1
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Varvelo L, Lynd JK, Citty B, Kühn O, Raccah DIGB. Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light-Harvesting 2 Antenna Nanoarray. J Phys Chem Lett 2023; 14:3077-3083. [PMID: 36947483 PMCID: PMC10069740 DOI: 10.1021/acs.jpclett.3c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
The photosynthetic apparatus of plants and bacteria combine atomically precise pigment-protein complexes with dynamic membrane architectures to control energy transfer on the 10-100 nm length scales. Recently, synthetic materials have integrated photosynthetic antenna proteins to enhance exciton transport, though the influence of artificial packing on the excited-state dynamics in these biohybrid materials is not fully understood. Here, we use the adaptive hierarchy of pure states (adHOPS) to perform a formally exact simulation of excitation energy transfer within artificial aggregates of light-harvesting complex 2 (LH2) with a range of packing densities. We find that LH2 aggregates support a remarkable exciton diffusion length ranging from 100 nm at a biological packing density to 300 nm at the densest packing previously suggested in an artificial aggregate. The unprecedented scale of these formally exact calculations also underscores the efficiency with which adHOPS simulates excited-state processes in molecular materials.
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Affiliation(s)
- Leonel Varvelo
- Department
of Chemistry, Southern Methodist University, P.O. Box 750314, Dallas, Texas 75275, United States
| | - Jacob K. Lynd
- Department
of Chemistry, Southern Methodist University, P.O. Box 750314, Dallas, Texas 75275, United States
| | - Brian Citty
- Department
of Chemistry, Southern Methodist University, P.O. Box 750314, Dallas, Texas 75275, United States
| | - Oliver Kühn
- Institute
of Physics, University of Rostock, Albert-Einstein-Strasse 23-24, 18059 Rostock, Germany
| | - Doran I. G. B. Raccah
- Department
of Chemistry, Southern Methodist University, P.O. Box 750314, Dallas, Texas 75275, United States
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2
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Onizhuk M, Sohoni S, Galli G, Engel GS. Spatial Patterns of Light-Harvesting Antenna Complex Arrangements Tune the Transfer-to-Trap Efficiency of Excitons in Purple Bacteria. J Phys Chem Lett 2021; 12:6967-6973. [PMID: 34283617 DOI: 10.1021/acs.jpclett.1c01537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In photosynthesis, the efficiency with which a photogenerated exciton reaches the reaction center is dictated by chromophore energies and the arrangement of chromophores in the supercomplex. Here, we explore the interplay between the arrangement of light-harvesting antennae and the efficiency of exciton transport in purple bacterial photosynthesis. Using a Miller-Abrahams-based exciton hopping model, we compare different arrangements of light-harvesting proteins on the intracytoplasmic membrane. We find that arrangements with aggregated LH1s have a higher efficiency than arrangements with randomly distributed LH1s in a wide range of physiological light fluences. This effect is robust to the introduction of defects on the intracytoplasmic membrane. Our result explains the absence of species with aggregated LH1 arrangements in low-light niches and the large increase seen in the expression of LH1 dimer complexes in high fluences. We suggest that the effect seen in our study is an adaptive strategy toward solar light fluence across different purple bacterial species.
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Affiliation(s)
- Mykyta Onizhuk
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Siddhartha Sohoni
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Giulia Galli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Gregory S Engel
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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3
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Tomasi S, Rouse DM, Gauger EM, Lovett BW, Kassal I. Environmentally Improved Coherent Light Harvesting. J Phys Chem Lett 2021; 12:6143-6151. [PMID: 34181855 DOI: 10.1021/acs.jpclett.1c01303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Coherence-enhanced light harvesting has not been directly observed experimentally, despite theoretical evidence that coherence can significantly enhance light-harvesting performance. The main experimental obstacle has been the difficulty in isolating the effect of coherence in the presence of confounding variables. Recent proposals for externally controlling coherence by manipulating the light's degree of polarization showed that coherent efficiency enhancements would be possible, but they were restricted to light-harvesting systems weakly coupled to their environment. Here, we show that increases in system-bath coupling strength can amplify coherent efficiency enhancements, rather than suppress them. This result dramatically broadens the range of systems that could be used to conclusively demonstrate coherence-enhanced light harvesting or to engineer coherent effects into artificial light-harvesting devices.
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Affiliation(s)
- Stefano Tomasi
- School of Chemistry and University of Sydney Nano Institute, University of Sydney Sydney, NSW 2006, Australia
| | - Dominic M Rouse
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Erik M Gauger
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K
| | - Brendon W Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Ivan Kassal
- School of Chemistry and University of Sydney Nano Institute, University of Sydney Sydney, NSW 2006, Australia
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4
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Schoffman H, Brown WM, Paltiel Y, Keren N, Gauger EM. Structure-based Hamiltonian model for IsiA uncovers a highly robust pigment-protein complex. J R Soc Interface 2020; 17:20200399. [PMID: 32842892 PMCID: PMC7482578 DOI: 10.1098/rsif.2020.0399] [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: 05/27/2020] [Accepted: 08/04/2020] [Indexed: 11/12/2022] Open
Abstract
The iron stress-induced protein A (IsiA) is a source of interest and debate in biological research. The IsiA supercomplex, binding over 200 chlorophylls, assembles in multimeric rings around photosystem I (PSI). Recently, the IsiA-PSI structure from Synechocystis sp. PCC 6803 was resolved to 3.48 Å. Based on this structure, we created a model simulating a single excitation event in an IsiA monomer. This model enabled us to calculate the fluorescence and the localization of the excitation in the IsiA structure. To further examine this system, noise was introduced to the model in two forms-thermal and positional. Introducing noise highlights the functional differences in the system between cryogenic temperatures and biologically relevant temperatures. Our results show that the energetics of the IsiA pigment-protein complex are very robust at room temperature. Nevertheless, shifts in the position of specific chlorophylls lead to large changes in their optical and fluorescence properties. Based on these results, we discuss the implication of highly robust structures, with potential for serving different roles in a context-dependent manner, on our understanding of the function and evolution of photosynthetic processes.
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Affiliation(s)
- Hanan Schoffman
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - William M. Brown
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Yossi Paltiel
- Applied Physics Department, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Erik M. Gauger
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
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5
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Tomasi S, Kassal I. Classification of Coherent Enhancements of Light-Harvesting Processes. J Phys Chem Lett 2020; 11:2348-2355. [PMID: 32119554 DOI: 10.1021/acs.jpclett.9b03490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Several kinds of coherence have recently been shown to affect the performance of light-harvesting systems, in some cases significantly improving their efficiency. Here, we classify the possible mechanisms of coherent efficiency enhancements, based on the types of coherence that can characterize a light-harvesting system and the types of processes these coherences can affect. We show that enhancements are possible only when coherences and dissipative effects are best described in different bases of states. Our classification allows us to predict a previously unreported coherent enhancement mechanism, where coherence between delocalized eigenstates can be used to localize excitons away from dissipation, thus reducing the rate of recombination and increasing efficiency.
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Affiliation(s)
- Stefano Tomasi
- School of Chemistry and University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Ivan Kassal
- School of Chemistry and University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
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6
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Claridge K, Padula D, Troisi A. On the arrangement of chromophores in light harvesting complexes: chance versus design. Faraday Discuss 2019; 221:133-149. [PMID: 31544201 DOI: 10.1039/c9fd00045c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used a homogeneous computational approach to derive the excitonic Hamiltonian for five light harvesting complexes containing only one type of chromophore and compare them in terms of statistical descriptors. We then studied the approximate exciton dynamics for the five complexes introducing a measure, the (averaged and time-dependent) inverse participation ratio, that enables the comparison between very diverse complexes on the same ground. We find that the global dynamics are very similar across the set of systems despite the variety of geometric structures of the complexes. In particular, the dynamics of four out of five light harvesting complexes are barely distinguishable with a small variation from the norm seen only for the Fenna-Matthews-Olson complex. We use the information from the realistic Hamiltonians to build a reduced model system that shows how the global dynamics are ultimately dominated by a single parameter, the degree of localization of the excitonic Hamiltonian eigenstates. Considering the physically plausible range of system parameters, the reduced model explains why the dynamics are so similar across most light harvesting complexes containing a single type of chromophore regardless of the detailed pattern of the inter-chromophore excitonic coupling.
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Affiliation(s)
- Kirsten Claridge
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK.
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7
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Bourne Worster S, Stross C, Vaughan FMWC, Linden N, Manby FR. Structure and Efficiency in Bacterial Photosynthetic Light Harvesting. J Phys Chem Lett 2019; 10:7383-7390. [PMID: 31714789 DOI: 10.1021/acs.jpclett.9b02625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photosynthetic organisms use networks of chromophores to absorb and deliver solar energy to reaction centers. We present a detailed model of the light-harvesting complexes in purple bacteria, including explicit interaction with sunlight, radiative and nonradiative energy loss, and dephasing and thermalizing effects of coupling to a vibrational bath. We capture the effect of slow vibrations by introducing time-dependent disorder. Our model describes the experimentally observed high efficiency of light harvesting, despite the absence of long-range quantum coherence. The one-exciton part of the quantum state fluctuates continuously but remains highly mixed at all times. These results suggest a relatively minor role for structure in determining efficiency. We build hypothetical models with randomly arranged chromophores but still observe high efficiency when nearest-neighbor distances are comparable to those in nature. This helps explain the high transport efficiency in organisms with widely differing antenna structures and suggests new design criteria for artificial light-harvesting devices.
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Affiliation(s)
- Susannah Bourne Worster
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
| | - Clement Stross
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
| | - Felix M W C Vaughan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
- Bristol Centre for Complexity Sciences , University of Bristol , Bristol BS2 8BB , U.K
| | - Noah Linden
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
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8
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Taylor N, Kassal I. Why are photosynthetic reaction centres dimeric? Chem Sci 2019; 10:9576-9585. [PMID: 32055331 PMCID: PMC6993572 DOI: 10.1039/c9sc03712h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 08/23/2019] [Indexed: 11/21/2022] Open
Abstract
All photosynthetic organisms convert solar energy into chemical energy through charge separation in dimeric reaction centres. It is unknown why early reaction centres dimerised and completely displaced their monomeric ancestors. Here, we discuss several proposed explanations for reaction-centre dimerism and conclude-with only weak assumptions about the primordial dimerisation event-that the most probable explanation for the dimerism is that it arose because it enhanced light-harvesting efficiency by deepening the excitonic trap, i.e., by enhancing the rate of exciton transfer from an antenna complex and decreasing the rate of back transfer. This effect would have outweighed the negative effect dimerisation would have had on charge transfer within the reaction centre. Our argument implies that dimerisation likely occurred after the evolution of the first antennas, and it explains why the lower-energy state of the special pair is bright.
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Affiliation(s)
- Natasha Taylor
- School of Chemistry and University of Sydney Nano Institute , University of Queensland , QLD 4072 , Australia
| | - Ivan Kassal
- School of Chemistry , University of Sydney Nano Institute , University of Sydney , NSW 2006 , Australia .
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9
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Brown WM, Gauger EM. Light Harvesting with Guide-Slide Superabsorbing Condensed-Matter Nanostructures. J Phys Chem Lett 2019; 10:4323-4329. [PMID: 31251067 DOI: 10.1021/acs.jpclett.9b01349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We establish design principles for light-harvesting antennae whose energy capture scales superlinearly with system size. Controlling the absorber dipole orientations produces sets of "guide-slide" states that promote steady-state superabsorbing characteristics in noisy condensed-matter nanostructures. Inspired by natural photosynthetic complexes, we discuss the example of ringlike dipole arrangements and show that, in our setup, vibrational relaxation enhances rather than impedes performance. Remarkably, the superabsorption effect proves to be robust to O(5%) disorder simultaneously for all relevant system parameters, showing promise for experimental exploration across a broad range of platforms.
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Affiliation(s)
- W M Brown
- SUPA, Institute of Photonics and Quantum Sciences , Heriot-Watt University , EH14 4AS Edinburgh , United Kingdom
| | - E M Gauger
- SUPA, Institute of Photonics and Quantum Sciences , Heriot-Watt University , EH14 4AS Edinburgh , United Kingdom
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10
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Rathbone HW, Davis JA, Michie KA, Goodchild SC, Robertson NO, Curmi PMG. Coherent phenomena in photosynthetic light harvesting: part two-observations in biological systems. Biophys Rev 2018; 10:1443-1463. [PMID: 30242555 PMCID: PMC6233342 DOI: 10.1007/s12551-018-0456-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/06/2018] [Indexed: 10/28/2022] Open
Abstract
Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or "quantum beats" via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.
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Affiliation(s)
- Harry W Rathbone
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Jeffery A Davis
- Centre for Quantum and Optical Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, 3122, Australia
| | - Katharine A Michie
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Sophia C Goodchild
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Neil O Robertson
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Paul M G Curmi
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia.
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11
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Du M, Martínez-Martínez LA, Ribeiro RF, Hu Z, Menon VM, Yuen-Zhou J. Theory for polariton-assisted remote energy transfer. Chem Sci 2018; 9:6659-6669. [PMID: 30310599 PMCID: PMC6115621 DOI: 10.1039/c8sc00171e] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022] Open
Abstract
Strong-coupling between light and matter produces hybridized states (polaritons) whose delocalization and electromagnetic character allow for novel modifications in spectroscopy and chemical reactivity of molecular systems. Recent experiments have demonstrated remarkable distance-independent long-range energy transfer between molecules strongly coupled to optical microcavity modes. To shed light on the mechanism of this phenomenon, we present the first comprehensive theory of polariton-assisted remote energy transfer (PARET) based on strong-coupling of donor and/or acceptor chromophores to surface plasmons. Application of our theory demonstrates that PARET up to a micron is indeed possible. In particular, we report two regimes for PARET: in one case, strong-coupling to a single type of chromophore leads to transfer mediated largely by surface plasmons while in the other case, strong-coupling to both types of chromophores creates energy transfer pathways mediated by vibrational relaxation. Importantly, we highlight conditions under which coherence enhances or deteriorates these processes. For instance, while exclusive strong-coupling to donors can enhance transfer to acceptors, the reverse turns out not to be true. However, strong-coupling to acceptors can shift energy levels in a way that transfer from acceptors to donors can occur, thus yielding a chromophore role-reversal or "carnival effect". This theoretical study demonstrates the potential for confined electromagnetic fields to control and mediate PARET, thus opening doors to the design of remote mesoscale interactions between molecular systems.
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Affiliation(s)
- Matthew Du
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093 , USA .
| | - Luis A Martínez-Martínez
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093 , USA .
| | - Raphael F Ribeiro
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093 , USA .
| | - Zixuan Hu
- Department of Chemistry , Department of Physics , Birck Nanotechnology Center , Purdue University , West Lafayette , IN 47907 , USA
- Qatar Environment and Energy Research Institute , College of Science and Engineering , HBKU , Doha , Qatar
| | - Vinod M Menon
- Department of Physics , City College , City University of New York , New York 10031 , USA
- Department of Physics , Graduate Center , City University of New York , New York 10016 , USA
| | - Joel Yuen-Zhou
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093 , USA .
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12
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Taylor NB, Kassal I. Generalised Marcus theory for multi-molecular delocalised charge transfer. Chem Sci 2018; 9:2942-2951. [PMID: 29732078 PMCID: PMC5915794 DOI: 10.1039/c8sc00053k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/11/2018] [Indexed: 01/07/2023] Open
Abstract
Transfer of charges delocalised over multiple molecules can be described using the properties of the component molecules.
Although Marcus theory is widely used to describe charge transfer in molecular systems, in its usual form it is restricted to transfer from one molecule to another. If a charge is delocalised across multiple donor molecules, this approach requires us to treat the entire donor aggregate as a unified supermolecule, leading to potentially expensive quantum-chemical calculations and making it more difficult to understand how the aggregate components contribute to the overall transfer. Here, we show that it is possible to describe charge transfer between groups of molecules in terms of the properties of the constituent molecules and couplings between them, obviating the need for expensive supermolecular calculations. We use the resulting theory to show that charge delocalisation between molecules in either the donor or acceptor aggregates can enhance the rate of charge transfer through a process we call supertransfer (or suppress it through subtransfer). The rate can also be enhanced above what is possible with a single donor and a single acceptor by judiciously tuning energy levels and reorganisation energies. We also describe bridge-mediated charge transfer between delocalised molecular aggregates. The equations of generalised Marcus theory are in closed form, providing qualitative insight into the impact of delocalisation on charge dynamics in molecular systems.
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Affiliation(s)
- Natasha B Taylor
- Centre for Engineered Quantum Systems and School of Mathematics and Physics , The University of Queensland , Queensland 4072 , Australia
| | - Ivan Kassal
- Centre for Engineered Quantum Systems and School of Mathematics and Physics , The University of Queensland , Queensland 4072 , Australia.,The University of Sydney Nano Institute and School of Chemistry , The University of Sydney , NSW 2006 , Australia .
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13
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Häse F, Kreisbeck C, Aspuru-Guzik A. Machine learning for quantum dynamics: deep learning of excitation energy transfer properties. Chem Sci 2017; 8:8419-8426. [PMID: 29619189 PMCID: PMC5863613 DOI: 10.1039/c7sc03542j] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Understanding the relationship between the structure of light-harvesting systems and their excitation energy transfer properties is of fundamental importance in many applications including the development of next generation photovoltaics. Natural light harvesting in photosynthesis shows remarkable excitation energy transfer properties, which suggests that pigment-protein complexes could serve as blueprints for the design of nature inspired devices. Mechanistic insights into energy transport dynamics can be gained by leveraging numerically involved propagation schemes such as the hierarchical equations of motion (HEOM). Solving these equations, however, is computationally costly due to the adverse scaling with the number of pigments. Therefore virtual high-throughput screening, which has become a powerful tool in material discovery, is less readily applicable for the search of novel excitonic devices. We propose the use of artificial neural networks to bypass the computational limitations of established techniques for exploring the structure-dynamics relation in excitonic systems. Once trained, our neural networks reduce computational costs by several orders of magnitudes. Our predicted transfer times and transfer efficiencies exhibit similar or even higher accuracies than frequently used approximate methods such as secular Redfield theory.
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Affiliation(s)
- Florian Häse
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; ; Tel: +1-617-384-8188
| | - Christoph Kreisbeck
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; ; Tel: +1-617-384-8188
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; ; Tel: +1-617-384-8188
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14
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A pathway for protective quenching in antenna proteins of Photosystem II. Sci Rep 2017; 7:2523. [PMID: 28566748 PMCID: PMC5451436 DOI: 10.1038/s41598-017-02892-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/19/2017] [Indexed: 11/08/2022] Open
Abstract
Photosynthesis is common in nature, converting sunlight energy into proton motive force and reducing power. The increased spectral range absorption of light exerted by pigments (i.e. chlorophylls, Chls) within Light Harvesting Complexes (LHCs) proves an important advantage under low light conditions. However, in the exposure to excess light, oxidative damages and ultimately cell death can occur. A down-regulatory mechanism, thus, has been evolved (non-photochemical quenching, NPQ). The mechanistic details of its major component (qE) are missing at the atomic scale. The research herein, initiates on solid evidence from the current NPQ state of the art, and reveals a detailed atomistic view by large scale Molecular Dynamics, Metadynamics and ab initio Simulations. The results demonstrate a complete picture of an elaborate common molecular design. All probed antenna proteins (major LHCII from spinach-pea, CP29 from spinach) show striking plasticity in helix-D, under NPQ conditions. This induces changes in Qy bands in excitation and absorption spectra of the near-by pigment pair (Chl613-614) that could emerge as a new quenching site. Zeaxanthin enhances this plasticity (and possibly the quenching) even at milder NPQ conditions.
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15
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Knee GC, Rowe P, Smith LD, Troisi A, Datta A. Structure-Dynamics Relation in Physically-Plausible Multi-Chromophore Systems. J Phys Chem Lett 2017; 8:2328-2333. [PMID: 28475337 DOI: 10.1021/acs.jpclett.7b00829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We study a large number of physically-plausible arrangements of chromophores, generated via a computational method involving stochastic real-space transformations of a naturally-occurring "reference" structure, illustrating our methodology using the well-studied Fenna-Matthews-Olson complex (FMO). To explore the idea that the natural structure has been tuned for efficient energy transport, we use an atomic transition charge method to calculate the excitonic couplings of each generated structure and a Lindblad master equation to study the quantum transport of an exciton from a "source" to a "drain" chromophore. We find significant correlations between structure and transport efficiency: High-performing structures tend to be more compact and, among those, the best structures display a certain orientation of the chromophores, particularly the chromophore closest to the source-to-drain vector. We conclude that, subject to reasonable, physically motivated constraints, the FMO complex is highly attuned to the purpose of energy transport, partly by exploiting these structural motifs.
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Affiliation(s)
| | - Patrick Rowe
- London Centre for Nanotechnology, Thomas Young Centre, and Department of Physics and Astronomy, University College London , 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | | | - Alessandro Troisi
- Department of Chemistry, University of Liverpool , Liverpool L69 7ZD, United Kingdom
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