Study Of Excitation Energy Transfer Research Articles

Energy transfer from phycobilisomes to photosystem I at 77 K

Phycobilisomes serve as a light-harvesting antenna of both photosystem I (PSI) and II (PSII) in cyanobacteria, yet direct energy transfer from phycobilisomes to PSI is not well documented. Here we recorded picosecond time-resolved fluorescence at wavelengths of 605–760 nm in isolated photosystem I (PSI), phycobilisomes and intact cells of a PSII-deficient mutant of Synechocystis sp. PCC 6803 at 77 K to study excitation energy transfer and trapping. By means of a simultaneous target analysis of the kinetics of isolated complexes and whole cells, the pathways and dynamics of energy transfer in vitro and in vivo were established. We establish that the timescale of the slowest equilibration between different terminal emitters in the phycobilisome is ≈800 ps. It was estimated that the terminal emitter in about 40% of the phycobilisomes transfers its energy with a rate constant of 42 ns−1 to PSI. This energy transfer rate is higher than the rates of equilibration within the phycobilisome – between the rods and the core or between the core cylinders – and is evidence for the existence of specific phycobilisome-PSI interactions. The rest of the phycobilisomes remain unconnected or slowly transferring energy to PSI.

Efficient propagation of the hierarchical equations of motion using the Tucker and hierarchical Tucker tensors.

We develop new methods to efficiently propagate the hierarchical equations of motion (HEOM) by using the Tucker and hierarchical Tucker (HT) tensors to represent the reduced density operator and auxiliary density operators. We first show that by employing the split operator method, the specific structure of the HEOM allows a simple propagation scheme using the Tucker tensor. When the number of effective modes in the HEOM increases and the Tucker representation becomes intractable, the split operator method is extended to the binary tree structure of the HT representation. It is found that to update the binary tree nodes related to a specific effective mode, we only need to propagate a short matrix product state constructed from these nodes. Numerical results show that by further employing the mode combination technique commonly used in the multi-configuration time-dependent Hartree approaches, the binary tree representation can be applied to study excitation energy transfer dynamics in a fairly large system including over 104 effective modes. The new methods may thus provide a promising tool in simulating quantum dynamics in condensed phases.

Theoretical study of excitation energy transfer and nonlinear spectroscopy of photosynthetic light‐harvesting complexes using the nonperturbative reduced dynamics method

AbstractThe highly efficient excitation energy transfer (EET) processes in photosynthetic light‐harvesting complexes have attracted much recent research interests. Experimentally, spectroscopic studies have provided important information on the energetics and EET dynamics. Theoretically, due to the large number of degrees of freedom and the complex interaction between the pigments and the protein environment, it is impossible to simulate the whole system quantum mechanically. Effective Hamiltonian models are often used, in which the most important degrees of freedom are treated explicitly and all the other degrees of freedom are treated as a thermal bath. However, even with such simplifications, solving the real‐time quantum dynamics could still be a difficult task. A particular challenging case in simulating the EET dynamics and related spectroscopic phenomena lies in the so‐called intermediate coupling regime, where the intermolecular electronic couplings and the electronic–vibrational couplings are of similar strength. In this article, we review theoretical studies of linear and nonlinear spectroscopic signals of photosynthetic light‐harvesting complexes, using the nonperturbative hierarchical equations of motion (HEOM) approach. Simulations were performed for the EET dynamics, various types of linear spectra, two‐dimensional electronic spectra, and pump–probe spectra. Benchmark tests of several approximate methods related to the HEOM approach were also discussed. The results show that the nonperturbative HEOM approach is an effective method in simulating the EET dynamics and spectroscopic signals of photosynthetic light‐harvesting complexes. Important insights into EET pathways, quantum effects including quantum delocalization, and quantum coherence in photosynthetic light‐harvesting complexes were also obtained through such simulations.This article is categorized under: Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics Theoretical and Physical Chemistry > Spectroscopy Software > Simulation Methods

Time-resolved fluorescence study of excitation energy transfer in the cyanobacterium Anabaena PCC 7120

Excitation energy transfer (EET) and trapping in Anabaena variabilis (PCC 7120) intact cells, isolated phycobilisomes (PBS) and photosystem I (PSI) complexes have been studied by picosecond time-resolved fluorescence spectroscopy at room temperature. Global analysis of the time-resolved fluorescence kinetics revealed two lifetimes of spectral equilibration in the isolated PBS, 30–35 ps and 110–130 ps, assigned primarily to energy transfer within the rods and between the rods and the allophycocyanin core, respectively. An additional intrinsic kinetic component with a lifetime of 500–700 ps was found, representing non-radiative decay or energy transfer in the core. Isolated tetrameric PSI complexes exhibited biexponential fluorescence decay kinetics with lifetimes of about 10 ps and 40 ps, representing equilibration between the bulk antenna chlorophylls with low-energy “red” states and trapping of the equilibrated excitations, respectively. The cascade of EET in the PBS and in PSI could be resolved in intact filaments as well. Virtually all energy absorbed by the PBS was transferred to the photosystems on a timescale of 180–190 ps.

Comparison of methods to study excitation energy transfer in molecular multichromophoric systems

We compare theoretical methods for calculating excitation energy transfer rates in multichromophoric systems. The employed methods are the multichromophoric Förster resonance energy transfer (MC-FRET), the numerical integration of the Schrödinger equation (NISE), and the Haken-Strobl-Reineker (HSR) model. As a reference, we use the numerically exact Hierarchy of Equations of Motion (HEOM). We examine these methods in various system and bath parameter regimes including the regime relevant to biological light-harvesting systems. We apply them to a model system of a monomeric donor coupled to a multichromophoric acceptor ring of varying size in two limiting configurations, namely symmetric and asymmetric. We find that the symmetric case is more sensitive to the approximations of the methods studied. The NISE method gives the most reasonable results throughout the parameter regimes tested, while still being computationally tractable.

Effect of Underdamped Vibration on Excitation Energy Transfer: Direct Comparison between Two Different Partitioning Schemes

We study excitation energy transfer (EET) in a model three-site system with a mixed-quantum classical dynamics method, by focusing on the effect of an underdamped vibration. We construct two types of models where the underdamped vibration mode is included either in the quantum subsystem or in the classical bath. We show that the two models yield practically equivalent results despite the different depictions of the vibration. In particular, both models consistently demonstrate accelerations of population relaxation induced by quasi-resonant vibration. This indicates that intricate features of EET dynamics that have been frequently ascribed to the quantal nature of vibrations, such as vibronic mixing, can be successfully reproduced by using physically equivalent but classically described bath modes. The mechanism behind the observed quantum-classical correspondence is proposed. We also systematically examine how the structure of the spectating continuum phonon modes affects the vibronic resonance and observe that phonon modes with different time scales influence the resonance in different manners.

The phycobilisome terminal emitter transfers its energy with a rate of (20 ps)\u20131 to photosystem II

Ultrafast time resolved emission spectra were measured in whole cells of a PSI-deficient mutant of Synechocystis sp. PCC 6803 at room temperature and at 77K to study excitation energy transfer and trapping. By means of a target analysis it was estimated that the terminal emitter of the phycobilisome, termed allophycocyanin 680, transfers its energy with a rate of (20 ps)–1 to PSII. This is faster than the intraphycobilisome energy transfer rates between a rod and a core cylinder, or between the core cylinders.

Excitation energy transfer in phycobiliproteins of the cyanobacterium Acaryochloris marina investigated by spectral hole burning.

The cyanobacterium Acaryochloris marina developed two types of antenna complexes, which contain chlorophyll-d (Chl d) and phycocyanobilin (PCB) as light-harvesting pigment molecules, respectively. The latter membrane-extrinsic complexes are denoted as phycobiliproteins (PBPs). Spectral hole burning was employed to study excitation energy transfer and electron-phonon coupling in PBPs. The data reveal a rich spectral substructure with a total of four low-energy electronic states whose absorption bands peak at 633, 644, 654, and at about 673nm. The electronic states at ~633 and 644nm can be tentatively attributed to phycocyanin (PC) and allophycocyanin (APC), respectively. The remaining low-energy electronic states including the terminal emitter at 673nm may be associated with different isoforms of PC, APC, or the linker protein. Furthermore, the hole burning data reveal a large number of excited state vibrational frequencies, which are characteristic for the chromophore PCB. In summary, the results are in good agreement with the low-energy level structure of PBPs and electron-phonon coupling parameters reported by Gryliuk et al. (BBA 1837:1490-1499, 2014) based on difference fluorescence line-narrowing experiments.

Hybrid QM/MM study of FMO complex with polarized protein-specific charge.

The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point calculations have been employed to predict the energy transfer pathways utilizing the polarized protein-specific charge (PPC), which provides a more realistic description of Coulomb interaction potential in the protein than conventional mean-field charge scheme. The recently discovered eighth pigment has also been included in this study. Comparing with the conventional mean-field charges, more stable structures of FMO complex were found under PPC scheme during molecular dynamic simulation. Based on the electronic structure calculations, an exciton model was constructed to consider the couplings during excitation. The results show that pigments 3 and 4 dominate the lowest exciton levels whereas the highest exciton level are mainly constituted of pigments 1 and 6. This observation agrees well with the assumption based on the spatial distribution of the pigments. Moreover, the obtained spectral density in this study gives a reliable description of the diverse local environment embedding each pigment.

Novel 1- and 9-aminoanthracene/3-aminobenzanthrone bichromophores exhibiting through-bond excitation energy transfer

New 1/9- aminoanthracene-triazine-3-aminobenzanthrone bichromophores for the study of excitation energy transfer were synthesized and characterised. Absorption and emission spectra and fluorescence quantum yields were measured. Equilibrium ground state conformations and singlet electronic excited states characteristics were calculated at semiempirical level. A decrease of qF in polar solvents may be explained by the CT state connected with electron transfer from the HOMO localized on the donor to the LUMO spread over the acceptor. A highly efficient energy transfer mediated by through-bond mechanism was observed for all compounds.

Variations in the first steps of photosynthesis for the diatom Cyclotella meneghiniana grown under different light conditions

In this work we have applied picosecond and steady-state fluorescence measurements to study excitation energy transfer and trapping in intact Cyclotella meneghiniana diatom cells grown at different light intensities. Different excitation and detection wavelengths were used to discriminate between Photosystem I and II (PSI and PSII) kinetics and to study excitation energy transfer from the outer antenna to the core of PSI and PSII. It is found that the light-harvesting fucoxanthin chlorophyll proteins (FCPs) transfer their excitation energy predominantly to PSII. It is also observed that the PSII antenna is slightly richer in red-absorbing fucoxanthin than the FCPs associated with PSI. The average excitation trapping time in PSI is around 75ps whereas this time is around 450ps for PSII in cells grown in 20μmol of photons per m2 per s. The latter time decreases to 425ps for 50μmol of photons and 360ps for 140μmol of photons. It is concluded that cells grown under higher photon flux densities have a smaller antenna size than the ones grown in low light. At the same time, the increase of growth light intensity leads to a decrease of the relative amount of PSI. This effect is accompanied by a substantial increase in the amount of chlorophyll a that is not active in excitation energy transfer and most probably attached to inactivated/disassembled PSII units.

Optimal number of pigments in photosynthetic complexes

We study excitation energy transfer in a simple model of a photosynthetic complex. The model, described by the Lindblad equation, consists of pigments interacting via dipole–dipole interaction. The overlapping of pigments induces an on-site energy disorder, providing a mechanism for blocking the excitation transfer. Based on the average efficiency as well as the robustness of random configurations of pigments, we calculate the optimal number of pigments that should be enclosed in a pigment–protein complex of a given size. The results suggest that a large fraction of pigment configurations are efficient as well as robust if the number of pigments is properly chosen. We compare the optimal results of the model to the structure of pigment–protein complexes as found in nature, finding good agreement.

Quantum Rabi Model forN-State Atoms

A tractable N-state Rabi Hamiltonian is introduced by extending the parity symmetry of the two-state model. The single-mode case provides a few-parameter description of a novel class of periodic systems, predicting that the ground state of certain four-state atom-cavity systems will undergo parity change at strong-coupling. A group-theoretical treatment provides physical insight into dynamics and a modified rotating wave approximation obtains accurate analytical energies. The dissipative case can be applied to study excitation energy transfer in molecular rings or chains.

Low-Temperature Frequency Domain Study of Excitation Energy Transfer in Ethynyl-Linked Chlorophyll Trefoils and Aggregates

Using hole-burning spectroscopy, we show that excitation energy transfer (EET) time in ethynyl-linked chlorophyll trefoil (ChlT1) monomer is very fast (∼2.5 ps) at liquid helium temperature. This is consistent with data obtained by femtosecond transient spectroscopy experiments performed at room temperature, in which an EET time of 1.8 ps was observed (Kelley, R. F. et al. Angew. Chem. Int. Ed. 2006, 45, 7979). This finding further supports the importance of through-bond electronic coupling at low temperature. In addition, we show that ChlT1 (even at very low concentrations) in methyl tetrahydrofuran-ethanol glass (1:200 v/v; T ∼ 5 K) forms different types of aggregates. It is demonstrated that the relative distribution of various types of aggregates (whose possible structures are briefly discussed) depends on the cooling rate and matrix composition. For example, the EET time in two types of ChlT1-based aggregates is slower by a factor of ∼5-7 with respect to that observed for ChlT1 monomer. This indicates that ChlT1 aggregates can retain ultrafast energy transfer properties similar to those observed in natural photosynthetic antennas. It is anticipated that such building blocks could be utilized in future photovoltaic devices.

The Eighth Bacteriochlorophyll Completes the Excitation Energy Funnel in the FMO Protein.

The Fenna-Matthews-Olson (FMO) light-harvesting protein connects the outer antenna system (chlorosome/baseplate) with the reaction center complex in green sulfur bacteria. Since its first structure determination in the mid-70s, this pigment-protein complex has become an important model system to study excitation energy transfer. Recently, an additional bacteriochlorophyll a (the eighth) pigment was discovered in each subunit of this homotrimer. Our structure-based calculations of the optical properties of the FMO protein demonstrate that the eighth pigment is the linker to the baseplate, confirming recent suggestions from crystallographic studies.

Ultrafast Excitation Energy Transfer in Small Semiconducting Carbon Nanotube Aggregates

We study excitation energy transfer in small aggregates of chirality enriched carbon nanotubes by transient absorption spectroscopy. Ground state photobleaching is used to monitor exciton population dynamics with sub-10 fs time resolution. Upon resonant excitation of the first exciton transition in (6,5) tubes, we find evidence for energy transfer to (7,5) tubes within our time resolution (<10 fs). Excitation in the visible spectral range, where the second excitonic transitions occur, is followed by fast intratube relaxation and subsequent energy transfer, in particular from the (8,4) tube toward other tubes, the latter process occurring in less than 10 fs.

Ab Initio Study of Excitation Energy Transfer between Quantum Dots and Dye Molecules

We investigate excitation energy transfer between a semiconductor nanocrystal (NC) and an organic dye molecule, using ab initio calculations. The electronic coupling is evaluated based on the full Coulombic interaction between the NC and dye transition densities. We explore the effect of the NC−dye relative configurations on the electronic coupling, using a (CdSe)6 cluster and a rhodamine cation as a simplified model system. Our analysis demonstrates the limitations of the commonly used Förster theory for the NC−dye system and highlights the importance of considering the full Coulombic interactions of donor and acceptor. We find that energy transfer involves several electronic states and can occur even from optically dark states of the NC. The consequences for larger NC−dye systems are discussed.

Theoretical study of excitation energy transfer in DNA photolyase.

Photolyase (PL) is a DNA repair enzyme which splits UV light-induced thymine dimers on DNA by an electron transfer reaction occurring between the photoactivated FADH(-) cofactor and the DNA dimer in the DNA/PL complex. The crystal structure of the DNA/photolyase complex from Anacystis nidulans has been solved. Here, using the experimental crystal structure, we re-examine the details of the repair electron transfer reaction and address the question of energy transfer from the antenna HDF to the redox active FADH(-) cofactor. The photoactivation of FADH(-) immediately preceding the electron transfer is a key step in the repair mechanism that is largely left unexamined theoretically. An important butterfly thermal motion of flavin is identified in ab initio calculations; we propose its role in the back electron transfer from DNA to photolyase. Molecular dynamics simulation of the whole protein/DNA complex is carried out to obtain relevant cofactor conformations for ZINDO/S spectroscopic absorption and fluorescence calculations. We find that significant thermal broadening of the spectral lines, due to protein dynamics, as well as the alignment of the donor HDF and the acceptor FADH(-) transition dipole moments both contribute to the efficiency of energy transfer. The geometric factor of Förster's dipolar coupling is calculated to be 1.82, a large increase from the experimentally estimated 0.67. Using Förster's mechanism, we find that the energy transfer occurs with remarkable efficiency, comparable with the experimentally determined value of 98%.

Near edge X-ray absorption fine structure spectroscopy (NEXAFS) of pigment–protein complexes: Peridinin–chlorophyll a protein (PCP) of Amphidinium carterae

Peridinin–chlorophyll a protein (PCP) is a unique water soluble antenna complex that employs the carotenoid peridinin as the main light-harvesting pigment. In the present study the near edge X-ray absorption fine structure (NEXAFS) spectrum of PCP was recorded at the carbon K-edge. Additionally, the NEXAFS spectra of the constituent pigments, chlorophyll a and peridinin, were measured. The energies of the lowest unoccupied molecular levels of these pigments appearing in the carbon NEXAFS spectrum were resolved. Individual contributions of the pigments and the protein to the measured NEXAFS spectrum of PCP were determined using a “building block” approach combining NEXAFS spectra of the pigments and the amino acids constituting the PCP apoprotein. The results suggest that absorption changes of the pigments in the carbon near K-edge region can be resolved following excitation using a suitable visible pump laser pulse. Consequently, it may be possible to study excitation energy transfer processes involving “optically dark” states of carotenoids in pigment–protein complexes by soft X-ray probe optical pump double resonance spectroscopy (XODR).

Fast Collapse but Slow Formation of Secondary Structure Elements in the Refolding Transition of E. coli Adenylate Kinase

The various models proposed for protein folding transition differ in their order of appearance of the basic steps during this process. In this study, steady state and time-resolved dynamic non-radiative excitation energy transfer (FRET and trFRET) combined with site specific labeling experiments were applied in order to characterize the initial transient ensemble of Escherichia coli adenylate kinase (AK) molecules upon shifting conditions from those favoring denaturation to refolding and from folding to denaturing. Three sets of labeled AK mutants were prepared, which were designed to probe the equilibrium and transient distributions of intramolecular segmental end-to-end distances. A 176 residue section (residues 28-203), which spans most of the 214 residue molecule, and two short secondary structure chain segments including an alpha-helix (residues 169-188) and a predominantly beta-strand region (residues 188-203), were labeled. Upon fast change of conditions from denaturing to folding, the end-to-end distance of the 176 residue chain section showed an immediate collapse to a mean value of 26 A. Under the same conditions, the two short secondary structure elements did not respond to this shift within the first ten milliseconds, and retained the characteristics of a fully unfolded state. Within the first 10 ms after changes of the solvent from folding to denaturing, only minor changes were observed at the local environments of residues 203 and 169. The response of these same local environments to the shift of conditions from denaturing to folding occurred within the dead time of the mixing device. Thus, the response of the CORE domain of AK to fast transfer from folding to unfolding conditions is slow at all three conformational levels that were probed, and for at least a few milliseconds the ensemble of folded molecules is maintained under unfolding conditions. A different order of the changes was observed upon initiation of refolding. The AK molecules undergo fast collapse to an ensemble of compact structures where the local environment of surface probes seems to be native-like but the two labeled secondary structure elements remain unfolded.