Excitation Energy

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D F Coker - One of the best experts on this subject based on the ideXlab platform.

  • modeling electronic nuclear interactions for Excitation Energy transfer processes in light harvesting complexes
    Journal of Physical Chemistry Letters, 2016
    Co-Authors: D F Coker
    Abstract:

    An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic–nuclear interactions relevant for modeling Excitation Energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to Excitation Energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron–intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based Excitation Energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna–Matthews–Olson pigment–protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provid...

  • iterative linearized density matrix propagation for modeling coherent Excitation Energy transfer in photosynthetic light harvesting
    Journal of Chemical Physics, 2010
    Co-Authors: Pengfei Huo, D F Coker
    Abstract:

    Rather than incoherent hopping between chromophores, experimental evidence suggests that the Excitation Energy transfer in some biological light harvesting systems initially occurs coherently, and involves coherent superposition states in which Excitation spreads over multiple chromophores separated by several nanometers. Treating such delocalized coherent superposition states in the presence of decoherence and dissipation arising from coupling to an environment is a significant challenge for conventional theoretical tools that either use a perturbative approach or make the Markovian approximation. In this paper, we extend the recently developed iterative linearized density matrix (ILDM) propagation scheme [E. R. Dunkel et al., J. Chem. Phys. 129, 114106 (2008)] to study coherent Excitation Energy transfer in a model of the Fenna–Matthews–Olsen light harvesting complex from green sulfur bacteria. This approach is nonperturbative and uses a discrete path integral description employing a short time approxim...

  • iterative linearized density matrix propagation for modeling coherent Excitation Energy transfer in photosynthetic light harvesting
    Journal of Chemical Physics, 2010
    Co-Authors: D F Coker
    Abstract:

    Rather than incoherent hopping between chromophores, experimental evidence suggests that the Excitation Energy transfer in some biological light harvesting systems initially occurs coherently, and involves coherent superposition states in which Excitation spreads over multiple chromophores separated by several nanometers. Treating such delocalized coherent superposition states in the presence of decoherence and dissipation arising from coupling to an environment is a significant challenge for conventional theoretical tools that either use a perturbative approach or make the Markovian approximation. In this paper, we extend the recently developed iterative linearized density matrix (ILDM) propagation scheme [E. R. Dunkel et al., J. Chem. Phys. 129, 114106 (2008)] to study coherent Excitation Energy transfer in a model of the Fenna–Matthews–Olsen light harvesting complex from green sulfur bacteria. This approach is nonperturbative and uses a discrete path integral description employing a short time approximation to the density matrix propagator that accounts for interference between forward and backward paths of the quantum excitonic system while linearizing the phase in the difference between the forward and backward paths of the environmental degrees of freedom resulting in a classical-like treatment of these variables. The approach avoids making the Markovian approximation and we demonstrate that it successfully describes the coherent beating of the site populations on different chromophores and gives good agreement with other methods that have been developed recently for going beyond the usual approximations, thus providing a new reliable theoretical tool to study coherent exciton transfer in light harvesting systems. We conclude with a discussion of decoherence in independent bilinearly coupled harmonic chromophore baths. The ILDM propagation approach in principle can be applied to more general descriptions of the environment.Rather than incoherent hopping between chromophores, experimental evidence suggests that the Excitation Energy transfer in some biological light harvesting systems initially occurs coherently, and involves coherent superposition states in which Excitation spreads over multiple chromophores separated by several nanometers. Treating such delocalized coherent superposition states in the presence of decoherence and dissipation arising from coupling to an environment is a significant challenge for conventional theoretical tools that either use a perturbative approach or make the Markovian approximation. In this paper, we extend the recently developed iterative linearized density matrix (ILDM) propagation scheme [E. R. Dunkel et al., J. Chem. Phys. 129, 114106 (2008)] to study coherent Excitation Energy transfer in a model of the Fenna–Matthews–Olsen light harvesting complex from green sulfur bacteria. This approach is nonperturbative and uses a discrete path integral description employing a short time approxim...

Thomas Renger - One of the best experts on this subject based on the ideXlab platform.

  • The Eighth Bacteriochlorophyll Completes the Excitation Energy Funnel in the FMO Protein
    2015
    Co-Authors: Marcel Schmidt Am Busch, Frank Müh, Mohamed El-amine Madjet, Thomas Renger
    Abstract:

    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

  • α helices direct Excitation Energy flow in the fenna matthews olson protein
    Proceedings of the National Academy of Sciences of the United States of America, 2007
    Co-Authors: Frank Muh, Julia Adolphs, Mohamed Madjet, Ayjamal Abdurahman, Bjorn Rabenstein, Hiroshi Ishikita, Ernstwalter Knapp, Thomas Renger
    Abstract:

    In photosynthesis, light is captured by antenna proteins. These proteins transfer the Excitation Energy with almost 100% quantum efficiency to the reaction centers, where charge separation takes place. The time scale and pathways of this transfer are controlled by the protein scaffold, which holds the pigments at optimal geometry and tunes their Excitation energies (site energies). The detailed understanding of the tuning of site energies by the protein has been an unsolved problem since the first high-resolution crystal structure of a light-harvesting antenna appeared >30 years ago [Fenna RE, Matthews BW (1975) Nature 258:573–577]. Here, we present a combined quantum chemical/electrostatic approach to compute site energies that considers the whole protein in atomic detail and provides the missing link between crystallography and spectroscopy. The calculation of site energies of the Fenna–Matthews–Olson protein results in optical spectra that are in quantitative agreement with experiment and reveals an unexpectedly strong influence of the backbone of two α-helices. The electric field from the latter defines the direction of Excitation Energy flow in the Fenna–Matthews–Olson protein, whereas the effects of amino acid side chains, hitherto thought to be crucial, largely compensate each other. This result challenges the current view of how Energy flow is regulated in pigment–protein complexes and demonstrates that attention has to be paid to the backbone architecture.

  • how proteins trigger Excitation Energy transfer in the fmo complex of green sulfur bacteria
    Biophysical Journal, 2006
    Co-Authors: Julia Adolphs, Thomas Renger
    Abstract:

    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.

  • ultrafast Excitation Energy transfer dynamics in photosynthetic pigment protein complexes
    Physics Reports, 2001
    Co-Authors: Thomas Renger, Volkhard May, Oliver Kuhn
    Abstract:

    Abstract Photosynthetically active membranes of certain bacteria and higher plants contain antenna systems which surround the reaction center to increase its absorption cross section for the incoming sun light. The Excitation Energy created in the antenna pigments is transferred via an exciton mechanism to the reaction center where charge separation takes place. Sub-picosecond laser spectroscopy makes it possible to follow the initial dynamic events of Excitation Energy (exciton) motion and exciton relaxation in real time. On the other hand, the success of structure resolution opened the door to the microscopic understanding of spectroscopic data and to an appreciation of the structure–function relationship realized in different systems. Here, it will be demonstrated how the combination of microscopically based theoretical models and numerical simulations pave the road from spectroscopic data to a deeper understanding of the functionality of photosynthetic antenna systems. The density matrix technique is introduced as the theoretical tool providing a unified description of the processes which follow ultrafast laser Excitation. This includes in particular coherent exciton motion, vibrational coherences, exciton relaxation, and exciton localization. It can be considered as a major result of recent investigations that a theoretical model of intermediate complexity was shown to be suitable to explain a variety of experiments on different photosynthetic antenna systems. We start with introducing the structural components of antenna systems and discuss their general function. In the second part the formulation of the appropriate theoretical model as well as the simulation of optical spectra is reviewed in detail. Emphasis is put on the mapping of the complex protein structure and its hierarchy of dynamic phenomena onto models of static and dynamic disorder. In particular, it is shown that the protein spectral density plays a key role in characterizing Excitation Energy dissipation. The theoretical concepts are illustrated in the third part by results of numerical simulations of linear and nonlinear optical experiments for three types of antennae: the peripheral light-harvesting complex 2 of purple bacteria, the Fenna–Mathew–Olson complex of green bacteria, and the light-harvesting complex of photosystem II of green plants.

Seiji Akimoto - One of the best experts on this subject based on the ideXlab platform.

  • Excitation Energy transfer and quenching in diatom psi fcpi upon p700 cation formation
    Journal of Physical Chemistry B, 2020
    Co-Authors: Ryo Nagao, Jianren Shen, Makio Yokono, Yoshifumi Ueno, Seiji Akimoto
    Abstract:

    Excitation-Energy transfer in photosystem I (PSI) is changed by a cation formation of a special pair chlorophyll P700 in the PSI core; however, it remains unclear how light-harvesting pigment–protein complexes are involved in the P700-related Energy-transfer mechanisms. Here, we report effects of the redox changes of P700 on Excitation-Energy dynamics in diatom PSI-fucoxanthin chlorophyll a/c-binding protein (PSI-FCPI) and PSI core complexes by means of time-resolved fluorescence (TRF) spectroscopy. For the TRF measurements, the PSI-FCPI and PSI were adapted under P700 neutral and cation conditions using chemical reagents. Upon the P700+ formation, fluorescence decay-associated (FDA) spectra constructed from the TRF spectra exhibit a larger fluorescence decay amplitude relative to a fluorescence rise magnitude within 100 ps in each of the PSI-FCPI and PSI. The decay components are shifted to lower wavelengths in each of the P700-cation PSI-FCPI and PSI than in the P700-neutral PSIs. The rapid fluorescence...

  • low Energy chlorophylls in fucoxanthin chlorophyll a c binding protein conduct Excitation Energy transfer to photosystem i in diatoms
    Journal of Physical Chemistry B, 2019
    Co-Authors: Ryo Nagao, Jianren Shen, Makio Yokono, Yoshifumi Ueno, Seiji Akimoto
    Abstract:

    Photosynthetic organisms handle solar Energy precisely to achieve efficient photochemical reactions. Because there are a wide variety of light-harvesting antennas in oxyphototrophs, the Excitation Energy transfer mechanisms are thought to differ significantly. In this study, we compared Excitation Energy dynamics between photosystem I (PSI) cores and a complex between PSI and fucoxanthin chlorophyll (Chl) a/ c-binding protein I (PSI-FCPI) isolated from a diatom, Chaetoceros gracilis, by means of picosecond time-resolved fluorescence analyses. Time-resolved spectra measured at 77 K clearly show that low-Energy Chls in the FCPI transfer not only most of the Excitation Energy to the reaction center Chls in the PSI cores but also the remaining Energy to carotenoids for quenching. Under room-temperature conditions, the Energy in the low-Energy Chls is rapidly equilibrated on Chls in the PSI cores by uphill Energy transfer within a few tens of picoseconds. These findings provide solid evidence that the low-Energy Chls in the FCPI contribute to the photochemical reactions in PSI.

  • Ultrafast Excitation Energy Dynamics in a Diatom Photosystem I‑Antenna Complex: A Femtosecond Fluorescence Upconversion Study
    2019
    Co-Authors: Ryo Nagao, Jianren Shen, Yoshifumi Ueno, Kohei Kagatani, Seiji Akimoto
    Abstract:

    Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) are unique light-harvesting antennas in diatoms. Recent time-resolved fluorescence analysis of photosystem I with FCP associated (PSI–FCPI) has mainly shown Excitation Energy transfer among Chls a from FCPI to PSI in tens of picoseconds. However, it remains unclear how each pigment, especially carotenoids and Chl c, in the FCPI is functionally related to the Energy transfer in a femtosecond time range. Here, we reveal ultrafast Excitation Energy transfer mechanism in the PSI–FCPI preparations isolated from a diatom, Chaetoceros gracilis, by means of femtosecond time-resolved fluorescence spectroscopy with an upconversion system. Compared with the fluorescence lifetime components of PSI core-like complexes, the Energy transfer of Chl c → Chl a in the FCPI was observed within hundreds of femtoseconds, and the Energy in the FCPI was transferred to PSI in ∼2 ps. The comparative fluorescence analyses provide physical insights into the Energy transfer machinery within FCPI and from FCPI to PSI

  • Low-Energy Chlorophylls in Fucoxanthin Chlorophyll a/c‑Binding Protein Conduct Excitation Energy Transfer to Photosystem I in Diatoms
    2018
    Co-Authors: Ryo Nagao, Jianren Shen, Makio Yokono, Yoshifumi Ueno, Seiji Akimoto
    Abstract:

    Photosynthetic organisms handle solar Energy precisely to achieve efficient photochemical reactions. Because there are a wide variety of light-harvesting antennas in oxyphototrophs, the Excitation Energy transfer mechanisms are thought to differ significantly. In this study, we compared Excitation Energy dynamics between photosystem I (PSI) cores and a complex between PSI and fucoxanthin chlorophyll (Chl) a/c-binding protein I (PSI−FCPI) isolated from a diatom, Chaetoceros gracilis, by means of picosecond time-resolved fluorescence analyses. Time-resolved spectra measured at 77 K clearly show that low-Energy Chls in the FCPI transfer not only most of the Excitation Energy to the reaction center Chls in the PSI cores but also the remaining Energy to carotenoids for quenching. Under room-temperature conditions, the Energy in the low-Energy Chls is rapidly equilibrated on Chls in the PSI cores by uphill Energy transfer within a few tens of picoseconds. These findings provide solid evidence that the low-Energy Chls in the FCPI contribute to the photochemical reactions in PSI

  • Control Mechanism of Excitation Energy Transfer in a Complex Consisting of Photosystem II and Fucoxanthin Chlorophyll a/c‑Binding Protein
    2015
    Co-Authors: Ryo Nagao, Makio Yokono, Tatsuya Tomo, Seiji Akimoto
    Abstract:

    Fucoxanthin chlorophyll (Chl) a/c-binding protein (FCP) is a unique light-harvesting antenna in diatoms, which are photosynthesizing algae ubiquitous in aquatic environments. However, it is unknown how Excitation Energy is trapped and quenched in a complex consisting of photosystem II and FCP (PSII–FCPII complex). Here, we report the control mechanism of Excitation Energy transfer in the PSII–FCPII complexes isolated from a diatom, Chaetoceros gracilis, as revealed by picosecond time-resolved fluorescence spectroscopy. The results showed that Chl-Excitation Energy is harvested in low-Energy Chls near/within FCPII under the 77 K conditions, whereas most of the Energy is trapped in reaction center Chls in PSII under the 283 K conditions. Surprisingly, Excitation Energy quenching was observed in a part of PSII–FCPII complexes with the time constants of hundreds of picosecond, thus indicating the large contribution of FCPII to Energy trapping and quenching. On the basis of these results, we discuss the light-harvesting strategy of diatoms

Shigeru Itoh - One of the best experts on this subject based on the ideXlab platform.

Ryo Nagao - One of the best experts on this subject based on the ideXlab platform.

  • enhancement of Excitation Energy quenching in fucoxanthin chlorophyll a c binding proteins isolated from a diatom phaeodactylum tricornutum upon excess light illumination
    Biochimica et Biophysica Acta, 2021
    Co-Authors: Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Minoru Kumazawa, Ka Ho Kato, Naoki Tsuboshita, Naoshi Dohmae, Kentaro Ifuku, Jianren Shen
    Abstract:

    Abstract Photosynthetic organisms regulate pigment composition and molecular oligomerization of light-harvesting complexes in response to solar light intensities, in order to improve light-harvesting efficiency. Here we report Excitation-Energy dynamics and relaxation of fucoxanthin chlorophyll a/c-binding protein (FCP) complexes isolated from a diatom Phaeodactylum tricornutum grown under high-light (HL) illumination. Two types of FCP complexes were prepared from this diatom under the HL condition, whereas one FCP complex was isolated from the cells grown under a low-light (LL) condition. The subunit composition and oligomeric states of FCP complexes under the HL condition are different from those under the LL condition. Absorption and fluorescence spectra at 77 K of the FCP complexes also vary between the two conditions, indicating modifications of the pigment composition and arrangement upon the HL illumination. Time-resolved fluorescence curves at 77 K of the FCP complexes under the HL condition showed shorter lifetime components compared with the LL condition. Fluorescence decay-associated spectra at 77 K showed distinct Excitation-Energy-quenching components and alterations of Energy-transfer pathways in the FCP complexes under the HL condition. These findings provide insights into molecular and functional mechanisms of the dynamic regulation of FCPs in this diatom under excess-light conditions.

  • Excitation Energy transfer and quenching in diatom psi fcpi upon p700 cation formation
    Journal of Physical Chemistry B, 2020
    Co-Authors: Ryo Nagao, Jianren Shen, Makio Yokono, Yoshifumi Ueno, Seiji Akimoto
    Abstract:

    Excitation-Energy transfer in photosystem I (PSI) is changed by a cation formation of a special pair chlorophyll P700 in the PSI core; however, it remains unclear how light-harvesting pigment–protein complexes are involved in the P700-related Energy-transfer mechanisms. Here, we report effects of the redox changes of P700 on Excitation-Energy dynamics in diatom PSI-fucoxanthin chlorophyll a/c-binding protein (PSI-FCPI) and PSI core complexes by means of time-resolved fluorescence (TRF) spectroscopy. For the TRF measurements, the PSI-FCPI and PSI were adapted under P700 neutral and cation conditions using chemical reagents. Upon the P700+ formation, fluorescence decay-associated (FDA) spectra constructed from the TRF spectra exhibit a larger fluorescence decay amplitude relative to a fluorescence rise magnitude within 100 ps in each of the PSI-FCPI and PSI. The decay components are shifted to lower wavelengths in each of the P700-cation PSI-FCPI and PSI than in the P700-neutral PSIs. The rapid fluorescence...

  • low Energy chlorophylls in fucoxanthin chlorophyll a c binding protein conduct Excitation Energy transfer to photosystem i in diatoms
    Journal of Physical Chemistry B, 2019
    Co-Authors: Ryo Nagao, Jianren Shen, Makio Yokono, Yoshifumi Ueno, Seiji Akimoto
    Abstract:

    Photosynthetic organisms handle solar Energy precisely to achieve efficient photochemical reactions. Because there are a wide variety of light-harvesting antennas in oxyphototrophs, the Excitation Energy transfer mechanisms are thought to differ significantly. In this study, we compared Excitation Energy dynamics between photosystem I (PSI) cores and a complex between PSI and fucoxanthin chlorophyll (Chl) a/ c-binding protein I (PSI-FCPI) isolated from a diatom, Chaetoceros gracilis, by means of picosecond time-resolved fluorescence analyses. Time-resolved spectra measured at 77 K clearly show that low-Energy Chls in the FCPI transfer not only most of the Excitation Energy to the reaction center Chls in the PSI cores but also the remaining Energy to carotenoids for quenching. Under room-temperature conditions, the Energy in the low-Energy Chls is rapidly equilibrated on Chls in the PSI cores by uphill Energy transfer within a few tens of picoseconds. These findings provide solid evidence that the low-Energy Chls in the FCPI contribute to the photochemical reactions in PSI.

  • Ultrafast Excitation Energy Dynamics in a Diatom Photosystem I‑Antenna Complex: A Femtosecond Fluorescence Upconversion Study
    2019
    Co-Authors: Ryo Nagao, Jianren Shen, Yoshifumi Ueno, Kohei Kagatani, Seiji Akimoto
    Abstract:

    Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) are unique light-harvesting antennas in diatoms. Recent time-resolved fluorescence analysis of photosystem I with FCP associated (PSI–FCPI) has mainly shown Excitation Energy transfer among Chls a from FCPI to PSI in tens of picoseconds. However, it remains unclear how each pigment, especially carotenoids and Chl c, in the FCPI is functionally related to the Energy transfer in a femtosecond time range. Here, we reveal ultrafast Excitation Energy transfer mechanism in the PSI–FCPI preparations isolated from a diatom, Chaetoceros gracilis, by means of femtosecond time-resolved fluorescence spectroscopy with an upconversion system. Compared with the fluorescence lifetime components of PSI core-like complexes, the Energy transfer of Chl c → Chl a in the FCPI was observed within hundreds of femtoseconds, and the Energy in the FCPI was transferred to PSI in ∼2 ps. The comparative fluorescence analyses provide physical insights into the Energy transfer machinery within FCPI and from FCPI to PSI

  • Low-Energy Chlorophylls in Fucoxanthin Chlorophyll a/c‑Binding Protein Conduct Excitation Energy Transfer to Photosystem I in Diatoms
    2018
    Co-Authors: Ryo Nagao, Jianren Shen, Makio Yokono, Yoshifumi Ueno, Seiji Akimoto
    Abstract:

    Photosynthetic organisms handle solar Energy precisely to achieve efficient photochemical reactions. Because there are a wide variety of light-harvesting antennas in oxyphototrophs, the Excitation Energy transfer mechanisms are thought to differ significantly. In this study, we compared Excitation Energy dynamics between photosystem I (PSI) cores and a complex between PSI and fucoxanthin chlorophyll (Chl) a/c-binding protein I (PSI−FCPI) isolated from a diatom, Chaetoceros gracilis, by means of picosecond time-resolved fluorescence analyses. Time-resolved spectra measured at 77 K clearly show that low-Energy Chls in the FCPI transfer not only most of the Excitation Energy to the reaction center Chls in the PSI cores but also the remaining Energy to carotenoids for quenching. Under room-temperature conditions, the Energy in the low-Energy Chls is rapidly equilibrated on Chls in the PSI cores by uphill Energy transfer within a few tens of picoseconds. These findings provide solid evidence that the low-Energy Chls in the FCPI contribute to the photochemical reactions in PSI