1
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Demchenko AP. Excitonic Properties of Organic Dye Aggregates: Contribution of Ukrainian Science. CHEM REC 2024; 24:e202300290. [PMID: 37873897 DOI: 10.1002/tcr.202300290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/08/2023] [Indexed: 10/25/2023]
Abstract
Unexpected discovery that molecules of organic dyes when they form regular structures can change dramatically their light absorption and fluorescence properties were attracting the minds of researchers for more than eight decades. The progress in investigation of this unique phenomenon described in terms of H- and J-aggregation has led to many practical applications. Here the author expresses his personal view on the dramatic story of switching this research area from empirical knowledge to that standing on strong background of molecular exciton theory. The author was a witness of some of these events and acquainted with several great personalities involved. The major trends of future developments are highlighted.
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Affiliation(s)
- Alexander P Demchenko
- Palladin Institute of Biochemistry, Leontovicha st. 9, Kyiv, 01030, Ukraine
- Yuriy Fedkovych National University, Chernivtsi, 58012, Ukraine
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2
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Timpmann K, Rätsep M, Freiberg A. Enhancing solar spectrum utilization in photosynthesis: exploring exciton and site energy shifts as key mechanisms. Sci Rep 2023; 13:22299. [PMID: 38102394 PMCID: PMC10724156 DOI: 10.1038/s41598-023-49729-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Photosynthesis is a critical process that harnesses solar energy to sustain life across Earth's intricate ecosystems. Central to this phenomenon is nuanced adaptation to a spectrum spanning approximately from 300 nm to nearly 1100 nm of solar irradiation, a trait enabling plants, algae, and phototrophic bacteria to flourish in their respective ecological niches. While the Sun's thermal radiance and the Earth's atmospheric translucence naturally constrain the ultraviolet extent of this range, a comprehension of how to optimize the utilization of near-infrared light has remained an enduring pursuit. This study unveils the remarkable capacity of the bacteriochlorophyll b-containing purple photosynthetic bacterium Blastochloris viridis to harness solar energy at extreme long wavelengths, a property attributed to a synergistic interplay of exciton and site energy shift mechanisms. Understanding the unique native adaptation mechanisms offers promising prospects for advancing sustainable energy technologies of solar energy conversion.
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Affiliation(s)
- Kõu Timpmann
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411, Tartu, Estonia.
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia.
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3
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Timpmann K, Rätsep M, Freiberg A. Dominant role of excitons in photosynthetic color-tuning and light-harvesting. Front Chem 2023; 11:1231431. [PMID: 37908232 PMCID: PMC10613661 DOI: 10.3389/fchem.2023.1231431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
Photosynthesis is a vital process that converts sunlight into energy for the Earth's ecosystems. Color adaptation is crucial for different photosynthetic organisms to thrive in their ecological niches. Although the presence of collective excitons in light-harvesting complexes is well known, the role of delocalized excited states in color tuning and excitation energy transfer remains unclear. This study evaluates the characteristics of photosynthetic excitons in sulfur and non-sulfur purple bacteria using advanced optical spectroscopic techniques at reduced temperatures. The exciton effects in these bacteriochlorophyll a-containing species are generally much stronger than in plant systems that rely on chlorophylls. Their exciton bandwidth varies based on multiple factors such as chromoprotein structure, surroundings of the pigments, carotenoid content, hydrogen bonding, and metal ion inclusion. The study nevertheless establishes a linear relationship between the exciton bandwidth and Qy singlet exciton absorption peak, which in case of LH1 core complexes from different species covers almost 130 nm. These findings provide important insights into bacterial color tuning and light-harvesting, which can inspire sustainable energy strategies and devices.
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Affiliation(s)
- Kõu Timpmann
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
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4
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Cupellini L, Qian P, Nguyen-Phan TC, Gardiner AT, Cogdell RJ. Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex. PHOTOSYNTHESIS RESEARCH 2023; 156:75-87. [PMID: 35672557 PMCID: PMC10070313 DOI: 10.1007/s11120-022-00925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique near-infrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
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Affiliation(s)
- Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Nordic 5, 5651 GTC, Eindhoven, The Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 01, Třeboň, Czech Republic
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
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5
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Turn-on Fluorescence of Davydov-Split Aggregate Particles for Protein Detection. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Mao R, Wang X, Gao J. Bridging Carotenoid-to-Bacteriochlorophyll Energy Transfer of Purple Bacteria LH2 With Temperature Variations: Insights From Conformational Changes. Front Chem 2021; 9:764107. [PMID: 34671594 PMCID: PMC8521103 DOI: 10.3389/fchem.2021.764107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Photosynthesis is a key process for converting light energy into chemical energy and providing food for lives on Earth. Understanding the mechanism for the energy transfers could provide insights into regulating energy transfers in photosynthesis and designing artificial photosynthesis systems. Many efforts have been devoted to exploring the mechanism of temperature variations affecting the excitonic properties of LH2. In this study, we performed all-atom molecular dynamics (MD) simulations and quantum mechanics calculations for LH2 complex from purple bacteria along with its membrane environment under three typical temperatures: 270, 300, and 330 K. The structural analysis from validated MD simulations showed that the higher temperature impaired interactions at N-terminus of both α and β polypeptide helices and led to the dissociation of this hetero polypeptide dimer. Rhodopin-β-D-glucosides (RG1) moved centripetally with α polypeptide helices when temperature increased and enlarged their distances with bacteriochlorophylls molecules that have the absorption peak at 850 nm (B850), which resulted in reducing the coupling strengths between RG1 and B850 molecules. The present study reported a cascading mechanism for temperature regulating the energy transfers in LH2 of purple bacteria.
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Affiliation(s)
- Ruichao Mao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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Timpmann K, Rätsep M, Kangur L, Lehtmets A, Wang-Otomo ZY, Freiberg A. Exciton Origin of Color-Tuning in Ca 2+-Binding Photosynthetic Bacteria. Int J Mol Sci 2021; 22:ijms22147338. [PMID: 34298960 PMCID: PMC8303132 DOI: 10.3390/ijms22147338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
Flexible color adaptation to available ecological niches is vital for the photosynthetic organisms to thrive. Hence, most purple bacteria living in the shade of green plants and algae apply bacteriochlorophyll a pigments to harvest near infra-red light around 850–875 nm. Exceptions are some Ca2+-containing species fit to utilize much redder quanta. The physical basis of such anomalous absorbance shift equivalent to ~5.5 kT at ambient temperature remains unsettled so far. Here, by applying several sophisticated spectroscopic techniques, we show that the Ca2+ ions bound to the structure of LH1 core light-harvesting pigment–protein complex significantly increase the couplings between the bacteriochlorophyll pigments. We thus establish the Ca-facilitated enhancement of exciton couplings as the main mechanism of the record spectral red-shift. The changes in specific interactions such as pigment–protein hydrogen bonding, although present, turned out to be secondary in this regard. Apart from solving the two-decade-old conundrum, these results complement the list of physical principles applicable for efficient spectral tuning of photo-sensitive molecular nano-systems, native or synthetic.
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Affiliation(s)
- Kõu Timpmann
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | - Liina Kangur
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | - Alexandra Lehtmets
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | | | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
- Correspondence:
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Biaggne A, Knowlton WB, Yurke B, Lee J, Li L. Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations. Molecules 2021; 26:molecules26030524. [PMID: 33498306 PMCID: PMC7863957 DOI: 10.3390/molecules26030524] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of withdrawing substituents (W-W pairs) exhibiting the most negative solvation energies, suggesting dyes with W-W pairs are more soluble than others. With respect to pristine Cy5, the transition dipole moment was relatively unaffected upon substitution while numerous W-W pairs and pairs of donating and withdrawing substituents (D-W pairs) enhanced the static dipole difference. The increase in static dipole difference was correlated with an increase in the magnitude of the sum of the Hammett constants of the substituents on the dye. The results of this study provide insight into how specific substituents affect Cy5 monomers and which pairs can be used to engineer dyes with desired properties.
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
- Correspondence:
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Reddy NR, Rhodes S, Ma Y, Fang J. Davydov Split Aggregates of Cyanine Dyes on Self-Assembled Nanotubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13649-13655. [PMID: 33143426 DOI: 10.1021/acs.langmuir.0c02537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Davydov splitting of dye aggregates represents unique molecular excitons. In this paper, we report the formation of Davydov split aggregates of 3,3'-diethylthiacarbocyanine iodide (DiSC2 (3)) and 3,3'-diethylthiadicarbocyanine iodide (DiSC2 (5)) templated by the helical nanotubes of lithocholic acid (LCA). The templated Davydiv split aggregates show a strong J-band and a weak H-band in the adsorption spectra. As the LCA helical nanotubes transform into a straight shape, the relative intensities of the J-band and the H-band of the templated Davydov split aggregates become roughly equal. The twisted angle change of the transition moment of DiSC2 (3) and DiSC2 (5) molecules in the templated Davydov split aggregates in response to the helical-to-straight shape transformation of LCA nanotubes is estimated. The templated Dvaydov split aggregates with well-defined shapes and molecular excitons are of interest for artificial light-harvesting and optoelectronic devices.
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Affiliation(s)
- Nitin Ramesh Reddy
- Department of Materials Science and Engineering and Advanced Materials Processing and Analysis Center, University of Central Florida, Orlando, Florida 32816, United States
| | - Samuel Rhodes
- Department of Materials Science and Engineering and Advanced Materials Processing and Analysis Center, University of Central Florida, Orlando, Florida 32816, United States
| | - Yiping Ma
- Department of Materials Science and Engineering and Advanced Materials Processing and Analysis Center, University of Central Florida, Orlando, Florida 32816, United States
| | - Jiyu Fang
- Department of Materials Science and Engineering and Advanced Materials Processing and Analysis Center, University of Central Florida, Orlando, Florida 32816, United States
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10
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Cupellini L, Lipparini F, Cao J. Absorption and Circular Dichroism Spectra of Molecular Aggregates With the Full Cumulant Expansion. J Phys Chem B 2020; 124:8610-8617. [PMID: 32901476 PMCID: PMC7901647 DOI: 10.1021/acs.jpcb.0c05180] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic
techniques such as linear absorption and circular dichroism. To compare calculated
Hamiltonians to experiments, a lineshape theory is needed, which takes into account the
coupling of the excitons with inter- and intramolecular vibrations. This coupling is
normally introduced in a perturbative way through the cumulant expansion formalism and
further approximated by assuming a Markovian exciton dynamics, for example with the
modified Redfield theory. Here, we present the implementation of the full cumulant
expansion (FCE) formalism (J. Chem.
Phys.142, 2015, 09410625747060) to
efficiently compute absorption and circular dichroism spectra of molecular aggregates
beyond the Markov approximation, without restrictions on the form of
exciton–phonon coupling. By employing the LH2 system of purple bacteria as a
challenging test case, we compare the FCE lineshapes with the Markovian lineshapes
obtained with the modified Redfield theory, showing that the latter presents a less
satisfying agreement with experiments. The FCE approach instead accurately describes the
lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the
FCE approach will become a valuable tool for accurately comparing model exciton
Hamiltonians with optical spectroscopy experiments.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Kangur L, Rätsep M, Timpmann K, Wang-Otomo ZY, Freiberg A. The two light-harvesting membrane chromoproteins of Thermochromatium tepidum expose distinct robustness against temperature and pressure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148205. [PMID: 32305413 DOI: 10.1016/j.bbabio.2020.148205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/17/2020] [Accepted: 04/14/2020] [Indexed: 01/26/2023]
Abstract
An increased robustness against high temperature and the much red-shifted near-infrared absorption spectrum of excitons in the LH1-RC core pigment-protein complex from the thermophilic photosynthetic purple sulfur bacterium Thermochromatium tepidum has recently attracted much interest. In the present work, thermal and hydrostatic pressure stability of the peripheral LH2 and core LH1-RC complexes from this bacterium were in parallel investigated by various optical spectroscopy techniques applied over a wide spectral range from far-ultraviolet to near-infrared. In contrast to expectations, very distinct robustness of the complexes was established, while the sturdiness of LH2 surpassed that of LH1-RC both with respect to temperatures between 288 and 360 K, and pressures between 1 bar and 14 kbar. Subtle structural variances related to the hydrogen bond network are likely responsible for the extra stability of LH2.
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Affiliation(s)
- Liina Kangur
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | | | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia; Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia.
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Bold BM, Sokolov M, Maity S, Wanko M, Dohmen PM, Kranz JJ, Kleinekathöfer U, Höfener S, Elstner M. Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes. Phys Chem Chem Phys 2020; 22:10500-10518. [PMID: 31950960 DOI: 10.1039/c9cp05753f] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.
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Affiliation(s)
- Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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Cardoso Ramos F, Nottoli M, Cupellini L, Mennucci B. The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling. Chem Sci 2019; 10:9650-9662. [PMID: 32055335 PMCID: PMC6988754 DOI: 10.1039/c9sc02886b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022] Open
Abstract
The light-harvesting in photosynthetic purple bacteria can be tuned in response to the light conditions during cell growth. One of the used strategies is to change the energy of the excitons in the major fight-harvesting complex, commonly known as LH2. In the present study we report the first systematic investigation of the microscopic origin of the exciton tuning using three complexes, namely the common (high-light) and the low-light forms of LH2 from Rps. acidophila plus a third complex analogous to the PucD complex from Rps. palustris. The study is based on the combination of classical molecular dynamics of each complex in a lipid membrane and excitonic calculations based on a multiscale quantum mechanics/molecular mechanics approach including a polarizable embedding. From the comparative analysis, it comes out that the mechanisms that govern the adaptation of the complex to different light conditions use the different H-bonding environment around the bacteriochlorophyll pigments to dynamically control both internal and inter-pigment degrees of freedom. While the former have a large effect on the site energies, the latter significantly change the electronic couplings, but only the combination of the two effects can fully reproduce the tuning of the final excitons and explain the observed spectroscopic differences.
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Affiliation(s)
- Felipe Cardoso Ramos
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
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Nottoli M, Stamm B, Scalmani G, Lipparini F. Quantum Calculations in Solution of Energies, Structures, and Properties with a Domain Decomposition Polarizable Continuum Model. J Chem Theory Comput 2019; 15:6061-6073. [DOI: 10.1021/acs.jctc.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benjamin Stamm
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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16
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Nottoli M, Jurinovich S, Cupellini L, Gardiner AT, Cogdell R, Mennucci B. The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria. PHOTOSYNTHESIS RESEARCH 2018; 137:215-226. [PMID: 29502240 DOI: 10.1007/s11120-018-0492-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/23/2018] [Indexed: 05/21/2023]
Abstract
The LH2 antenna complexes of purple bacteria occur, depending on light conditions, in various different spectroscopic forms, with a similar structure but different absorption spectra. The differences are related to point changes in the primary amino acid sequence, but the molecular-level relationship between these changes and the resulting spectrum is still not well understood. We undertook a systematic quantum chemical analysis of all the main factors that contribute to the exciton structure, looking at how the environment modulates site energies and couplings in the B800-850 and B800-820 spectroscopic forms of LH2. A multiscale approach combining quantum chemistry and an atomistic classical embedding has been used where mutual polarization effects between the two parts are taken into account. We find that the loss of hydrogen bonds following amino acid changes can only explain a part of the observed blue-shift in the B850 band. The coupling of excitonic states to charge-transfer states, which is different in the two forms, contributes with a similar amount to the overall blue-shift.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Alastair T Gardiner
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow, G12 8TA, Scotland, UK
| | - Richard Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow, G12 8TA, Scotland, UK
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy.
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17
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Montemayor D, Rivera E, Jang SJ. Computational Modeling of Exciton-Bath Hamiltonians for Light Harvesting 2 and Light Harvesting 3 Complexes of Purple Photosynthetic Bacteria at Room Temperature. J Phys Chem B 2018. [PMID: 29533664 DOI: 10.1021/acs.jpcb.8b00358] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light harvesting 2 (LH2) complex is the primary component of the photosynthetic unit of purple bacteria that is responsible for harvesting and relaying excitons. The electronic absorption line shape of LH2 contains two major bands at 800 and 850 nm wavelength regions. Under low light conditions, some species of purple bacteria replace LH2 with light harvesting 3 (LH3), a variant form with almost the same structure as the former but with distinctively different spectral features. The major difference between the absorption line shapes of LH2 and LH3 is the shift of the 850 nm band of the former to a new 820 nm region. The microscopic origin of this difference has been the subject of some theoretical/computational investigations. However, the genuine molecular level source of such a difference is not clearly understood yet. This work reports a comprehensive computational study of LH2 and LH3 complexes so as to clarify different molecular level features of LH2 and LH3 complexes and to construct simple exciton-bath models with a common form. All-atomistic molecular dynamics simulations of both LH2 and LH3 complexes provide detailed molecular level structural differences of bacteriochlorophylls (BChls) in the two complexes, in particular, in their patterns of hydrogen bonding (HB) and torsional angles of the acetyl group. Time-dependent density functional theory calculation of the excitation energies of BChls for structures sampled from the MD simulations suggests that the observed differences in the HB and torsional angles cannot fully account for the experimentally observed spectral shift of LH3. Potential sources that can explain the actual spectral shift of LH3 are discussed, and their magnitudes are assessed through fitting of experimental line shapes. These results demonstrate the feasibility of developing simple exciton-bath models for both LH2 and LH3, which can be employed for large-scale exciton quantum dynamics in their aggregates.
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Affiliation(s)
- Daniel Montemayor
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Eva Rivera
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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18
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Cannon BL, Patten LK, Kellis DL, Davis PH, Lee J, Graugnard E, Yurke B, Knowlton WB. Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates. J Phys Chem A 2018; 122:2086-2095. [PMID: 29420037 DOI: 10.1021/acs.jpca.7b12668] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, we have demonstrated that our dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics, optical information processing, and quantum computing.
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Affiliation(s)
- Brittany L Cannon
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Lance K Patten
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Donald L Kellis
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
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19
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Pan J, Gelzinis A, Chorošajev V, Vengris M, Senlik SS, Shen JR, Valkunas L, Abramavicius D, Ogilvie JP. Ultrafast energy transfer within the photosystem II core complex. Phys Chem Chem Phys 2018; 19:15356-15367. [PMID: 28574545 DOI: 10.1039/c7cp01673e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.
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Affiliation(s)
- Jie Pan
- Department of Physics, University of Michigan, Ann Arbor, 48109, USA.
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20
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Rätsep M, Muru R, Freiberg A. High temperature limit of photosynthetic excitons. Nat Commun 2018; 9:99. [PMID: 29311621 PMCID: PMC5758513 DOI: 10.1038/s41467-017-02544-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/06/2017] [Indexed: 11/24/2022] Open
Abstract
Excitons in light-harvesting complexes are known to significantly improve solar-energy harnessing. Here we demonstrate photosynthetic excitons at super-physiological temperatures reaching 60–80 °C in different species of mesophilic photosynthetic bacteria. It is shown that the survival of light-harvesting excitons in the peripheral LH2 antennae is restricted by thermal decomposition of the pigment–protein complex rather than by any intrinsic property of excitons. The regular spatial organization of the bacteriochlorophyll a pigments supporting excitons in this complex is lost upon the temperature-induced breakdown of its tertiary structure. Secondary structures of the complexes survive even higher temperatures. The discovered pivotal role of the protein scaffold in the stabilization of excitons comprises an important aspect of structure–function relationship in biology. These results also intimately entangle the fundamental issues of quantum mechanical concepts in biology and in the folding of proteins. Excitons in light-harvesting complexes are known to significantly improve solar energy harnessing. Here, the authors investigate and explain extreme robustness against temperature of excitons in purple photosynthetic bacteria.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411, Tartu, Estonia
| | - Renata Muru
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411, Tartu, Estonia. .,Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
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21
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Cannon BL, Kellis DL, Patten LK, Davis PH, Lee J, Graugnard E, Yurke B, Knowlton WB. Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System. J Phys Chem A 2017; 121:6905-6916. [PMID: 28813152 DOI: 10.1021/acs.jpca.7b04344] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.
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Affiliation(s)
- Brittany L Cannon
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Donald L Kellis
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Lance K Patten
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
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22
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Chorošajev V, Marčiulionis T, Abramavicius D. Temporal dynamics of excitonic states with nonlinear electron-vibrational coupling. J Chem Phys 2017; 147:074114. [DOI: 10.1063/1.4985910] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Vladimir Chorošajev
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Tomas Marčiulionis
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
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23
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Ma F, Yu LJ, Llansola-Portoles MJ, Robert B, Wang-Otomo ZY, van Grondelle R. Metal Cations Induced αβ-BChl a
Heterogeneity in LH1 as Revealed by Temperature-Dependent Fluorescence Splitting. Chemphyschem 2017; 18:2295-2301. [DOI: 10.1002/cphc.201700551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/09/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Fei Ma
- Department of Biophysics; Faculty of Sciences; VU University Amsterdam; De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Long-Jiang Yu
- Faculty of Science; Ibaraki University; Mito Ibaraki 310-8512 Japan
| | - Manuel J. Llansola-Portoles
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Univ Paris-Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette cedex France
| | - Bruno Robert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Univ Paris-Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette cedex France
| | | | - Rienk van Grondelle
- Department of Biophysics; Faculty of Sciences; VU University Amsterdam; De Boelelaan 1081 1081 HV Amsterdam The Netherlands
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24
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Kell A, Jassas M, Acharya K, Hacking K, Cogdell RJ, Jankowiak R. Conformational Complexity in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum Revealed by Hole-Burning Spectroscopy. J Phys Chem A 2017; 121:4435-4446. [PMID: 28531352 DOI: 10.1021/acs.jpca.7b03188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800R and B800B. The energy differences between average site energies of conformations 1 and 2, and B800R and B800B are similar (∼200 cm-1), suggesting weak and strong hydrogen bonds linking two major subpopulations of BChls and the protein scaffolding. Although conformations 1 and 2 of the B850 chromophores, and B800R and B800B, exist in the ground state, selective excitation leads to 1 → 2 and B800R → B800B phototransformations. Different static inhomogeneous broadening is revealed for the lowest energy exciton states of B850 (fwhm ∼195 cm-1) and B800R (fwhm ∼140 cm-1). To describe the 5 K absorption spectrum and the above-mentioned conformations, we employ an exciton model with dichotomous protein conformation disorder. We show that both experimental data and the modeling study support a two-site model with strongly and weakly hydrogen-bonded B850 and B800 BChls, which under illumination undergo conformational changes, most likely caused by proton dynamics.
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Affiliation(s)
| | | | | | - Kirsty Hacking
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8TA, Scotland
| | - Richard J Cogdell
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8TA, Scotland
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25
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Segatta F, Cupellini L, Jurinovich S, Mukamel S, Dapor M, Taioli S, Garavelli M, Mennucci B. A Quantum Chemical Interpretation of Two-Dimensional Electronic Spectroscopy of Light-Harvesting Complexes. J Am Chem Soc 2017; 139:7558-7567. [DOI: 10.1021/jacs.7b02130] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Segatta
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), 38123 Trento, Italy
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi
13, 56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi
13, 56124 Pisa, Italy
| | - Shaul Mukamel
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Maurizio Dapor
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), 38123 Trento, Italy
| | - Simone Taioli
- European Center for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), 38123 Trento, Italy
- Faculty
of Mathematics and Physics, Charles University, Prague 116 36, Czech Republic
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi
13, 56124 Pisa, Italy
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26
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Chorošajev V, Gelzinis A, Valkunas L, Abramavicius D. Benchmarking the stochastic time-dependent variational approach for excitation dynamics in molecular aggregates. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Cupellini L, Jurinovich S, Campetella M, Caprasecca S, Guido CA, Kelly SM, Gardiner AT, Cogdell R, Mennucci B. An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence. J Phys Chem B 2016; 120:11348-11359. [PMID: 27791372 DOI: 10.1021/acs.jpcb.6b06585] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Marco Campetella
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Stefano Caprasecca
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Ciro A Guido
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Sharon M Kelly
- Life Sciences Biomolecular Sci, Joseph Black Building, University of Glasgow , Glasgow G12 8QQ, Scotland
| | - Alastair T Gardiner
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow , 126 University Place, Glasgow G12 8TA, Scotland
| | - Richard Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow , 126 University Place, Glasgow G12 8TA, Scotland
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
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28
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Freiberg A, Chenchiliyan M, Rätsep M, Timpmann K. Spectral and kinetic effects accompanying the assembly of core complexes of Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1727-1733. [PMID: 27514285 DOI: 10.1016/j.bbabio.2016.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/03/2016] [Accepted: 08/06/2016] [Indexed: 11/19/2022]
Abstract
In the present work, spectral and kinetic changes accompanying the assembly of the light-harvesting 1 (LH1) complex with the reaction center (RC) complex into monomeric RC-LH1 and dimeric RC-LH1-PufX core complexes of the photosynthetic purple bacterium Rhodobacter sphaeroides are systematically studied over the temperature range of 4.5-300K. The samples were interrogated with a combination of optical absorption, hole burning, fluorescence excitation, steady state and picosecond time resolved fluorescence spectroscopy. Fair additivity of the LH1 and RC absorption spectra suggests rather weak electronic coupling between them. A low-energy tail revealed at cryogenic temperatures in the absorption spectra of both monomeric and dimeric core complexes is proved to be due to the special pair of the RC. At selected excitation intensity and temperature, the fluorescence decay time of core complexes is shown to be a function of multiple factors, most importantly of the presence/absence of RCs, the supramolecular architecture (monomeric or dimeric) of the complexes, and whether the complexes were studied in a native membrane environment or in a detergent - purified state.
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Affiliation(s)
- Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Manoop Chenchiliyan
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia
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29
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Chorošajev V, Rancova O, Abramavicius D. Polaronic effects at finite temperatures in the B850 ring of the LH2 complex. Phys Chem Chem Phys 2016; 18:7966-77. [DOI: 10.1039/c5cp06871a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Energy transfer and relaxation dynamics in the B850 ring of LH2 molecular aggregates are described, taking into account the polaronic effects, by a stochastic time-dependent variational approach.
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Affiliation(s)
- Vladimir Chorošajev
- Department of Theoretical Physics
- Faculty of Physics
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | - Olga Rancova
- Department of Theoretical Physics
- Faculty of Physics
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics
- Faculty of Physics
- Vilnius University
- LT-10222 Vilnius
- Lithuania
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30
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Shi Y, Zhao NJ, Wang P, Fu LM, Yu LJ, Zhang JP, Wang-Otomo ZY. Thermal Adaptability of the Light-Harvesting Complex 2 from Thermochromatium tepidum: Temperature-Dependent Excitation Transfer Dynamics. J Phys Chem B 2015; 119:14871-9. [DOI: 10.1021/acs.jpcb.5b09023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Shi
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Ning-Jiu Zhao
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Peng Wang
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Li-Min Fu
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
| | - Long-Jiang Yu
- Faculty
of Science, Ibaraki University, Mito 310-8512, Japan
| | - Jian-Ping Zhang
- Department
of Chemistry, Renmin University of China, Beijing 1000872, P. R. China
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31
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Rätsep M, Pajusalu M, Linnanto JM, Freiberg A. Subtle spectral effects accompanying the assembly of bacteriochlorophylls into cyclic light harvesting complexes revealed by high-resolution fluorescence spectroscopy. J Chem Phys 2015; 141:155102. [PMID: 25338912 DOI: 10.1063/1.4897637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have observed that an assembly of the bacteriochloropyll a molecules into B850 and B875 groups of cyclic bacterial light-harvesting complexes LH2 and LH1, respectively, results an almost total loss of the intra-molecular vibronic structure in the fluorescence spectrum, and simultaneously, an essential enhancement of its phonon sideband due to electron-phonon coupling. While the suppression of the vibronic coupling in delocalized (excitonic) molecular systems is predictable, as also confirmed by our model calculations, a boost of the electron-phonon coupling is rather unexpected. The latter phenomenon is explained by exciton self-trapping, promoted by mixing the molecular exciton states with charge transfer states between the adjacent chromophores in the tightly packed B850 and B875 arrangements. Similar, although less dramatic trends were noted for the light-harvesting complexes containing chlorophyll pigments.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Mihkel Pajusalu
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | | | - Arvi Freiberg
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia and Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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32
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Schlau-Cohen GS. Principles of light harvesting from single photosynthetic complexes. Interface Focus 2015; 5:20140088. [PMID: 26052423 DOI: 10.1098/rsfs.2014.0088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Photosynthetic systems harness sunlight to power most life on Earth. In the initial steps of photosynthetic light harvesting, absorbed energy is converted to chemical energy with near-unity quantum efficiency. This is achieved by an efficient, directional and regulated flow of energy through a network of proteins. Here, we discuss the following three key principles of this flow and of photosynthetic light harvesting: thermal fluctuations of the protein structure; intrinsic conformational switches with defined functional consequences; and environmentally triggered conformational switches. Through these principles, photosynthetic systems balance two types of operational costs: metabolic costs, or the cost of maintaining and running the molecular machinery, and opportunity costs, or the cost of losing any operational time. Understanding how the molecular machinery and dynamics are designed to balance these costs may provide a blueprint for improved artificial light-harvesting devices. With a multi-disciplinary approach combining knowledge of biology, this blueprint could lead to low-cost and more effective solar energy conversion. Photosynthetic systems achieve widespread light harvesting across the Earth's surface; in the face of our growing energy needs, this is functionality we need to replicate, and perhaps emulate.
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Affiliation(s)
- G S Schlau-Cohen
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue, 6-225, Cambridge, MA 02139 , USA
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33
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Chorošajev V, Gelzinis A, Valkunas L, Abramavicius D. Dynamics of exciton-polaron transition in molecular assemblies: the variational approach. J Chem Phys 2015; 140:244108. [PMID: 24985619 DOI: 10.1063/1.4884275] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamics of excitonic polaron formation in molecular systems coupled to an overdamped bath are investigated using the Dirac-Frenkel variational principle and Davydov D1 Ansatz. Using a two-site model system we show that a few qualitatively distinct relaxation regimes of an optically created exciton are possible, depending on the timescale of bath fluctuations. A slow bath always leads to adiabatic polaron formation. Non-adiabatic exciton self-trapping occurs when the system is strongly coupled to a fast bath. Weak coupling to such bath does not perturb the excitonic picture. The complex system-bath dynamics can then be mapped to an effective model where the resonant coupling between sites is quenched during relaxation. The timescale of the polaron formation can be defined by the timescale of resonant coupling quenching, and is found to directly correlate with the bath relaxation time.
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Affiliation(s)
- Vladimir Chorošajev
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Andrius Gelzinis
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
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34
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Sawaya NPD, Huh J, Fujita T, Saikin SK, Aspuru-Guzik A. Fast delocalization leads to robust long-range excitonic transfer in a large quantum chlorosome model. NANO LETTERS 2015; 15:1722-1729. [PMID: 25694170 DOI: 10.1021/nl504399d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chlorosomes are efficient light-harvesting antennas containing up to hundreds of thousands of bacteriochlorophyll molecules. With massively parallel computer hardware, we use a nonperturbative stochastic Schrödinger equation, while including an atomistically derived spectral density, to study excitonic energy transfer in a realistically sized chlorosome model. We find that fast short-range delocalization leads to robust long-range transfer due to the antennae's concentric-roll structure. Additionally, we discover anomalous behavior arising from different initial conditions, and outline general considerations for simulating excitonic systems on the nanometer to micrometer scale.
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Affiliation(s)
- Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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35
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van der Vegte CP, Prajapati JD, Kleinekathöfer U, Knoester J, Jansen TLC. Atomistic Modeling of Two-Dimensional Electronic Spectra and Excited-State Dynamics for a Light Harvesting 2 Complex. J Phys Chem B 2015; 119:1302-13. [DOI: 10.1021/jp509247p] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. P. van der Vegte
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - J. D. Prajapati
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - U. Kleinekathöfer
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - J. Knoester
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - T. L. C. Jansen
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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36
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Pajusalu M, Kunz R, Rätsep M, Timpmann K, Köhler J, Freiberg A. Unified analysis of ensemble and single-complex optical spectral data from light-harvesting complex-2 chromoproteins for gaining deeper insight into bacterial photosynthesis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052709. [PMID: 26651725 DOI: 10.1103/physreve.92.052709] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 05/15/2023]
Abstract
Bacterial light-harvesting pigment-protein complexes are very efficient at converting photons into excitons and transferring them to reaction centers, where the energy is stored in a chemical form. Optical properties of the complexes are known to change significantly in time and also vary from one complex to another; therefore, a detailed understanding of the variations on the level of single complexes and how they accumulate into effects that can be seen on the macroscopic scale is required. While experimental and theoretical methods exist to study the spectral properties of light-harvesting complexes on both individual complex and bulk ensemble levels, they have been developed largely independently of each other. To fill this gap, we simultaneously analyze experimental low-temperature single-complex and bulk ensemble optical spectra of the light-harvesting complex-2 (LH2) chromoproteins from the photosynthetic bacterium Rhodopseudomonas acidophila in order to find a unique theoretical model consistent with both experimental situations. The model, which satisfies most of the observations, combines strong exciton-phonon coupling with significant disorder, characteristic of the proteins. We establish a detailed disorder model that, in addition to containing a C_{2}-symmetrical modulation of the site energies, distinguishes between static intercomplex and slow conformational intracomplex disorders. The model evaluations also verify that, despite best efforts, the single-LH2-complex measurements performed so far may be biased toward complexes with higher Huang-Rhys factors.
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Affiliation(s)
- Mihkel Pajusalu
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
| | - Ralf Kunz
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research, University of Bayreuth, 95440 Bayreuth, Germany
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
| | - Jürgen Köhler
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research, University of Bayreuth, 95440 Bayreuth, Germany
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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37
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Rancova O, Abramavicius D. Static and Dynamic Disorder in Bacterial Light-Harvesting Complex LH2: A 2DES Simulation Study. J Phys Chem B 2014; 118:7533-7540. [DOI: 10.1021/jp5043156] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Olga Rancova
- Department of Theoretical
Physics, Faculty of Physics, Vilnius University, Sauletekio av. 9 III bld., LT-10222 Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical
Physics, Faculty of Physics, Vilnius University, Sauletekio av. 9 III bld., LT-10222 Vilnius, Lithuania
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38
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Kunz R, Timpmann K, Southall J, Cogdell RJ, Köhler J, Freiberg A. Fluorescence-Excitation and Emission Spectra from LH2 Antenna Complexes of Rhodopseudomonas acidophila as a Function of the Sample Preparation Conditions. J Phys Chem B 2013; 117:12020-9. [DOI: 10.1021/jp4073697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ralf Kunz
- Experimental Physics
IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
| | - Kõu Timpmann
- Institute
of Physics, University of Tartu, Riia 142, Tartu EE-51014, Estonia
| | - June Southall
- Institute of Molecular,
Cell and Systems Biology, College of Medical, Veterinary and Life
Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular,
Cell and Systems Biology, College of Medical, Veterinary and Life
Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Jürgen Köhler
- Experimental Physics
IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
| | - Arvi Freiberg
- Institute
of Physics, University of Tartu, Riia 142, Tartu EE-51014, Estonia
- Institute of Molecular
and Cell Biology, University of Tartu, Riia 23, Tartu EE-51010, Estonia
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39
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Meldaikis J, Zerlauskiene O, Abramavicius D, Valkunas L. Manifestation of protein conformations in the B850 absorption band of light-harvesting complex LH2. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Linnanto JM, Korppi-Tommola JEI. Exciton Description of Chlorosome to Baseplate Excitation Energy Transfer in Filamentous Anoxygenic Phototrophs and Green Sulfur Bacteria. J Phys Chem B 2013; 117:11144-61. [DOI: 10.1021/jp4011394] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juha M. Linnanto
- Department of Chemistry, P.O.
Box 35, University of Jyväskylä, FIN-40014, Finland
- University of Tartu, Institute of Physics, Riia 142,
EE-51014 Tartu, Estonia
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41
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Structural implications of hydrogen-bond energetics in membrane proteins revealed by high-pressure spectroscopy. Biophys J 2013; 103:2352-60. [PMID: 23283234 DOI: 10.1016/j.bpj.2012.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/09/2012] [Accepted: 10/23/2012] [Indexed: 11/23/2022] Open
Abstract
The light-harvesting 1 (LH1) integral membrane complex of Rhodobacter sphaeroides provides a convenient model system in which to examine the poorly understood role of hydrogen bonds (H-bonds) as stabilizing factors in membrane protein complexes. We used noncovalently bound arrays of bacteriochlorophyll chromophores within native and genetically modified variants of LH1 complexes to monitor local changes in the chromophore binding sites induced by externally applied hydrostatic pressure. Whereas membrane-bound complexes demonstrated very high resilience to pressures reaching 2.1 GPa, characteristic discontinuous shifts and broadenings of the absorption spectra were observed around 1 GPa for detergent-solubilized proteins, in similarity to those observed when specific (α or β) H-bonds between the chromophores and the surrounding protein were selectively removed by mutagenesis. These pressure effects, which were reversible upon decompression, allowed us to estimate the rupture energies of H-bonds to the chromophores in LH1 complexes. A quasi-independent, additive role of H-bonds in the α- and β-sublattices in reinforcing the wild-type LH1 complex was established. A comparison of a reaction-center-deficient LH1 complex with complexes containing reaction centers also demonstrated a stabilizing effect of the reaction center. This study thus provides important insights into the design principles of natural photosynthetic complexes.
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42
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Freiberg A, Pajusalu M, Rätsep M. Excitons in intact cells of photosynthetic bacteria. J Phys Chem B 2013; 117:11007-14. [PMID: 23379598 DOI: 10.1021/jp3098523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Live cells and regular crystals seem fundamentally incompatible. Still, effects characteristic to ideal crystals, such as coherent sharing of excitation, have been recently used in many studies to explain the behavior of several photosynthetic complexes, especially the inner workings of the light-harvesting apparatus of the oldest known photosynthetic organisms, the purple bacteria. To this date, there has been no concrete evidence that the same effects are instrumental in real living cells, leaving a possibility that this is an artifact of unnatural study conditions, not a real effect relevant to the biological operation of bacteria. Hereby, we demonstrate survival of collective coherent excitations (excitons) in intact cells of photosynthetic purple bacteria. This is done by using excitation anisotropy spectroscopy for tracking the temperature-dependent evolution of exciton bands in light-harvesting systems of increasing structural complexity. The temperature was gradually raised from 4.5 K to ambient temperature, and the complexity of the systems ranged from detergent-isolated complexes to complete bacterial cells. The results provide conclusive evidence that excitons are indeed one of the key elements contributing to the energetic and dynamic properties of photosynthetic organisms.
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Affiliation(s)
- Arvi Freiberg
- Institute of Physics, University of Tartu , Riia 142, Tartu 51014, Estonia
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43
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Kunz R, Timpmann K, Southall J, Cogdell RJ, Freiberg A, Köhler J. Exciton Self Trapping in Photosynthetic Pigment–Protein Complexes Studied by Single-Molecule Spectroscopy. J Phys Chem B 2012; 116:11017-23. [DOI: 10.1021/jp3040456] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ralf Kunz
- Experimental Physics IV and
Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
| | - Kõu Timpmann
- Institute of Physics, University of Tartu, Riia 142, Tartu EE-51014, Estonia
| | - June Southall
- Institute of Molecular, Cell and
Systems Biology, College of Medical Veterinary and Life Sciences,
Biomedical Research Building, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular, Cell and
Systems Biology, College of Medical Veterinary and Life Sciences,
Biomedical Research Building, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Riia 142, Tartu EE-51014, Estonia
- Institute of Molecular and Cell
Biology, University of Tartu, Riia 23,
Tartu EE-51010, Estonia
| | - Jürgen Köhler
- Experimental Physics IV and
Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, 95440 Bayreuth, Germany
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44
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Zhao Y, Luo B, Zhang Y, Ye J. Dynamics of a Holstein polaron with off-diagonal coupling. J Chem Phys 2012; 137:084113. [PMID: 22938224 DOI: 10.1063/1.4748140] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yang Zhao
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798.
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45
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Trinkunas G, Zerlauskiene O, Urbonienė V, Chmeliov J, Gall A, Robert B, Valkunas L. Exciton Band Structure in Bacterial Peripheral Light-Harvesting Complexes. J Phys Chem B 2012; 116:5192-8. [DOI: 10.1021/jp302042w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gediminas Trinkunas
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu
Avenue 231, LT-02300 Vilnius, Lithuania
- Department of Theoretical Physics,
Faculty of Physics, Vilnius University,
Sauletekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Oksana Zerlauskiene
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu
Avenue 231, LT-02300 Vilnius, Lithuania
| | - Vidita Urbonienė
- Department of General Physics
and Spectroscopy, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Jevgenij Chmeliov
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu
Avenue 231, LT-02300 Vilnius, Lithuania
- Department of Theoretical Physics,
Faculty of Physics, Vilnius University,
Sauletekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Andrew Gall
- Institute of Biology and Technology of Saclay, CNRS-URA2096, CEA-Saclay,
91911 Gif sur Yvette, France
| | - Bruno Robert
- Institute of Biology and Technology of Saclay, CNRS-URA2096, CEA-Saclay,
91911 Gif sur Yvette, France
| | - Leonas Valkunas
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu
Avenue 231, LT-02300 Vilnius, Lithuania
- Department of Theoretical Physics,
Faculty of Physics, Vilnius University,
Sauletekio Avenue 9, LT-10222 Vilnius, Lithuania
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46
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Freiberg A, Rätsep M, Timpmann K. A comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded LH2 light-harvesting complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:1471-82. [PMID: 22172735 DOI: 10.1016/j.bbabio.2011.11.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/18/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
Integral membrane proteins constitute more than third of the total number of proteins present in organisms. Solubilization with mild detergents is a common technique to study the structure, dynamics, and catalytic activity of these proteins in purified form. However beneficial the use of detergents may be for protein extraction, the membrane proteins are often denatured by detergent solubilization as a result of native lipid membrane interactions having been modified. Versatile investigations of the properties of membrane-embedded and detergent-isolated proteins are, therefore, required to evaluate the consequences of the solubilization procedure. Herein, the spectroscopic and kinetic fingerprints have been established that distinguish excitons in individual detergent-solubilized LH2 light-harvesting pigment-protein complexes from them in the membrane-embedded complexes of purple photosynthetic bacteria Rhodobacter sphaeroides. A wide arsenal of spectroscopic techniques in visible optical range that include conventional broadband absorption-fluorescence, fluorescence anisotropy excitation, spectrally selective hole burning and fluorescence line-narrowing, and transient absorption-fluorescence have been applied over broad temperature range between physiological and liquid He temperatures. Significant changes in energetics and dynamics of the antenna excitons upon self-assembly of the proteins into intracytoplasmic membranes are observed, analyzed, and discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Affiliation(s)
- Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia.
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