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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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52
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Adolphs J, Berrer M, Renger T. Hole-Burning Spectroscopy on Excitonically Coupled Pigments in Proteins: Theory Meets Experiment. J Am Chem Soc 2016; 138:2993-3001. [PMID: 26811003 PMCID: PMC4786881 DOI: 10.1021/jacs.5b08246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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A theory for the calculation of resonant
and nonresonant hole-burning
(HB) spectra of pigment–protein complexes is presented and
applied to the water-soluble chlorophyll-binding protein (WSCP) from
cauliflower. The theory is based on a non-Markovian line shape theory
(Renger and Marcus2002, 116, 9997) and includes exciton delocalization, vibrational
sidebands, and lifetime broadening. An earlier approach by Reppert
(2011, 2, 2716) is found to describe nonresonant HB spectra only. Here we present
a theory that can be used for a quantitative description of HB data
for both nonresonant and resonant burning conditions. We find that
it is important to take into account the excess energy of the excitation
in the HB process. Whereas excitation of the zero-phonon transition
of the lowest exciton state, that is, resonant burning allows the
protein to access only its conformational substates in the neighborhood
of the preburn state, any higher excitation gives the protein full
access to all conformations present in the original inhomogeneous
ensemble. Application of the theory to recombinant WSCP from cauliflower,
reconstituted with chlorophyll a or chlorophyll b, gives excellent agreement with experimental data by Pieper
et al. (2011, 115, 405321417356) and allows us to obtain an upper bound of the lifetime of the upper
exciton state directly from the HB experiments in agreement with lifetimes
measured recently in time domain 2D experiments by Alster et al. (2014, 118, 352424627983).
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Affiliation(s)
- Julian Adolphs
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
| | - Manuel Berrer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
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53
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Jurinovich S, Viani L, Prandi IG, Renger T, Mennucci B. Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II. Phys Chem Chem Phys 2016; 17:14405-16. [PMID: 25872495 DOI: 10.1039/c4cp05647g] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light-harvesting pigment-protein complexes (PPC) represent the fundamental units through which the photosynthetic organisms absorb sunlight and funnel the energy to the reaction centre for carrying out the primary energy conversion reactions of photosynthesis. Here we apply a multiscale computational strategy to a specific PPC present in the photosystem II of plants and algae (CP29) to investigate in what detail should the environment effects due to protein and membrane/solvent be included for an accurate description of optical spectra. We find that a refinement of the crystal structure is needed before any meaningful quantum chemical calculations of pigment transition energies can be performed. For this purpose we apply classical molecular dynamics simulations of the PPC within its natural environment and we perform ab initio computations of the exciton Hamiltonian of the complex, including the environment either implicitly by the polarizable continuum model (PCM) or explicitly using the polarizable QM/MM methodology (MMPol). However, PCM essentially leads to an unspecific redshift of all transition energies, and MMPol is able to reveal site-specific changes in the optical properties of the pigments. Based on the latter and the excitonic couplings obtained within a polarizable QM/MM methodology, optical spectra are calculated, which are in good qualitative agreement with experimental data. A weakness of the approach is however found in the overestimation of the fluctuations of the excitonic parameters of the pigments along the MD trajectory. An explanation for such a finding in terms of the limits of the force fields commonly used for protein cofactors is presented and discussed.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 3, I-56124 Pisa, Italy.
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54
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Mohamed A, Nagao R, Noguchi T, Fukumura H, Shibata Y. Structure-Based Modeling of Fluorescence Kinetics of Photosystem II: Relation between Its Dimeric Form and Photoregulation. J Phys Chem B 2016; 120:365-76. [PMID: 26714062 DOI: 10.1021/acs.jpcb.5b09103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Ahmed Mohamed
- Department of Chemistry, Graduate School of Science, Tohoku University , Aramaki Aza Aoba, Aoba-Ku, Sendai 980-8578, Japan
| | - Ryo Nagao
- Division of Material Science (Physics), Graduate School of Science, Nagoya University , Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science (Physics), Graduate School of Science, Nagoya University , Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Hiroshi Fukumura
- Department of Chemistry, Graduate School of Science, Tohoku University , Aramaki Aza Aoba, Aoba-Ku, Sendai 980-8578, Japan
| | - Yutaka Shibata
- Department of Chemistry, Graduate School of Science, Tohoku University , Aramaki Aza Aoba, Aoba-Ku, Sendai 980-8578, Japan
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55
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The quest for energy traps in the CP43 antenna of photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:286-300. [DOI: 10.1016/j.jphotobiol.2015.05.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 05/13/2015] [Accepted: 05/28/2015] [Indexed: 01/08/2023]
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56
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Song K, Bai S, Shi Q. A time domain two-particle approximation to calculate the absorption and circular dichroism line shapes of molecular aggregates. J Chem Phys 2015; 143:064109. [DOI: 10.1063/1.4928584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Shuming Bai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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57
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Fujihashi Y, Kimura A. Assignment of Exciton Domain in Light Harvesting Systems Based on the Variational Polaron Approach. J Phys Chem B 2015; 119:8349-56. [DOI: 10.1021/acs.jpcb.5b04503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuta Fujihashi
- Graduate School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
| | - Akihiro Kimura
- Graduate School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
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58
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Craddock TJA, Friesen D, Mane J, Hameroff S, Tuszynski JA. The feasibility of coherent energy transfer in microtubules. J R Soc Interface 2015; 11:20140677. [PMID: 25232047 DOI: 10.1098/rsif.2014.0677] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
It was once purported that biological systems were far too 'warm and wet' to support quantum phenomena mainly owing to thermal effects disrupting quantum coherence. However, recent experimental results and theoretical analyses have shown that thermal energy may assist, rather than disrupt, quantum coherent transport, especially in the 'dry' hydrophobic interiors of biomolecules. Specifically, evidence has been accumulating for the necessary involvement of quantum coherent energy transfer between uniquely arranged chromophores in light harvesting photosynthetic complexes. The 'tubulin' subunit proteins, which comprise microtubules, also possess a distinct architecture of chromophores, namely aromatic amino acids, including tryptophan. The geometry and dipolar properties of these aromatics are similar to those found in photosynthetic units indicating that tubulin may support coherent energy transfer. Tubulin aggregated into microtubule geometric lattices may support such energy transfer, which could be important for biological signalling and communication essential to living processes. Here, we perform a computational investigation of energy transfer between chromophoric amino acids in tubulin via dipole excitations coupled to the surrounding thermal environment. We present the spatial structure and energetic properties of the tryptophan residues in the microtubule constituent protein tubulin. Plausibility arguments for the conditions favouring a quantum mechanism of signal propagation along a microtubule are provided. Overall, we find that coherent energy transfer in tubulin and microtubules is biologically feasible.
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Affiliation(s)
- Travis John Adrian Craddock
- Center for Psychological Studies, Graduate School of Computer and Information Sciences, and College of Osteopathic Medicine, Nova Southeastern University, Ft Lauderdale, FL 33328, USA Institute for Neuro-Immune Medicine, Nova Southeastern University, Ft Lauderdale, FL 33328, USA
| | - Douglas Friesen
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Jonathan Mane
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Stuart Hameroff
- Departments of Anesthesiology and Psychology, Center for Consciousness Studies, The University of Arizona Health Sciences Center, Tucson, AZ 210202, USA
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2 Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2E1
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59
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Carbonera D, Di Valentin M, Spezia R, Mezzetti A. The unique photophysical properties of the Peridinin-Chlorophyll-α-Protein. Curr Protein Pept Sci 2015; 15:332-50. [PMID: 24678668 PMCID: PMC4030626 DOI: 10.2174/1389203715666140327111139] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 11/22/2013] [Accepted: 03/16/2014] [Indexed: 11/22/2022]
Abstract
Peridinin-Chlorophyll-a-Proteins (PCPs) are water-soluble light harvesting complexes from dinoflagellates.
They have unique light-harvesting and energy transfer properties which have been studied in details in the last 15 years.
This review aims to give an overview on all the main aspects of PCPs photophysics, with an emphasis on some aspects
which have not been reviewed in details so far, such as vibrational spectroscopy studies, theoretical calculations, and
magnetic resonance studies. A paragraph on the present development of PCPs towards technological applications is also
included.
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Affiliation(s)
| | | | | | - Alberto Mezzetti
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy.
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60
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Collette F, Renger T, Schmidt am Busch M. Revealing the functional states in the active site of BLUF photoreceptors from electrochromic shift calculations. J Phys Chem B 2014; 118:11109-19. [PMID: 25153778 PMCID: PMC4174740 DOI: 10.1021/jp506400y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/22/2014] [Indexed: 11/28/2022]
Abstract
Photoexcitation with blue light of the flavin chromophore in BLUF photoreceptors induces a switch into a metastable signaling state that is characterized by a red-shifted absorption maximum. The red shift is due to a rearrangement in the hydrogen bond pattern around Gln63 located in the immediate proximity of the isoalloxazine ring system of the chromophore. There is a long-lasting controversy between two structural models, named Q63A and Q63J in the literature, on the local conformation of the residues Gln63 and Tyr21 in the dark state of the photoreceptor. As regards the mechanistic details of the light-activation mechanism, rotation of Gln63 is opposed by tautomerism in the Q63A and Q63J models, respectively. We provide a structure-based simulation of electrochromic shifts of the flavin chromophore in the wild type and in various site-directed mutants. The excellent overall agreement between experimental and computed data allows us to evaluate the two structural models. Compelling evidence is obtained that the Q63A model is incorrect, whereas the Q63J is fully consistent with the present computations. Finally, we confirm independently that a keto-enol tautomerization of the glutamine at position 63, which was proposed as molecular mechanism for the transition between the dark and the light-adapted state, explains the measured 10 to 15 nm red shift in flavin absorption between these two states of the protein. We believe that the accurateness of our results provides evidence that the BLUF photoreceptors absorption is fine-tuned through electrostatic interactions between the chromophore and the protein matrix, and finally that the simplicity of our theoretical model is advantageous as regards easy reproducibility and further extensions.
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Affiliation(s)
- Florimond Collette
- Institut für Theoretische
Physik, Johannes Kepler Universität
Linz, Altenberger Strasse
69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische
Physik, Johannes Kepler Universität
Linz, Altenberger Strasse
69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische
Physik, Johannes Kepler Universität
Linz, Altenberger Strasse
69, 4040 Linz, Austria
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61
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Jennings RC, Zucchelli G. Antenna entropy in plant photosystems does not reduce the free energy for primary charge separation. Biophys Chem 2014; 195:16-21. [PMID: 25190479 DOI: 10.1016/j.bpc.2014.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/12/2014] [Accepted: 08/12/2014] [Indexed: 11/17/2022]
Abstract
We have investigated the concept of the so-called "antenna entropy" of higher plant photosystems. Several interesting points emerge: 1. In the case of a photosystemwhich harbours an excited state, the “antenna entropy” is equivalent to the configurational (mixing) entropy of a thermodynamic canonical ensemble. The energy associated with this parameter has been calculated for a hypothetical isoenergetic photosystem, photosystem I and photosystem II, and comes out in the range of 3.5 - 8% of the photon energy considering 680 nm. 2. The “antenna entropy” seems to be a rather unique thermodynamic phenomenon, in as much as it does not modify the free energy available for primary photochemistry, as has been previously suggested. 3. It is underlined that this configurational (mixing) entropy, unlike heat dispersal in a thermal system, does not involve energy dilution. This points out an important difference between thermal and electronic energy dispersal.
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Affiliation(s)
- Robert C Jennings
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, sede di Milano, via Giovanni Celoria 26, 20133 Milan, Italy; Dipartimento di Bioscienze, Università degli Studi di Milano, via Giovanni Celoria 26, 20133 Milan, Italy.
| | - Giuseppe Zucchelli
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, sede di Milano, via Giovanni Celoria 26, 20133 Milan, Italy; Dipartimento di Bioscienze, Università degli Studi di Milano, via Giovanni Celoria 26, 20133 Milan, Italy
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62
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Müh F, Lindorfer D, Schmidt am Busch M, Renger T. Towards a structure-based exciton Hamiltonian for the CP29 antenna of photosystem II. Phys Chem Chem Phys 2014; 16:11848-63. [PMID: 24603694 DOI: 10.1039/c3cp55166k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The exciton Hamiltonian pertaining to the first excited states of chlorophyll (Chl) a and b pigments in the minor light-harvesting complex CP29 of plant photosystem II is determined based on the recent crystal structure at 2.8 Å resolution applying a combined quantum chemical/electrostatic approach as used earlier for the major light-harvesting complex LHCII. Two electrostatic methods for the calculation of the local transition energies (site energies), referred to as the Poisson-Boltzmann/quantum chemical (PBQC) and charge density coupling (CDC) method, which differ in the way the polarizable environment of the pigments is described, are compared and found to yield comparable results, when tested against fits of measured optical spectra (linear absorption, linear dichroism, circular dichroism, and fluorescence). The crystal structure shows a Chl a/b ratio of 2.25, whereas a ratio between 2.25 and 3.0 can be estimated from the simulation of experimental spectra. Thus, it is possible that up to one Chl b is lost in CP29 samples. The lowest site energy is found to be located at Chl a604 close to neoxanthin. This assignment is confirmed by the simulation of wild-type-minus-mutant difference spectra of reconstituted CP29, where a tyrosine residue next to Chl a604 is modified in the mutant. Nonetheless, the terminal emitter domain (TED), i.e. the pigments contributing mostly to the lowest exciton state, is found at the Chl a611-a612-a615 trimer due to strong excitonic coupling between these pigments, with the largest contributions from Chls a611 and a612. A major difference between CP29 and LHCII is that Chl a610 is not the energy sink in CP29, which is presumably to a large extent due to the replacement of a lysine residue with alanine close to the TED.
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Affiliation(s)
- Frank Müh
- Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria.
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63
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Shibata Y, Katoh W, Chiba T, Namie K, Ohnishi N, Minagawa J, Nakanishi H, Noguchi T, Fukumura H. Development of a novel cryogenic microscope with numerical aperture of 0.9 and its application to photosynthesis research. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:880-7. [PMID: 24650629 DOI: 10.1016/j.bbabio.2014.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/05/2014] [Accepted: 03/10/2014] [Indexed: 01/15/2023]
Abstract
A novel cryogenic optical-microscope system was developed in which the objective lens is set inside of the cryostat adiabatic vacuum space. Being isolated from the sample when it was cooled, the objective lens was maintained at room temperature during the cryogenic measurement. Therefore, the authors were able to use a color-aberration corrected objective lens with a numerical aperture of 0.9. The lens is equipped with an air vent for compatibility to the vacuum. The theoretically expected spatial resolutions of 0.39μm along the lateral direction and 1.3μm along the axial direction were achieved by the developed system. The system was applied to the observations of non-uniform distributions of the photosystems in the cells of a green alga, Chlamydomonas reinhardtii, at 94K. Gaussian decomposition analysis of the fluorescence spectra at all the pixels clearly demonstrated a non-uniform distribution of the two photosystems, as reflected in the variable ratios of the fluorescence intensities assigned to photosystem II and to those assigned to photosystem I. The system was also applied to the fluorescence spectroscopy of single isolated photosystem I complexes at 90K. The fluorescence, assigned to be emitted from a single photosystem I trimer, showed an intermittent fluctuation called blinking, which is typical for a fluorescence signal from a single molecule. The vibronic fluorescence bands at around 790nm were observed for single photosystem I trimers, suggesting that the color aberration is not serious up to the 800nm spectral region.
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Affiliation(s)
- Yutaka Shibata
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan.
| | - Wataru Katoh
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tomofumi Chiba
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Keisuke Namie
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Norikazu Ohnishi
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Hanayo Nakanishi
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hiroshi Fukumura
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan
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64
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Schlodder E, Lendzian F, Meyer J, Çetin M, Brecht M, Renger T, Karapetyan N. Long-wavelength limit of photochemical energy conversion in Photosystem I. J Am Chem Soc 2014; 136:3904-18. [PMID: 24517238 PMCID: PMC3959156 DOI: 10.1021/ja412375j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Indexed: 11/30/2022]
Abstract
In Photosystem I (PS I) long-wavelength chlorophylls (LWC) of the core antenna are known to extend the spectral region up to 750 nm for absorbance of light that drives photochemistry. Here we present clear evidence that even far-red light with wavelengths beyond 800 nm, clearly outside the LWC absorption bands, can still induce photochemical charge separation in PS I throughout the full temperature range from 295 to 5 K. At room temperature, the photoaccumulation of P700(+•) was followed by the absorbance increase at 826 nm. At low temperatures (T < 100 K), the formation of P700(+•)FA/B(-•) was monitored by the characteristic EPR signals of P700(+•) and FA/B(-•) and by the characteristic light-minus-dark absorbance difference spectrum in the QY region. P700 oxidation was observed upon selective excitation at 754, 785, and 808 nm, using monomeric and trimeric PS I core complexes of Thermosynechococcus elongatus and Arthrospira platensis, which differ in the amount of LWC. The results show that the LWC cannot be responsible for the long-wavelength excitation-induced charge separation at low temperatures, where thermal uphill energy transfer is frozen out. Direct energy conversion of the excitation energy from the LWC to the primary radical pair, e.g., via a superexchange mechanism, is excluded, because no dependence on the content of LWC was observed. Therefore, it is concluded that electron transfer through PS I is induced by direct excitation of a proposed charge transfer (CT) state in the reaction center. A direct signature of this CT state is seen in absorbance spectra of concentrated PS I samples, which reveal a weak and featureless absorbance band extending beyond 800 nm, in addition to the well-known bands of LWC (C708, C719 and C740) in the range between 700 and 750 nm. The present findings suggest that nature can exploit CT states for extending the long wavelength limit in PSI even beyond that of LWC. Similar mechanisms may work in other photosynthetic systems and in chemical systems capable of photoinduced electron transfer processes in general.
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Affiliation(s)
- Eberhard Schlodder
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Friedhelm Lendzian
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Jenny Meyer
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Marianne Çetin
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Marc Brecht
- Institut für
Physikalische und Theoretische Physik, Eberhard-Karls-Universität
Tübingen, Auf
der Morgenstelle 14, 71976 Tübingen, Germany
| | - Thomas Renger
- Institut
für Theoretische Physik, Johannes
Kepler Universität, Abteilung Theoretische
Biophysik, Altenberger
Str. 69, Linz, Austria
| | - Navasard
V. Karapetyan
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
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65
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Haverkort F, Stradomska A, de Vries AH, Knoester J. First-principles calculation of the optical properties of an amphiphilic cyanine dye aggregate. J Phys Chem A 2014; 118:1012-23. [PMID: 24422675 DOI: 10.1021/jp4112487] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a first-principles approach, we calculate electronic and optical properties of molecular aggregates of the dye amphi-pseudoisocyanine, whose structures we obtained from molecular dynamics (MD) simulations of the self-aggregation process. Using quantum chemistry methods, we translate the structural information into an effective time-dependent Frenkel exciton Hamiltonian for the dominant optical transitions in the aggregate. This Hamiltonian is used to calculate the absorption spectrum. Detailed analysis of the dynamic fluctuations in the molecular transition energies and intermolecular excitation transfer interactions in this Hamiltonian allows us to elucidate the origin of the relevant time scales; short time scales, on the order of up to a few hundreds of femtoseconds, result from internal motions of the dye molecules, while the longer (a few picosecond) time scales we ascribe to environmental motions. The absorption spectra of the aggregate structures obtained from MD feature a blue-shifted peak compared to that of the monomer; thus, our aggregates can be classified as H-aggregates, although considerable oscillator strength is carried by states along the entire exciton band. Comparison to the experimental absorption spectrum of amphi-PIC aggregates shows that the simulated line shape is too wide, pointing to too much disorder in the internal structure of the simulated aggregates.
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Affiliation(s)
- Frank Haverkort
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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66
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Cole DJ, Chin AW, Hine NDM, Haynes PD, Payne MC. Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex. J Phys Chem Lett 2013; 4:4206-4212. [PMID: 26296166 DOI: 10.1021/jz402000c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present progress toward a first-principles parametrization of the Hamiltonian of the Fenna-Matthews-Olson pigment-protein complex, a molecule that has become key to understanding the role of quantum dynamics in photosynthetic exciton energy transfer. To this end, we have performed fully quantum mechanical calculations on each of the seven bacteriochlorophyll pigments that make up the complex, including a significant proportion of their protein environment (more than 2000 atoms), using linear-scaling density functional theory exploiting a recent development for the computation of excited states. Local pigment transition energies and interpigment coupling between optical transitions have been calculated and are in good agreement with the literature consensus. Comparisons between simulated and experimental optical spectra point toward future work that may help to elucidate important design principles in these nanoscale devices.
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Affiliation(s)
- Daniel J Cole
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
- ‡Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Alex W Chin
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Nicholas D M Hine
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
- §Departments of Materials and Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Peter D Haynes
- §Departments of Materials and Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Mike C Payne
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
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67
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Croce R, van Amerongen H. Light-harvesting in photosystem I. PHOTOSYNTHESIS RESEARCH 2013; 116:153-66. [PMID: 23645376 PMCID: PMC3825136 DOI: 10.1007/s11120-013-9838-x] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/23/2013] [Indexed: 05/18/2023]
Abstract
This review focuses on the light-harvesting properties of photosystem I (PSI) and its LHCI outer antenna. LHCI consists of different chlorophyll a/b binding proteins called Lhca's, surrounding the core of PSI. In total, the PSI-LHCI complex of higher plants contains 173 chlorophyll molecules, most of which are there to harvest sunlight energy and to transfer the created excitation energy to the reaction center (RC) where it is used for charge separation. The efficiency of the complex is based on the capacity to deliver this energy to the RC as fast as possible, to minimize energy losses. The performance of PSI in this respect is remarkable: on average it takes around 50 ps for the excitation to reach the RC in plants, without being quenched in the meantime. This means that the internal quantum efficiency is close to 100% which makes PSI the most efficient energy converter in nature. In this review, we describe the light-harvesting properties of the complex in relation to protein and pigment organization/composition, and we discuss the important parameters that assure its very high quantum efficiency. Excitation energy transfer and trapping in the core and/or Lhcas, as well as in the supercomplexes PSI-LHCI and PSI-LHCI-LHCII are described in detail with the aim of giving an overview of the functional behavior of these complexes.
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Affiliation(s)
- Roberta Croce
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands,
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68
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Renger T, Madjet MEA, Schmidt am Busch M, Adolphs J, Müh F. Structure-based modeling of energy transfer in photosynthesis. PHOTOSYNTHESIS RESEARCH 2013; 116:367-388. [PMID: 23921525 DOI: 10.1007/s11120-013-9893-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment-protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton-vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria,
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69
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Chmeliov J, Songaila E, Rancova O, Gall A, Robert B, Abramavicius D, Valkunas L. Excitons in the LH3 complexes from purple bacteria. J Phys Chem B 2013; 117:11058-68. [PMID: 23570515 DOI: 10.1021/jp400239z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The noncovalently bound and structurally identical bacteriochlorophyll a chromophores in the peripheral light-harvesting complexes LH2 (B800-850) and LH3 (B800-820) from photosynthetic purple bacteria ensure the variability of the exciton spectra in the near-infrared (820-850 nm) wavelength region. As a result, the spectroscopic properties of the antenna complexes, such as positions of the maxima in the exciton absorption spectra, give rise to very efficient excitation transfer toward the reaction center. In this work, we investigated the possible molecular origin of the excitonically coupled B820 bacteriochlorophylls in LH3 using femtosecond transient absorption spectroscopy, deconvolution of steady-state absorption spectra, and modeling of the electrostatic intermolecular interactions using a charge density coupling approach. Compared to LH2, the upper excitonic level is red-shifted from 755 to 790 nm and is associated with an approximate 2-fold decrease of B820 intrapigment coupling. The absorption properties of LH3 cannot be reproduced by only changing the B850 site energy but also require a different scaling factor to be used to calculate interpigment couplings and a change of histidine protonation state. Several protonation patterns for distinct amino acid groups are presented, giving values of 162-173 cm(-1) at 100 K for the intradimer resonance interaction in the B820 ring.
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Affiliation(s)
- Jevgenij Chmeliov
- Institute of Physics, Center for Physical Sciences and Technology , Gostauto 11, LT-01108 Vilnius, Lithuania
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70
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Shibata Y, Nishi S, Kawakami K, Shen JR, Renger T. Photosystem II does not possess a simple excitation energy funnel: time-resolved fluorescence spectroscopy meets theory. J Am Chem Soc 2013; 135:6903-14. [PMID: 23537277 PMCID: PMC3650659 DOI: 10.1021/ja312586p] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The experimentally
obtained time-resolved fluorescence spectra
of photosystem II (PS II) core complexes, purified from a thermophilic
cyanobacterium Thermosynechococcus vulcanus, at 5–180 K are compared with simulations. Dynamic localization
effects of excitons are treated implicitly by introducing exciton
domains of strongly coupled pigments. Exciton relaxations within a
domain and exciton transfers between domains are treated on the basis
of Redfield theory and generalized Förster theory, respectively.
The excitonic couplings between the pigments are calculated by a quantum
chemical/electrostatic method (Poisson-TrEsp). Starting with previously
published values, a refined set of site energies of the pigments is
obtained through optimization cycles of the fits of stationary optical
spectra of PS II. Satisfactorily agreement between the experimental
and simulated spectra is obtained for the absorption spectrum including
its temperature dependence and the linear dichroism spectrum of PS
II core complexes (PS II-CC). Furthermore, the refined site energies
well reproduce the temperature dependence of the time-resolved fluorescence
spectrum of PS II-CC, which is characterized by the emergence of a
695 nm fluorescence peak upon cooling down to 77 K and the decrease
of its relative intensity upon further cooling below 77 K. The blue
shift of the fluorescence band upon cooling below 77 K is explained
by the existence of two red-shifted chlorophyll pools emitting at
around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43
in CP43 (Chl numbering according to the nomenclature of Loll et al. Nature2005, 438, 1040) while
the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll
is suggested to attract excitations from the peripheral light-harvesting
complexes and might also be involved in photoprotection.
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Affiliation(s)
- Yutaka Shibata
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya, Japan.
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71
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König C, Neugebauer J. Protein Effects on the Optical Spectrum of the Fenna–Matthews–Olson Complex from Fully Quantum Chemical Calculations. J Chem Theory Comput 2013; 9:1808-20. [DOI: 10.1021/ct301111q] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Carolin König
- Theoretische Organische
Chemie, Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster,
Germany
| | - Johannes Neugebauer
- Theoretische Organische
Chemie, Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster,
Germany
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72
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Viani L, Curutchet C, Mennucci B. Spatial and Electronic Correlations in the PE545 Light-Harvesting Complex. J Phys Chem Lett 2013; 4:372-377. [PMID: 26281726 DOI: 10.1021/jz301987u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The recent discovery of long-lasting quantum coherence effects in photosynthetic pigment-protein complexes has challenged our view of the role that protein motions play in light-harvesting processes. Several groups have suggested that correlated fluctuations involving the pigments site energies and couplings could be at the origin of such unexpected behavior. Here we combine molecular dynamics simulations with quantum mechanics/molecular mechanics calculations to analyze the degree of correlated fluctuations in the PE545 complex of Rhodomonas sp. strain CS24. We find that correlations between the motions of the chromophores, which are significantly assisted by the water solvent, do not translate into appreciable site energy correlations but do lead to significant cross-correlations of energies and couplings. Such behavior, not observed in a recent study on the Fenna-Mathews-Olson complex, seems to provide phycobiliproteins with an additional fundamental mechanism to control quantum coherence and light-harvesting efficiency compared with chlorophyll-containing complexes.
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Affiliation(s)
- Lucas Viani
- †Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Carles Curutchet
- ‡Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- †Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
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73
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Renger T, Müh F. Understanding photosynthetic light-harvesting: a bottom up theoretical approach. Phys Chem Chem Phys 2013; 15:3348-71. [PMID: 23361062 DOI: 10.1039/c3cp43439g] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Linz, Austria.
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74
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Zarea M, Powell D, Renaud N, Wasielewski MR, Ratner MA. Decoherence and Quantum Interference in a Four-Site Model System: Mechanisms and Turnovers. J Phys Chem B 2013; 117:1010-20. [DOI: 10.1021/jp3102942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mahdi Zarea
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Daniel Powell
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Nicolas Renaud
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Mark A. Ratner
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
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75
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Renger T, Klinger A, Steinecker F, Schmidt am Busch M, Numata J, Müh F. Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons. J Phys Chem B 2012; 116:14565-80. [PMID: 23163520 PMCID: PMC3557933 DOI: 10.1021/jp3094935] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/19/2012] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
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76
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Renaud N, Powell D, Zarea M, Movaghar B, Wasielewski MR, Ratner MA. Quantum Interferences and Electron Transfer in Photosystem I. J Phys Chem A 2012; 117:5899-908. [DOI: 10.1021/jp308216y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Daniel Powell
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Mahdi Zarea
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Bijan Movaghar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
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77
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Curutchet C, Novoderezhkin VI, Kongsted J, Muñoz-Losa A, van Grondelle R, Scholes GD, Mennucci B. Energy Flow in the Cryptophyte PE545 Antenna Is Directed by Bilin Pigment Conformation. J Phys Chem B 2012; 117:4263-73. [DOI: 10.1021/jp305033d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica,
Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | | | - Jacob Kongsted
- Department
of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Aurora Muñoz-Losa
- Dipartimento di Chimica e Chimica
Industriale, Università di Pisa,
via Risorgimento 35, 56126 Pisa, Italy
| | - Rienk van Grondelle
- Department of Physics and Astronomy,
Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gregory D. Scholes
- Department of Chemistry, 80 St. George
Street, Institute for Optical Sciences, and Centre for Quantum Information
and Quantum Control, University of Toronto, Toronto, Ontario, M5S 3H6 Canada
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica
Industriale, Università di Pisa,
via Risorgimento 35, 56126 Pisa, Italy
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78
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Kim HW, Kelly A, Park JW, Rhee YM. All-Atom Semiclassical Dynamics Study of Quantum Coherence in Photosynthetic Fenna–Matthews–Olson Complex. J Am Chem Soc 2012; 134:11640-51. [DOI: 10.1021/ja303025q] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyun Woo Kim
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Aaron Kelly
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Jae Woo Park
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Young Min Rhee
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
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79
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Rancova O, Sulskus J, Abramavicius D. Insight into the Structure of Photosynthetic LH2 Aggregate from Spectroscopy Simulations. J Phys Chem B 2012; 116:7803-14. [DOI: 10.1021/jp302817p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Olga Rancova
- Department of Theoretical
Physics, Vilnius University, Saulėtekio
al. 9-III, LT-10222
Vilnius, Lithuania
| | - Juozas Sulskus
- Department of Theoretical
Physics, Vilnius University, Saulėtekio
al. 9-III, LT-10222
Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical
Physics, Vilnius University, Saulėtekio
al. 9-III, LT-10222
Vilnius, Lithuania
- State
Key Laboratory of Supramolecular
Structure and Materials, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
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80
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Müh F, Madjet MEA, Renger T. Structure-based simulation of linear optical spectra of the CP43 core antenna of photosystem II. PHOTOSYNTHESIS RESEARCH 2012; 111:87-101. [PMID: 21809112 DOI: 10.1007/s11120-011-9675-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 07/18/2011] [Indexed: 05/31/2023]
Abstract
The linear optical spectra (absorbance, linear dichroism, circular dichroism, fluorescence) of the CP43 (PsbC) antenna of the photosystem II core complex (PSIIcc) pertaining to the S(0) → S(1) (Q(Y)) transitions of the chlorophyll (Chl) a pigments are simulated by applying a combined quantum chemical/electrostatic method to obtain excitonic couplings and local transition energies (site energies) on the basis of the 2.9 Å resolution crystal structure (Guskov et al., Nat Struct Mol Biol 16:334-342, 2009). The electrostatic calculations identify three Chls with low site energies (Chls 35, 37, and 45 in the nomenclature of Loll et al. (Nature 438:1040-1044, 2005). A refined simulation of experimental spectra of isolated CP43 suggests a modified set of site energies within 143 cm(-1) of the directly calculated values (root mean square deviation: 80 cm(-1)). In the refined set, energy sinks are at Chls 37, 43, and 45 in agreement with earlier fitting results (Raszewski and Renger, J Am Chem Soc 130:4431-4446, 2008). The present structure-based simulations reveal that a large part of the redshift of Chl 37 is due to a digalactosyldiacylglycerol lipid. This finding suggests a new role for lipids in PSIIcc, namely the tuning of optical spectra and the creation of an excitation energy funnel towards the reaction center. The analysis of electrostatic pigment-protein interactions is used to identify amino acid residues that are of potential interest for an experimental approach to an assignment of site energies and energy sinks by site-directed mutagenesis.
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Affiliation(s)
- Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria.
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81
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Renger T, Müh F. Theory of excitonic couplings in dielectric media : foundation of Poisson-TrEsp method and application to photosystem I trimers. PHOTOSYNTHESIS RESEARCH 2012; 111:47-52. [PMID: 21912923 DOI: 10.1007/s11120-011-9685-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/25/2011] [Indexed: 05/20/2023]
Abstract
The Poisson-TrEsp method (where TrEsp stands for transition charges from electrostatic potentials) has been successfully applied to calculate excitonic couplings in a variety of pigment-protein complexes. It relies on an isomorphism that allows for relating the excitonic coupling between transition densities in dielectric media to their Coulomb coupling. This isomorphism was derived by Hsu et al. (J. Chem. Phys. 114, 3065, (2001)) using time-dependent density functional response theory. In this article, we provide an alternative and simple derivation by first-order perturbation theory. An application of Poisson-TrEsp to photosystem I trimers reveals that the local field correction/screening factor depends on the mutual orientation of the pigments and on the dielectric boundaries rather than on distance. A mean correction factor of f = 0.69 is determined for this system.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria.
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82
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Müh F, Renger T. Refined structure-based simulation of plant light-harvesting complex II: linear optical spectra of trimers and aggregates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1446-60. [PMID: 22387396 DOI: 10.1016/j.bbabio.2012.02.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 02/09/2012] [Accepted: 02/15/2012] [Indexed: 11/27/2022]
Abstract
Linear optical spectra of solubilized trimers and small lamellar aggregates of the major light-harvesting complex II (LHCII) of higher plants are simulated employing excitonic couplings and site energies of chlorophylls (Chls) computed on the basis of the two crystal structures by a combined quantum chemical/electrostatic approach. A good agreement between simulation and experiment is achieved (except for the circular dichroism in the Chl b region), if vibronic transitions of Chls are taken into account. Site energies are further optimized by refinement fits of optical spectra. The differences between refined and directly calculated values are not significant enough to decide, whether the crystal structures are closer to trimers or aggregates. Changes in the linear dichroism spectrum upon aggregation are related to site energy shifts of Chls b601, b607, a603, a610, and a613, and are interpreted in terms of conformational changes of violaxanthin and the two luteins involving their ionone rings. Chl a610 is the energy sink at 77K in both conformations. An analysis of absorption spectra of trimers perpendicular and parallel to the C(3)-axis (van Amerongen et al. Biophys. J. 67 (1994) 837-847) shows that only Chl a604 close to neoxanthin is significantly reoriented in trimers compared to the crystal structures. Whether this pigment is orientated in aggregates as in the crystal structures, can presently not be determined faithfully. To finally decide about pigment reorientations that could be of relevance for non-photochemical quenching, further polarized absorption and fluorescence measurements of aggregates or detergent-depleted LHCII would be helpful. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Affiliation(s)
- Frank Müh
- Johannes Kepler Universitat Linz, Linz, Austria.
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83
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Jing Y, Zheng R, Li HX, Shi Q. Theoretical Study of the Electronic–Vibrational Coupling in the Qy States of the Photosynthetic Reaction Center in Purple Bacteria. J Phys Chem B 2012; 116:1164-71. [DOI: 10.1021/jp209575q] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yuanyuan Jing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Renhui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Hui-Xue Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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84
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Utecht M, Klamroth T, Saalfrank P. Optical absorption and excitonic coupling in azobenzenes forming self-assembled monolayers: a study based on density functional theory. Phys Chem Chem Phys 2011; 13:21608-14. [PMID: 22071571 DOI: 10.1039/c1cp22793a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the analysis of optical absorption spectra, it has recently been speculated that the excitonic coupling between individual azobenzene-functionalized alkanethiols arranged in a self-assembled monolayer (SAM) on a gold surface could be strong enough to hinder collective trans-cis isomerization-on top of steric hindrance [Gahl et al., J. Am. Chem. Soc., 2010, 132, 1831]. Using models of SAMs of increasing complexity (dimer, linear N-mers, and two-dimensionally arranged N-mers) and density functional theory on the (TD-) B3LYP/6-31G* level, we determine optical absorption spectra, the nature and magnitude of excitonic couplings, and the corresponding spectral shifts. It is found that at inter-monomer distances of about 20 Å and above, TD-B3LYP excitation frequencies (and signal intensities) can be well described by the frequently used point-dipole approximation. Further, calculated blue shifts in optical absorption spectra account for the experimental observations made for azobenzene/gold SAMs, and hint to the fact that they can indeed be responsible for reduced switching probability in densely packed self-assembled structures.
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Affiliation(s)
- Manuel Utecht
- Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
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85
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König C, Neugebauer J. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. Chemphyschem 2011; 13:386-425. [PMID: 22287108 DOI: 10.1002/cphc.201100408] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Indexed: 11/07/2022]
Abstract
The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.
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Affiliation(s)
- Carolin König
- Institute for Physical and Theoretical Chemistry, Technical University Braunschweig, Braunschweig, Germany
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86
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Vassiliev S, Mahboob A, Bruce D. Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes. PHOTOSYNTHESIS RESEARCH 2011; 110:25-38. [PMID: 21964859 DOI: 10.1007/s11120-011-9689-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 09/15/2011] [Indexed: 05/26/2023]
Abstract
The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or "site." Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment-proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment-protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna-Mathews-Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.
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Affiliation(s)
- Serguei Vassiliev
- Department of Biology, Brock University, 500 Glenridge Avenue, St. Catharines, ON L2S 3A1, Canada.
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87
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Mennucci B, Curutchet C. The role of the environment in electronic energy transfer: a molecular modeling perspective. Phys Chem Chem Phys 2011; 13:11538-50. [PMID: 21597605 DOI: 10.1039/c1cp20601j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The key role of the environment in electronic energy transfer has been underscored in recent experimental and theoretical studies. In this perspective, we provide an overview of novel quantum-mechanical methodologies aimed at describing environment effects in energy transfers. The techniques described include continuum dielectric and atomistic descriptions of the surroundings. We discuss the advantages and limitations of each technique, as well as the main insights that have emerged from their application to solvated dyads and photosynthetic pigment-protein complexes. We finally highlight the aspects that still need to be solved in order to provide a full theoretical route to the study of energy transfer phenomena in complex environments.
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Affiliation(s)
- Benedetta Mennucci
- Department of Chemistry, University of Pisa, via Risorgimento 35, 56126 Pisa, Italy.
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88
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Renger T, Schlodder E. Optical properties, excitation energy and primary charge transfer in photosystem II: theory meets experiment. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2011; 104:126-41. [PMID: 21531572 DOI: 10.1016/j.jphotobiol.2011.03.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 03/04/2011] [Accepted: 03/21/2011] [Indexed: 11/29/2022]
Abstract
In this review we discuss structure-function relationships of the core complex of photosystem II, as uncovered from analysis of optical spectra of the complex and its subunits. Based on descriptions of optical difference spectra including site directed mutagenesis we propose a revision of the multimer model of the symmetrically arranged reaction center pigments, described by an asymmetric exciton Hamiltonian. Evidence is provided for the location of the triplet state, the identity of the primary electron donor, the localization of the cation and the secondary electron transfer pathway in the reaction center. We also discuss the stationary and time-dependent optical properties of the CP43 and CP47 subunits and the excitation energy transfer and trapping-by-charge-transfer kinetics in the core complex.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität, Abteilung Theoretische Biophysik, Austria.
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89
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König C, Neugebauer J. First-principles calculation of electronic spectra of light-harvesting complex II. Phys Chem Chem Phys 2011; 13:10475-90. [PMID: 21369568 DOI: 10.1039/c0cp02808h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a fully quantum chemical investigation of important structural and environmental effects on the site energies of chlorophyll pigments in green-plant light-harvesting complex II (LHC II). Among the tested factors are technical and structural aspects as well as effects of neighboring residues and exciton couplings in the chlorophyll network. By employing a subsystem time-dependent density functional theory (TDDFT) approach based on the frozen density embedding (FDE) method we are able to determine site energies and electronic couplings separately in a systematic way. This approach allows us to treat much larger systems in a quantum chemical way than would be feasible with a conventional density functional theory. Based on this method, we have simulated a series of mutagenesis experiments to investigate the effect of a lack of one pigment in the chlorophyll network on the excitation properties of the other pigments. From these calculations, we can conclude that conformational changes within the chlorophyll molecules, direct interactions with neighboring residues, and interactions with other chlorophyll pigments can lead to non-negligible changes in excitation energies. All of these factors are important when site energies shall be calculated with high accuracy. Moreover, the redistribution of the oscillator strengths due to exciton coupling has a large impact on the calculated absorption spectra. This indicates that modeling mutagenesis experiments requires us to consider the entire set of chlorophyll molecules in the wild type and in the mutant, rather than just considering the missing chlorophyll pigment. An analysis of the mixing of particular excitations and the coupling elements in the FDEc calculation indicates that some pigments in the chlorophyll network act as bridges which mediate the interaction between other pigments. These bridges are also supported by the calculations on the "mutants" lacking the bridging pigment.
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Affiliation(s)
- Carolin König
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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90
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Schmidt Am Busch M, Müh F, El-Amine Madjet M, Renger T. The Eighth Bacteriochlorophyll Completes the Excitation Energy Funnel in the FMO Protein. J Phys Chem Lett 2011; 2:93-98. [PMID: 26295526 DOI: 10.1021/jz101541b] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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.
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Affiliation(s)
- Marcel Schmidt Am Busch
- †Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- ‡Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| | - Mohamed El-Amine Madjet
- ‡Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| | - Thomas Renger
- †Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Strasse 69, 4040 Linz, Austria
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91
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Müh F, Madjet MEA, Renger T. Structure-Based Identification of Energy Sinks in Plant Light-Harvesting Complex II. J Phys Chem B 2010; 114:13517-35. [DOI: 10.1021/jp106323e] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frank Müh
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, D-14195 Berlin, Germany, and Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Mohamed El-Amine Madjet
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, D-14195 Berlin, Germany, and Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, D-14195 Berlin, Germany, and Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
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