ultrafast long-distance excitation energy transport in donor-bridge-acceptor systems

The excited-state dynamics of two energy donor-bridge-acceptor (D-B-A) systems consisting of a zinc tetraphenylporphyrin (ZnP) and a free base tetraphenylporphyrin (FbP) bridged by oligo-p-phenyleneethynylene units with different substituents has been investigated using ultrafast spectroscopy. These systems differ by the location of the lowest singlet excited state of the bridge, just above or below the S(2) porphyrin states. In the first case, Soret band excitation of the porphyrins is followed by internal conversion to the local S(1) state of both molecules and by a S(1) energy transfer from the ZnP to the FbP end on the 10 ns time scale, as expected for a center-to-center distance of about 4.7 nm. On the other hand, if the bridge is excited, the energy is efficiently transferred within 1 ps to both porphyrin ends. Selective bridge excitation is not possible with the second system, because of the overlap of the absorption bands. However, the time-resolved spectroscopic data suggest a reversible conversion between the D*(S(2))-B-A and D-B*(S(1))-A states as well as a transition from the D-B*(S(1))-A to the D-B-A* states on the picosecond time scale. This implies that the local S(2) energy of the ZnP end can be transported stepwise to the FbP end, i.e., over about 4.7 nm, within 1 ps with an efficiency of more than 0.2.