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Forde A, Maity S, Freixas VM, Fernandez-Alberti S, Neukirch AJ, Kleinekathöfer U, Tretiak S. Stabilization of Charge-Transfer Excited States in Biological Systems: A Computational Focus on the Special Pair in Photosystem II Reaction Centers. J Phys Chem Lett 2024; 15:4142-4150. [PMID: 38593451 DOI: 10.1021/acs.jpclett.4c00362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Charge-transfer (CT) excited states play an important role in many biological processes. However, many computational approaches often inadequately address the equilibration effects of nuclear and environmental degrees of freedom on these states. One prominent example of systems in which CT states are of utmost importance is reaction centers (RC) in photosystems. Here we use a multiscale approach combined with time-dependent density functional theory to explore the lowest CT excited state of the special pair PD1-PD2 in the Photosystem II-RC of a cyanobacterium. We find that the nonequilibrium CT excited state resides near the Soret band, making an exciton the lowest-energy excited state. However, accounting for nuclear and state-specific dielectric equilibration along the CT potential energy surface (PES), the CT state PD1--PD2+ stabilizes energetically below the excitonic state. This underscores the crucial role of state-specific solvation in mapping the PES of CT states, as demonstrated in a simplified dimer model.
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Affiliation(s)
- Aaron Forde
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sayan Maity
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Victor M Freixas
- Departamento de Ciencia y Tecnologiia, Univresidad Nacional de Quilmes/CONICET, B1876BXD Bernal, Argentina
| | | | - Amanda J Neukirch
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | | | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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2
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Runeson JE, Fay TP, Manolopoulos DE. Exciton dynamics from the mapping approach to surface hopping: comparison with Förster and Redfield theories. Phys Chem Chem Phys 2024; 26:4929-4938. [PMID: 38265093 PMCID: PMC10849040 DOI: 10.1039/d3cp05926j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
We compare the recently introduced multi-state mapping approach to surface hopping (MASH) with the Förster and Redfield theories of excitation energy transfer. Whereas Förster theory relies on weak coupling between chromophores, and Redfield theory assumes the electronic excitations to be weakly coupled to fast chromophore vibrations, MASH is free from any perturbative or Markovian approximations. We illustrate this with an example application to the rate of energy transfer in a Frenkel-exciton dimer, showing that MASH interpolates correctly between the opposing regimes in which the Förster and Redfield results are reliable. We then compare the three methods for a realistic model of the Fenna-Matthews-Olson complex with a structured vibrational spectral density and static disorder in the excitation energies. In this case there are no exact results for comparison so we use MASH to assess the validity of Förster and Redfield theories. We find that Förster theory is the more accurate of the two on the picosecond timescale, as has been shown previously for a simpler model of this particular light-harvesting complex. We also explore various ways to sample the initial electronic state in MASH and find that they all give very similar results for exciton dynamics.
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Affiliation(s)
- Johan E Runeson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Thomas P Fay
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David E Manolopoulos
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.
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3
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Razjivin AP, Kozlovsky VS, Ashikhmin AA, Pishchalnikov RY. Gaussian Decomposition vs. Semiclassical Quantum Simulation: Obtaining the High-Order Derivatives of a Spectrum in the Case of Photosynthetic Pigment Optical Properties Studying. SENSORS (BASEL, SWITZERLAND) 2023; 23:8248. [PMID: 37837078 PMCID: PMC10574941 DOI: 10.3390/s23198248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
In this paper, a procedure for obtaining undistorted high derivatives (up to the eighth order) of the optical absorption spectra of biomolecule pigments has been developed. To assess the effectiveness of the procedure, the theoretical spectra of bacteriochlorophyll a, chlorophyll a, spheroidene, and spheroidenone were simulated by fitting the experimental spectra using the differential evolution algorithm. The experimental spectra were also approximated using sets of Gaussians to calculate the model absorption spectra. Theoretical and model spectra can be differentiated without smoothing (high-frequency noise filtering) to obtain high derivatives. Superimposition of the noise track on the model spectra allows us to obtain test spectra similar to the experimental ones. Comparison of the high derivatives of the model spectra with those of the test spectra allows us to find the optimal parameters of the filter, the application of which leads to minimal differences between the high derivatives of the model and test spectra. For all four studied pigments, it was shown that smoothing the experimental spectra with optimal filters makes it possible to obtain the eighth derivatives of the experimental spectra, which were close to the eighth derivatives of their theoretical spectra.
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Affiliation(s)
- Andrei P. Razjivin
- Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia;
| | - Vladimir S. Kozlovsky
- Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia;
| | - Aleksandr A. Ashikhmin
- Institute of Basic Biological Problems, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Roman Y. Pishchalnikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia
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4
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Thwaites O, Christianson BM, Cowan AJ, Jäckel F, Liu LN, Gardner AM. Unravelling the Roles of Integral Polypeptides in Excitation Energy Transfer of Photosynthetic RC-LH1 Supercomplexes. J Phys Chem B 2023; 127:7283-7290. [PMID: 37556839 PMCID: PMC10461223 DOI: 10.1021/acs.jpcb.3c04466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/24/2023] [Indexed: 08/11/2023]
Abstract
Elucidating the photosynthetic processes that occur within the reaction center-light-harvesting 1 (RC-LH1) supercomplexes from purple bacteria is crucial for uncovering the assembly and functional mechanisms of natural photosynthetic systems and underpinning the development of artificial photosynthesis. Here, we examined excitation energy transfer of various RC-LH1 supercomplexes of Rhodobacter sphaeroides using transient absorption spectroscopy, coupled with lifetime density analysis, and studied the roles of the integral transmembrane polypeptides, PufX and PufY, in energy transfer within the RC-LH1 core complex. Our results show that the absence of PufX increases both the LH1 → RC excitation energy transfer lifetime and distribution due to the role of PufX in defining the interaction and orientation of the RC within the LH1 ring. While the absence of PufY leads to the conformational shift of several LH1 subunits toward the RC, it does not result in a marked change in the excitation energy transfer lifetime.
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Affiliation(s)
- Owen Thwaites
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Physics, University of Liverpool, Liverpool L69 7ZE, U.K.
| | - Bern M. Christianson
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Alexander J. Cowan
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Frank Jäckel
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Physics, University of Liverpool, Liverpool L69 7ZE, U.K.
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
- College
of Marine Life Sciences, and Frontiers Science Center for Deep Ocean
Multispheres and Earth System, Ocean University
of China, Qingdao 266003, China
| | - Adrian M. Gardner
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
- Early Career
Laser Laboratory, University of Liverpool, Liverpool L69 3BX, U.K.
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5
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Cina JA. Dynamics of an excitation-transfer trimer: Interference, coherence, Berry's phase development, and vibrational control of non-adiabaticity. J Chem Phys 2023; 158:124307. [PMID: 37003733 DOI: 10.1063/5.0139174] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
We detail several interesting features in the dynamics of an equilaterally shaped electronic excitation-transfer (EET) trimer with distance-dependent intermonomer excitation-transfer couplings. In the absence of electronic-vibrational coupling, symmetric and antisymmetric superpositions of two single-monomer excitations are shown to exhibit purely constructive, oscillatory, and purely destructive interference in the EET to the third monomer, respectively. In the former case, the transfer is modulated by motion in the symmetrical framework-expansion vibration induced by the Franck-Condon excitation. Distortions in the shape of the triangular framework degrade that coherent EET while activating excitation transfer in the latter case of an antisymmetric initial state. In its symmetrical configuration, two of the three single-exciton states of the trimer are degenerate. This degeneracy is broken by the Jahn-Teller-active framework distortions. The calculations illustrate closed, approximately circular pseudo-rotational wave-packet dynamics on both the lower and the upper adiabatic potential energy surfaces of the degenerate manifold, which lead to the acquisition after one cycle of physically meaningful geometric (Berry) phases of π. Another manifestation of Berry-phase development is seen in the evolution of the vibrational probability density of a wave packet on the lower Jahn-Teller adiabatic potential comprising a superposition of clockwise and counterclockwise circular motions. The circular pseudo-rotation on the upper cone is shown to stabilize the adiabatic electronic state against non-adiabatic internal conversion via the conical intersection, a dynamical process analogous to Slonczewski resonance. Strategies for initiating and monitoring these various dynamical processes experimentally using pre-resonant impulsive Raman excitation, short-pulse absorption, and multi-dimensional wave-packet interferometry are outlined in brief.
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Affiliation(s)
- Jeffrey A Cina
- Department of Chemistry and Biochemistry, Oregon Center for Optical, Molecular, and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
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Kundu S, Dani R, Makri N. Tight inner ring architecture and quantum motion of nuclei enable efficient energy transfer in bacterial light harvesting. SCIENCE ADVANCES 2022; 8:eadd0023. [PMID: 36288310 PMCID: PMC9604522 DOI: 10.1126/sciadv.add0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
The efficient, directional transfer of absorbed solar energy between photosynthetic light-harvesting complexes continues to pose intriguing questions. In this work, we identify the pathways of energy flow between the B800 and B850 rings in the LH2 complex of Rhodopseudomonas molischianum using fully quantum mechanical path integral methods to simulate the excited-state dynamics of the 24 bacteriochlorophyll molecules and their coupling to 50 normal mode vibrations in each chromophore. While all pigments are identical, the tighter packing of the inner B850 ring is responsible for the thermodynamic stabilization of the inner ring. Molecular vibrations enable the 1-ps flow of energy to the B850 states, which would otherwise be kinetically inaccessible. A classical treatment of the vibrations leads to uniform equilibrium distribution of the excitation, with only 67% transferred to the inner ring. However, spontaneous fluctuations associated with the quantum motion of the nuclei increase the transfer efficiency to 90%.
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Affiliation(s)
- Sohang Kundu
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Reshmi Dani
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Nancy Makri
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
- Department of Physics, University of Illinois, Urbana, IL 61801, USA
- Illinois Quantum Information Science and Technology Center, University of Illinois, Urbana, IL 61801, USA
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Runeson JE, Lawrence JE, Mannouch JR, Richardson JO. Explaining the Efficiency of Photosynthesis: Quantum Uncertainty or Classical Vibrations? J Phys Chem Lett 2022; 13:3392-3399. [PMID: 35404611 PMCID: PMC9036581 DOI: 10.1021/acs.jpclett.2c00538] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Photosynthetic organisms are known to use a mechanism of vibrationally assisted exciton energy transfer to efficiently harvest energy from light. The importance of quantum effects in this mechanism is a long-standing topic of debate, which has traditionally focused on the role of excitonic coherences. Here, we address another recent claim: that the efficient energy transfer in the Fenna-Matthews-Olson complex relies on nuclear quantum uncertainty and would not function if the vibrations were classical. We present a counter-example to this claim, showing by trajectory-based simulations that a description in terms of quantum electrons and classical nuclei is indeed sufficient to describe the funneling of energy to the reaction center. We analyze and compare these findings to previous classical-nuclear approximations that predicted the absence of an energy funnel and conclude that the key difference and the reason for the discrepancy is the ability of the trajectories to properly account for Newton's third law.
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Do TN, Nguyen HL, Caffarri S, Tan HS. Two-dimensional electronic spectroscopy of the Q x to Q y relaxation of chlorophylls a in photosystem II core complex. J Chem Phys 2022; 156:145102. [DOI: 10.1063/5.0079500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using two-dimensional electronic spectroscopy, we measured the Qx to Qy transfer dynamics of the chlorophyll a (Chl a) manifold in the photosystem II (PSII) monomeric core complex from Arabidopsis thaliana. A PSII monomeric core consists of 35 Chls a and no Chl b, thus allowing for a clear window to study Chl a Qx dynamics in a large pigment-protein complex. Initial excitation in the Qx band results in a transfer to the Qy band in less than 60 fs. Upon the ultrafast transfer, regardless of the excitation frequency within the Qx band, the quasi-transient absorption spectra are very similar. This observation indicates that Chl a’s Qx to Qy transfer is not frequency selective. Using a simple model, we determined that this is not due to the lifetime broadening of the ultrafast transfer but predominantly due to a lack of correlation between the PSII core complex’s Chl a Qx and Qy bands. We suggest the origin to be the intrinsic loss of correlation during the Qx to Qy internal conversion as observed in previous studies of molecular Chl a dissolved in solvents.
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Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Stefano Caffarri
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, LGBP Team, 13009 Marseille, France
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
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Searching for a Unique Exciton Model of Photosynthetic Pigment–Protein Complexes: Photosystem II Reaction Center Study by Differential Evolution. MATHEMATICS 2022. [DOI: 10.3390/math10060959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Studying the optical properties of photosynthetic pigment–protein complexes (PPCs) in the visible light range, both experimentally and theoretically, is one of the ways of gaining knowledge about the function of the photosynthetic machinery of living species. To simulate the PPC optical response, it is necessary to use semiclassical theories describing the effect of external fields–matter interaction, energy migration in molecular crystals, and electron–phonon coupling. In this paper, we report the results of photosystem II reaction center (PSIIRC) linear optical response simulations. Applying the multimode Brownian oscillator model and the theory of molecular excitons, we have demonstrated that the absorption, circular and linear dichroism, and steady-state fluorescence of PSIIRC can be accurately fitted with the help of differential evolution (DE), the multiparametric evolutionary optimization algorithm. To explore the effectiveness of DE, we used the simulated experimental data as the target functions instead of those actually measured. Only 2 of 10 DE strategies have shown the best performance of the optimization algorithm. With the best tuning parameters of DE/rand-to-best/1/exp strategy determined from the strategy tests, we found the exact solution for the PSIIRC exciton model and fitted the spectra with a reasonable convergence rate.
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10
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Chrysafoudi A, Maity S, Kleinekathöfer U, Daskalakis V. Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study. J Phys Chem Lett 2021; 12:9626-9633. [PMID: 34585934 DOI: 10.1021/acs.jpclett.1c02498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diatoms generate a large portion of the oxygen produced on earth due to their exceptional light-harvesting properties involving fucoxanthin and chlorophyll-binding proteins (FCP). At the same time, an efficient adaptation of these complexes to fluctuating light conditions is necessary to protect the diatoms against photodamage. So far, structural and dynamic data for the interaction between FCP and the photoprotective LHCX family of proteins in diatoms are lacking. In this computational study, we provide a structural basis for a remarkable pH-dependent adaptation at the molecular level. Upon binding of the LHCX1 protein to the FCP complex together with a change in pH, conformational changes within the FCP protein result in a variation of the electronic coupling in a specific chlorophyll-fucoxanthin pair, leading to a change in the exciton transfer rate by almost an order of magnitude. A common strategy for photoprotection between diatoms and higher plants is identified and discussed.
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Affiliation(s)
- Anthi Chrysafoudi
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3603 Limassol, Cyprus
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11
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The Relationship between the Spatial Arrangement of Pigments and Exciton Transition Moments in Photosynthetic Light-Harvesting Complexes. Int J Mol Sci 2021; 22:ijms221810031. [PMID: 34576194 PMCID: PMC8470053 DOI: 10.3390/ijms221810031] [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: 08/19/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Considering bacteriochlorophyll molecules embedded in the protein matrix of the light-harvesting complexes of purple bacteria (known as LH2 and LH1-RC) as examples of systems of interacting pigment molecules, we investigated the relationship between the spatial arrangement of the pigments and their exciton transition moments. Based on the recently reported crystal structures of LH2 and LH1-RC and the outcomes of previous theoretical studies, as well as adopting the Frenkel exciton Hamiltonian for two-level molecules, we performed visualizations of the LH2 and LH1 exciton transition moments. To make the electron transition moments in the exciton representation invariant with respect to the position of the system in space, a system of pigments must be translated to the center of mass before starting the calculations. As a result, the visualization of the transition moments for LH2 provided the following pattern: two strong transitions were outside of LH2 and the other two were perpendicular and at the center of LH2. The antenna of LH1-RC was characterized as having the same location of the strongest moments in the center of the complex, exactly as in the B850 ring, which actually coincides with the RC. Considering LH2 and LH1 as supermolecules, each of which has excitation energies and corresponding transition moments, we propose that the outer transitions of LH2 can be important for inter-complex energy exchange, while the inner transitions keep the energy in the complex; moreover, in the case of LH1, the inner transitions increased the rate of antenna-to-RC energy transfer.
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