Exciton dynamics in FMO bacteriochlorophyll protein at low temperatures

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.

Probing exciton dynamics with spectral selectivity through the use of quantum entangled photons

Quantum light is increasingly recognized as a promising resource for developing optical measurement techniques. Particular attention has been paid to enhancing the precision of the measurements beyond classical techniques by using nonclassical correlations between quantum entangled photons. Recent advances in the quantum optics technology have made it possible to manipulate spectral and temporal properties of entangled photons, and photon correlations can facilitate the extraction of matter information with relatively simple optical systems compared to conventional schemes. In these respects, the applications of entangled photons to time-resolved spectroscopy can open new avenues for unambiguously extracting information on dynamical processes in complex molecular and materials systems. Here, we propose time-resolved spectroscopy in which specific signal contributions are selectively enhanced by harnessing nonclassical correlations of entangled photons. The entanglement time characterizes the mutual delay between an entangled twin and determines the spectral distribution of photon correlations. The entanglement time plays a dual role as the knob for controlling the accessible time region of dynamical processes and the degrees of spectral selectivity. In this sense, the role of the entanglement time is substantially equivalent to the temporal width of the classical laser pulse. The results demonstrate that the application of quantum entangled photons to time-resolved spectroscopy leads to monitoring dynamical processes in complex molecular and materials systems by selectively extracting desired signal contributions from congested spectra. We anticipate that more elaborately engineered photon states would broaden the availability of quantum light spectroscopy.

Open hardware microsecond dispersive transient absorption spectrometer for linear optical response

Abstract

An open hardware design and implementation for a transient absorption spectrometer are presented that has microsecond time resolution and measures full difference spectra in the visible spectral region from 380 to 750 nm. The instrument has been designed to allow transient absorption spectroscopy measurements of either low or high quantum yield processes by combining intense sub-microsecond excitation flashes using a xenon lamp together with stroboscopic non-actinic white light probing using LED sources driven under high pulsed current from a capacitor bank. The instrument is sensitive to resolve 0.15 mOD flash-induced differences within 1000 measurements at 20 Hz repetition rate using an inexpensive CCD sensor with 200 μm pixel dimension, 40 K electrons full well capacity and a dynamic range of 1800. The excitation flash has 230 ns pulse duration and the 2 mJ flash energy allows spectral filtering while retaining high power density with focussing to generate mOD signals in the 10^–4–10^–1 ΔOD range. We present the full electronics design and construction of the flash and probe sources, the optics as well as the timing electronics and CCD spectrometer operation and modification for internal signal referencing. The performance characterisation and example measurements are demonstrated using microsecond TAS of Congo red dye, as an example of a low quantum yield photoreaction at 2% with up to 78% of molecules excited. The instrument is fully open hardware and combines inexpensive selection of commercial components, optics and electronics and allows linear response measurements of photoinduced reactions for the purpose of accurate global analysis of chemical dynamics.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s43630-021-00127-6.

Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

The intermolecular contribution to the spectral density of the exciton-vibrational coupling of the homotrimeric Fenna-Matthews-Olson (FMO) light-harvesting protein of green sulfur bacteria P. aestuarii is analyzed by combining a normal mode analysis of the protein with the charge density coupling method for the calculation of local transition energies of the pigments. Correlations in site energy fluctuations across the whole FMO trimer are found at low vibrational frequencies. Including, additionally, the high-frequency intrapigment part of the spectral density, extracted from line-narrowing spectra, we study intra- and intermonomer exciton transfer. Whereas the intrapigment part of the spectral density is important for fast intramonomer exciton relaxation, the intermolecular contributions (due to pigment-environment coupling) determine the intermonomer exciton transfer. Neither the variations of the local Huang-Rhys factors nor the correlations in site energy fluctuations have a critical influence on energy transfer. At room temperature, the intermonomer transfer in the FMO protein occurs on a 10 ps time scale, whereas intramonomer exciton equilibration is roughly two orders of magnitude faster. At cryogenic temperatures, intermonomer transfer limits the lifetimes of the lowest exciton band. The lifetimes are found to increase between 20 ps in the center of this band up to 100 ps toward lower energies, which is in very good agreement with the estimates from hole burning data. Interestingly, exciton delocalization in the FMO monomers is found to slow down intermonomer energy transfer, at both physiological and cryogenic temperatures.

On uncorrelated inter-monomer Förster energy transfer in Fenna-Matthews-Olson complexes

The Fenna-Matthews-Olson (FMO) light-harvesting antenna protein of green sulfur bacteria is a long-studied pigment-protein complex which funnels energy from the chlorosome to the reaction centre where photochemistry takes place. The structure of the FMO protein from Chlorobaculum tepidum is known as a homotrimeric complex containing eight bacteriochlorophyll a per monomer. Owing to this structure FMO has strong intra-monomer and weak inter-monomer electronic coupling constants. While long-lived (sub-picosecond) coherences within a monomer have been a prevalent topic of study over the past decade, various experimental evidence supports the presence of subsequent inter-monomer energy transfer on a picosecond time scale. The latter has been neglected by most authors in recent years by considering only sub-picosecond time scales or assuming that the inter-monomer coupling between low-energy states is too weak to warrant consideration of the entire trimer. However, Förster theory predicts that energy transfer of the order of picoseconds is possible even for very weak (less than 5 cm^-1) electronic coupling between chromophores. This work reviews experimental data (with a focus on emission and hole-burned spectra) and simulations of exciton dynamics which demonstrate inter-monomer energy transfer. It is shown that the lowest energy 825 nm absorbance band cannot be properly described by a single excitonic state. The energy transfer through FMO is modelled by generalized Förster theory using a non-Markovian, reduced density matrix approach to describe the electronic structure. The disorder-averaged inter-monomer transfer time across the 825 nm band is about 27 ps. While only isolated FMO proteins are presented, the presence of inter-monomer energy transfer in the context of the overall photosystem is also briefly discussed.

Impact of Single-Point Mutations on the Excitonic Structure and Dynamics in a Fenna-Matthews-Olson Complex

Hole burning (HB) spectroscopy and modeling studies reveal significant changes in the excitonic structure and dynamics in several mutants of the FMO trimer from the Chlorobaculum tepidum. The excited-state decay times ( T₁) of the high-energy excitons are significantly modified when mutation occurs near bacteriochlorophyll (BChl) 1 (V152N mutant) or BChl 6 (W184F). Longer (averaged) T₁ times of highest-energy excitons in V152N and W184F mutants suggest that site energies of BChls 1 and 6, believed to play an important role in receiving excitation from the baseplate BChls, likely play a critical role to ensure the femtosecond (fs) energy relaxation observed in wild-type FMO. HB spectroscopy reveals preferentially slower T₁ times (about 1 ps on average) because fs times prohibit HB due to an extremely low HB quantum yield. Uncorrelated (incoherent) excitation energy transfer times between monomers, the composition of exciton states, and average, frequency-dependent, excited-state decay times ( T₁) are discussed.

Ultrafast Spectroscopic Investigation of Energy Transfer in Site-Directed Mutants of the Fenna-Matthews-Olson (FMO) Antenna Complex from Chlorobaculum tepidum

Ultrafast transient absorption (TA) and time-resolved fluorescence (TRF) spectroscopic studies were performed on several mutants of the bacteriochlorophyll (BChl) a-containing Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum. These mutants were generated to perturb a particular BChl a site and determine its effects on the optical spectroscopic properties of the pigment-protein complex. Measurements conducted at 77 K under both oxidizing and reducing conditions revealed changes in the dynamics of the various spectral components as compared to the data set from wild-type FMO. TRF results show that under reducing conditions all FMO samples decay with a similar lifetime in the ∼2 ns range. The oxidized samples revealed varying fluorescence lifetimes of the terminal BChl a emitter, considerably shorter than those recorded for the reduced samples, indicating that the quenching mechanism in wild-type FMO is still present in the mutants. Global fitting of TA data yielded similar overall results, and in addition, the lifetimes of early decaying components were determined. Target analyses of TA data for select FMO samples generated kinetic models that better simulate the TA data. A comparison of the lifetime of excitonic components for all samples reveals that the mutations affect mainly the early kinetic components, but not that of the lowest energy exciton, which reflects the flexibility of energy transfer in FMO.

Dynamics of Energy and Electron Transfer in the FMO-Reaction Center Core Complex from the Phototrophic Green Sulfur Bacterium Chlorobaculum tepidum

The reaction center core (RCC) complex and the RCC with associated Fenna-Matthews-Olson protein (FMO-RCC) complex from the green sulfur bacterium Chlorobaculum tepidum were studied comparatively by steady-state and time-resolved fluorescence (TRF) and femtosecond time-resolved transient absorption (TA) spectroscopies. The energy transfer efficiency from the FMO to the RCC complex was calculated to be ∼40% based on the steady-state fluorescence. TRF showed that most of the FMO complexes (66%), regardless of the fact that they were physically attached to the RCC, were not able to transfer excitation energy to the reaction center. The TA spectra of the RCC complex showed a 30-38 ps lifetime component regardless of the excitation wavelengths, which is attributed to charge separation. Excitonic equilibration was shown in TA spectra of the RCC complex when excited into the BChl a Qx band at 590 nm and the Chl a Qy band at 670 nm, while excitation at 840 nm directly populated the low-energy excited state and equilibration within the excitonic BChl a manifold was not observed. The TA spectra for the FMO-RCC complex excited into the BChl a Qx band could be interpreted by a combination of the excited FMO protein and RCC complex. The FMO-RCC complex showed an additional fast kinetic component compared with the FMO protein and the RCC complex, which may be due to FMO-to-RCC energy transfer.

Visualization of Hot Exciton Energy Relaxation from Coherent to Diffusive Regimes in Conjugated Polymers: A Theoretical Analysis

The unified coherent-to-diffusive energy relaxation of hot exciton in organic aggregates or polymers, which still remains largely unclear and is also a great challenge theoretically, is investigated from a time-dependent wavepacket diffusive approach. The results demonstrate that in the multiple time scale energy relaxation dynamics, the fast relaxation time essentially corresponds to the dephasing time of excitonic coherence motion, whereas the slow time is related to a hopping migration, and a suggested kinetic model successfully connects these two processes. The dependencies of those times on the initial energy and delocalization of exciton wavepacket as well as exciton-phonon interactions are further analyzed. The proposed method together with quantum chemistry calculations has explained an experimental observation of hot exciton energy relaxation in the low-bandgap copolymer PBDTTPD.

On the Controversial Nature of the 825 nm Exciton Band in the FMO Protein Complex

The nature of the low-energy 825 nm band of the Fenna-Matthews-Olson (FMO) protein complex from Chlorobaculum tepidum at 5 K is discussed. It is shown, using hole-burning (HB) spectroscopy and excitonic calculations, that the 825 nm absorption band of the FMO trimer cannot be explained by a single electronic transition or overlap of electronic transitions of noninteracting pigments. To explain the shape of emission and nonresonant HB spectra, downward uncorrelated excitation energy transfer (EET) between trimer subunits should be taken into account. Modeling studies reveal the presence of three sub-bands within the 825 nm band, in agreement with nonresonant HB and emission spectra. We argue that after light induced coherences vanish, uncorrelated EET between the lowest exciton levels of each monomer takes place. HB induced spectral shifts provide a new insight on the energy landscape of the FMO protein.

Freestanding sample holder for ultrafast optical spectroscopy at low temperatures

Ultrafast optical spectroscopy techniques are often employed to gain information about samples that are liquid at room temperature and frozen at cryogenic temperatures. However, the measurements suffer from the presence of unwanted, non-resonant signals originating in the sample cell walls. Most of these artifacts can be avoided in the measurements performed at room temperature by using liquid jet systems, i.e., by removing the sample cell. However, these systems cannot be used in low temperature measurements, when the sample is frozen. Herein we describe a freestanding sample holder that allows low temperature ultrafast spectroscopy measurements free of artifacts caused by the sample cell.

Understanding photosynthetic light-harvesting: a bottom up theoretical approach

We discuss a bottom up approach for modeling photosynthetic light-harvesting. Methods are reviewed for a full structure-based parameterization of the Hamiltonian of pigment-protein complexes (PPCs). These parameters comprise (i) the local transition energies of the pigments in their binding sites in the protein, the site energies; (ii) the couplings between optical transitions of the pigments, the excitonic couplings; and (iii) the spectral density characterizing the dynamic modulation of pigment transition energies and excitonic couplings by protein vibrations. Starting with quantum mechanics perturbation theory, we provide a microscopic foundation for the standard PPC Hamiltonian and relate the expressions obtained for its matrix elements to quantities that can be calculated with classical molecular mechanics/electrostatics approaches including the whole PPC in atomic detail and using charge and transition densities obtained with quantum chemical calculations on the isolated building blocks of the PPC. In the second part of this perspective, the Hamiltonian is utilized to describe the quantum dynamics of excitons. Situations are discussed that differ in the relative strength of excitonic and exciton-vibrational coupling. The predictive power of the approaches is demonstrated in application to different PPCs, and challenges for future work are outlined.

Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons

We report a method for the structure-based calculation of the spectral density of the pigment-protein coupling in light-harvesting complexes that combines normal-mode analysis with the charge density coupling (CDC) and transition charge from electrostatic potential (TrEsp) methods for the computation of site energies and excitonic couplings, respectively. The method is applied to the Fenna-Matthews-Olson (FMO) protein in order to investigate the influence of the different parts of the spectral density as well as correlations among these contributions on the energy transfer dynamics and on the temperature-dependent decay of coherences. The fluctuations and correlations in excitonic couplings as well as the correlations between coupling and site energy fluctuations are found to be 1 order of magnitude smaller in amplitude than the site energy fluctuations. Despite considerable amplitudes of that part of the spectral density which contains correlations in site energy fluctuations, the effect of these correlations on the exciton population dynamics and dephasing of coherences is negligible. The inhomogeneous charge distribution of the protein, which causes variations in local pigment-protein coupling constants of the normal modes, is responsible for this effect. It is seen thereby that the same building principle that is used by nature to create an excitation energy funnel in the FMO protein also allows for efficient dissipation of the excitons' excess energy.

Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex

A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear, and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents, to our knowledge, one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.

A comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded LH2 light-harvesting complexes

Integral membrane proteins constitute more than third of the total number of proteins present in organisms. Solubilization with mild detergents is a common technique to study the structure, dynamics, and catalytic activity of these proteins in purified form. However beneficial the use of detergents may be for protein extraction, the membrane proteins are often denatured by detergent solubilization as a result of native lipid membrane interactions having been modified. Versatile investigations of the properties of membrane-embedded and detergent-isolated proteins are, therefore, required to evaluate the consequences of the solubilization procedure. Herein, the spectroscopic and kinetic fingerprints have been established that distinguish excitons in individual detergent-solubilized LH2 light-harvesting pigment-protein complexes from them in the membrane-embedded complexes of purple photosynthetic bacteria Rhodobacter sphaeroides. A wide arsenal of spectroscopic techniques in visible optical range that include conventional broadband absorption-fluorescence, fluorescence anisotropy excitation, spectrally selective hole burning and fluorescence line-narrowing, and transient absorption-fluorescence have been applied over broad temperature range between physiological and liquid He temperatures. Significant changes in energetics and dynamics of the antenna excitons upon self-assembly of the proteins into intracytoplasmic membranes are observed, analyzed, and discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex

The experimental observation of long-lived quantum coherences in the Fenna-Matthews-Olson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search of explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings is analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian, linear and two-dimensional spectra are determined. The thus-obtained linear absorption line shape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.

Characterization of an FMO variant of Chlorobaculum tepidum carrying bacteriochlorophyll a esterified by geranylgeraniol

The Fenna-Matthews-Olson light-harvesting antenna (FMO) protein has been a model system for understanding pigment-protein interactions in the energy transfer process in photosynthesis. All previous studies have utilized wild-type FMO proteins from several species. Here we report the purification and characterization of the first FMO protein variant generated via replacement of the esterifying alcohol at the C-17 propionate residue of bacteriochlorophyll (BChl) a, phytol, with geranylgeraniol, which possesses three more double bonds. The FMO protein still assembles with the modified pigment, but both the whole cell absorption and the biochemical purification indicate that the mutant cells contain a much less mature FMO protein. The gene expression was checked using qRT-PCR, and none of the genes encoding BChl a-binding proteins are strongly regulated at the transcriptional level. The smaller amount of the FMO protein in the mutant cell is probably due to the degradation of the apo-FMO protein at different stages after it does not bind the normal pigment. The absorption, fluorescence, and CD spectra of the purified FMO variant protein are similar to those of the wild-type FMO protein except the conformations of most pigments are more heterogeneous, which broadens the spectral bands. Interestingly, the lowest-energy pigment binding site seems to be unchanged and is the only peak that can be well resolved in 77 K absorption spectra. The excited-state lifetime of the variant FMO protein is unchanged from that of the wild type and shows a temperature-dependent modulation similar to that of the wild type. The variant FMO protein is less thermally stable than the wild type. The assembly of the FMO protein and also the implications of the decreased FMO/chlorosome stoichiometry are discussed in terms of the topology of these two antennas on the cytoplasmic membrane.

Dynamics of light harvesting in photosynthesis

We review recent theoretical and experimental advances in the elucidation of the dynamics of light harvesting in photosynthesis, focusing on recent theoretical developments in structure-based modeling of electronic excitations in photosynthetic complexes and critically examining theoretical models for excitation energy transfer. We then briefly describe two-dimensional electronic spectroscopy and its application to the study of photosynthetic complexes, in particular the Fenna-Matthews-Olson complex from green sulfur bacteria. This review emphasizes recent experimental observations of long-lasting quantum coherence in photosynthetic systems and the implications of quantum coherence in natural photosynthesis.

Calculation of pigment transition energies in the FMO protein: from simplicity to complexity and back

The Fenna-Matthews-Olson (FMO) protein of green sulfur bacteria represents an important model protein for the study of elementary pigment-protein couplings. We have previously used a simple approach [Adolphs and Renger (2006) Biophys J 91:2778-2797] to study the shift in local transition energies (site energies) of the FMO protein of Prosthecochloris aestuarii by charged amino acid residues, assuming a standard protonation pattern of the titratable groups. Recently, we have found strong evidence that besides the charged amino acids also the neutral charge density of the protein is important, by applying a combined quantum chemical/electrostatic approach [Müh et al. (2007) Proc Natl Acad Sci USA, in press]. Here, we extract the essential parts from this sophisticated method to obtain a relatively simple method again. It is shown that the main contribution to the site energy shifts is due to charge density coupling (CDC) between the pigments and their pigment, protein and water surroundings and that polarization effects for qualitative considerations can be approximated by screening the Coulomb coupling by an effective dielectric constant.

How proteins trigger excitation energy transfer in the FMO complex of green sulfur bacteria

A simple electrostatic method for the calculation of optical transition energies of pigments in protein environments is presented and applied to the Fenna-Matthews-Olson (FMO) complex of Prosthecochloris aestuarii and Chlorobium tepidum. The method, for the first time, allows us to reach agreement between experimental optical spectra and calculations based on transition energies of pigments that are calculated in large part independently, rather than fitted to the spectra. In this way it becomes possible to understand the molecular mechanism allowing the protein to trigger excitation energy transfer reactions. The relative shift in excitation energies of the seven bacteriochlorophyll-a pigments of the FMO complex of P. aestuarii and C. tepidum are obtained from calculations of electrochromic shifts due to charged amino acids, assuming a standard protonation pattern of the protein, and by taking into account the three different ligand types of the pigments. The calculations provide an explanation of some of the earlier results for the transition energies obtained from fits of optical spectra. In addition, those earlier fits are verified here by using a more advanced theory of optical spectra, a genetic algorithm, and excitonic couplings obtained from electrostatic calculations that take into account the influence of the dielectric protein environment. The two independent calculations of site energies strongly favor one of the two possible orientations of the FMO trimer relative to the photosynthetic membrane, which were identified by electron microscopic studies and linear dichroism experiments. Efficient transfer of excitation energy to the reaction center requires bacteriochlorophylls 3 and 4 to be the linker pigments. The temporal and spatial transfer of excitation energy through the FMO complex is calculated to proceed along two branches, with transfer times that differ by an order of magnitude.

Excitonic interactions in wild-type and mutant PSI reaction centers

Femtosecond excitation of the red edge of the chlorophyll a Q(Y) transition band in photosystem I (PSI), with light of wavelength > or = 700 nm, leads to wide transient (subpicosecond) absorbance changes: positive DeltaA between 635 and 665 nm, and four negative DeltaA bands at 667, 675, 683, and 695 nm. Here we compare the transient absorbance changes after excitation at 700, 705, and 710 nm at 20 K in several PSI preparations of Chlamydomonas reinhardtii where amino acid ligands of the primary donor, primary acceptor, or connecting chlorophylls have been mutated. Most of these mutations influence the spectrum of the absorbance changes. This supports the view that the chlorophylls of the electron transfer chain as well as the connecting chlorophylls are engaged in the observed absorbance changes. The wide absorption spectrum of the electron transfer chain revealed by the transient measurements may contribute to the high efficiency of energy trapping in photosystem 1. Exciton calculations, based on the recent PSI structure, allow an assignment of the DeltaA bands to particular chlorophylls: the bands at 675 and 695 nm to the dimers of primary acceptor and accessory chlorophyll and the band at 683 nm to the connecting chlorophylls. The subpicosecond transient absorption bands decay may reflect rapid charge separation in the PSI reaction center.