1
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Dutta R, Cabral DGA, Lyu N, Vu NP, Wang Y, Allen B, Dan X, Cortiñas RG, Khazaei P, Schäfer M, Albornoz ACCD, Smart SE, Nie S, Devoret MH, Mazziotti DA, Narang P, Wang C, Whitfield JD, Wilson AK, Hendrickson HP, Lidar DA, Pérez-Bernal F, Santos LF, Kais S, Geva E, Batista VS. Simulating Chemistry on Bosonic Quantum Devices. J Chem Theory Comput 2024. [PMID: 39068594 DOI: 10.1021/acs.jctc.4c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Bosonic quantum devices offer a novel approach to realize quantum computations, where the quantum two-level system (qubit) is replaced with the quantum (an)harmonic oscillator (qumode) as the fundamental building block of the quantum simulator. The simulation of chemical structure and dynamics can then be achieved by representing or mapping the system Hamiltonians in terms of bosonic operators. In this Perspective, we review recent progress and future potential of using bosonic quantum devices for addressing a wide range of challenging chemical problems, including the calculation of molecular vibronic spectra, the simulation of gas-phase and solution-phase adiabatic and nonadiabatic chemical dynamics, the efficient solution of molecular graph theory problems, and the calculations of electronic structure.
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Affiliation(s)
- Rishab Dutta
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Delmar G A Cabral
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ningyi Lyu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Nam P Vu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Yuchen Wang
- Department of Chemistry, Department of Physics, and Purdue Quantum Science and Engineering Institute, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Xiaohan Dan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Rodrigo G Cortiñas
- Department of Applied Physics and Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Pouya Khazaei
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Max Schäfer
- Department of Applied Physics and Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Alejandro C C D Albornoz
- Department of Applied Physics and Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Scott E Smart
- Division of Physical Sciences, College of Letters and Science and Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Scott Nie
- Division of Physical Sciences, College of Letters and Science and Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Michel H Devoret
- Department of Applied Physics and Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - David A Mazziotti
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Prineha Narang
- Division of Physical Sciences, College of Letters and Science and Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Chen Wang
- Department of Physics, University of Massachusetts - Amherst, Amherst, Massachusetts 01003, United States
| | - James D Whitfield
- Department of Physics and Astronomy, Dartmouth College, Hanover, New Hampshire 01003, United States
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Daniel A Lidar
- Department of Electrical & Computer Engineering, Department of Chemistry, Department of Physics & Astronomy, and Center for Quantum Information Science & Technology, University of Southern California, Los Angeles, California 90089, United States
| | - Francisco Pérez-Bernal
- Departamento de Ciencias Integradas y Centro de Estudios Avanzados en Física, Matemáticas y Computación, Universidad de Huelva, Huelva 21071, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada 18071, Spain
| | - Lea F Santos
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Sabre Kais
- Department of Chemistry, Department of Physics, and Purdue Quantum Science and Engineering Institute, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
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2
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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3
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Lyu N, Miano A, Tsioutsios I, Cortiñas RG, Jung K, Wang Y, Hu Z, Geva E, Kais S, Batista VS. Mapping Molecular Hamiltonians into Hamiltonians of Modular cQED Processors. J Chem Theory Comput 2023; 19:6564-6576. [PMID: 37733472 DOI: 10.1021/acs.jctc.3c00620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
We introduce a general method based on the operators of the Dyson-Masleev transformation to map the Hamiltonian of an arbitrary model system into the Hamiltonian of a circuit Quantum Electrodynamics (cQED) processor. Furthermore, we introduce a modular approach to programming a cQED processor with components corresponding to the mapping Hamiltonian. The method is illustrated as applied to quantum dynamics simulations of the Fenna-Matthews-Olson (FMO) complex and the spin-boson model of charge transfer. Beyond applications to molecular Hamiltonians, the mapping provides a general approach to implement any unitary operator in terms of a sequence of unitary transformations corresponding to powers of creation and annihilation operators of a single bosonic mode in a cQED processor.
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Affiliation(s)
- Ningyi Lyu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alessandro Miano
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, United States
- Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Ioannis Tsioutsios
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, United States
- Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Rodrigo G Cortiñas
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, United States
- Department of Physics, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Kenneth Jung
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Yuchen Wang
- Department of Chemistry, Department of Physics and Purdue Quantum Science and Engineering Institute, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zixuan Hu
- Department of Chemistry, Department of Physics and Purdue Quantum Science and Engineering Institute, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sabre Kais
- Department of Chemistry, Department of Physics and Purdue Quantum Science and Engineering Institute, Purdue University, West Lafayette, Indiana 47907, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Yale Quantum Institute, Yale University, New Haven, Connecticut 06511, United States
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4
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Rolczynski BS, Díaz SA, Kim YC, Mathur D, Klein WP, Medintz IL, Melinger JS. Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms. Phys Chem Chem Phys 2023; 25:3651-3665. [PMID: 36648290 DOI: 10.1039/d2cp04960k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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5
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Heshmatpour C, Hauer J, Šanda F. Correlated spectral fluctuations quantified by line shape analysis of fifth-order two-dimensional electronic spectra. J Chem Phys 2022; 156:084114. [DOI: 10.1063/5.0081053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Correlated spectral fluctuations were suggested to coordinate excitation transport inside natural light harvesting complexes. We demonstrate the capacities of 2D line shapes from fifth-order coherent electronic signals (R5-2D) to report on such fluctuations in molecular aggregates and present a stochastic approach to fluctuations in correlated site and bi-exciton binding energies in the optical dynamics of Frenkel excitons. The model is applied to R5-2D line shapes of a homodimer, and we show that the peak tilt dynamics are a measure for site energy disorder, inter-site correlation, and the strength of bi-exciton binding energy fluctuations.
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Affiliation(s)
- Constantin Heshmatpour
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
- Professur für Dynamische Spektroskopien, Fakultät für Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching b. München, Germany
| | - Jürgen Hauer
- Professur für Dynamische Spektroskopien, Fakultät für Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching b. München, Germany
| | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
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6
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Mass OA, Wilson CK, Barcenas G, Terpetschnig EA, Obukhova OM, Kolosova OS, Tatarets AL, Li L, Yurke B, Knowlton WB, Pensack RD, Lee J. Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:3475-3488. [PMID: 35242270 PMCID: PMC8883467 DOI: 10.1021/acs.jpcc.1c08981] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/15/2022] [Indexed: 06/01/2023]
Abstract
Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn-Renger-May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm-1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
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Affiliation(s)
- Olga A. Mass
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - German Barcenas
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | | | - Olena M. Obukhova
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Olga S. Kolosova
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Anatoliy L. Tatarets
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Lan Li
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ryan. D. Pensack
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Chemistry and Biochemistry, Boise State
University, Boise, Idaho 83725, United
States
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7
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Cho KH, Rhee YM. Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes. Phys Chem Chem Phys 2021; 23:26623-26639. [PMID: 34842245 DOI: 10.1039/d1cp04615b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes.
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Affiliation(s)
- Kwang Hyun Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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8
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Rolczynski BS, Díaz SA, Kim YC, Medintz IL, Cunningham PD, Melinger JS. Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes. J Phys Chem A 2021; 125:9632-9644. [PMID: 34709821 DOI: 10.1021/acs.jpca.1c07205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Structural DNA nanotechnology is a promising approach to create chromophore networks with modular structures and Hamiltonians to control the material's functions. The functional behaviors of these systems depend on the interactions of the chromophores' vibronic states, as well as interactions with their environment. To optimize their functions, it is necessary to characterize the chromophore network's structural and energetic properties, including the electronic delocalization in some cases. In this study, parameters of interest are deduced in DNA-scaffolded Cyanine 3 and Cyanine 5 dimers. The methods include steady-state optical measurements, physical modeling, and a genetic algorithm approach. The parameters include the chromophore network's vibronic Hamiltonian, molecular positions, transition dipole orientations, and environmentally induced energy broadening. Additionally, the study uses temperature-dependent optical measurements to characterize the spectral broadening further. These combined results reveal the quantum mechanical delocalization, which is important for functions like coherent energy transport and quantum information applications.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Paul D Cunningham
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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9
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Du M, Qin M, Cui H, Wang C, Xu Y, Ma X, Yi X. Role of Spatially Correlated Fluctuations in Photosynthetic Excitation Energy Transfer with an Equilibrium and a Nonequilibrium Initial Bath. J Phys Chem B 2021; 125:6417-6430. [PMID: 34105973 DOI: 10.1021/acs.jpcb.1c02041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of excitation energy in photosynthetic light-harvesting complexes has inspired growing interest for its scientific and engineering significance. Recent experimental findings have suggested that spatially correlated environmental fluctuations may account for the existence of long-lived quantum coherent energy transfer observed even at physiological temperature. In this paper, we investigate the effects of spatial correlations on the excitation energy transfer dynamics by including a nonequilibrium initial bath in a simulated donor-acceptor model. The initial bath state, which is assumed to be either equilibrium or nonequilibrium, is expanded in powers of coupling strength within the polaron formalism of a quantum master equation. The spatial correlations of bath fluctuations strongly influence the decay of coherence in the dynamics. The role of a nonequilibrium initial bath is also influenced by spatial correlations and becomes the most conspicuous for certain degrees of spatial correlations from which we propose a picture that the spatial correlations of bath fluctuations open up new energy transfer pathways, playing a role of protecting coherence. Besides, we apply the polaron master equation approach to study the dynamics in a two-site subsystem of the FMO complex and provide a practical example that shows the versatility of this approach.
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Affiliation(s)
- Min Du
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Ming Qin
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Haitao Cui
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Chunyang Wang
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Yuqing Xu
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xiaoguang Ma
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xuexi Yi
- Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
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10
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Bradbury NC, Chuang C, Deshmukh AP, Rabani E, Baer R, Caram JR, Neuhauser D. Stochastically Realized Observables for Excitonic Molecular Aggregates. J Phys Chem A 2020; 124:10111-10120. [PMID: 33251807 DOI: 10.1021/acs.jpca.0c07953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We show that a stochastic approach enables calculations of the optical properties of large 2-dimensional and nanotubular excitonic molecular aggregates. Previous studies of such systems relied on numerically diagonalizing the dense and disordered Frenkel Hamiltonian, which scales approximately as O(N3) for N dye molecules. Our approach scales much more efficiently as O(Nlog(N)), enabling quick study of systems with a million of coupled molecules on the micrometer size scale. We calculate several important experimental observables, including the optical absorption spectrum and density of states, and develop a stochastic formalism for the participation ratio. Quantitative agreement with traditional matrix diagonalization methods is demonstrated for both small- and intermediate-size systems. The stochastic methodology enables the study of the effects of spatial-correlation in site energies on the optical signatures of large 2D aggregates. Our results demonstrate that stochastic methods present a path forward for screening structural parameters and validating experiments and theoretical predictions in large excitonic aggregates.
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Affiliation(s)
- Nadine C Bradbury
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Chern Chuang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Eran Rabani
- Department of Chemistry, University of California and Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Roi Baer
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Daniel Neuhauser
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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11
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Mass OA, Wilson CK, Roy SK, Barclay MS, Patten LK, Terpetschnig EA, Lee J, Pensack RD, Yurke B, Knowlton WB. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. J Phys Chem B 2020; 124:9636-9647. [PMID: 33052691 DOI: 10.1021/acs.jpcb.0c06480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations-transverse dimer, adjacent dimer, and tetramer-were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.
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Affiliation(s)
| | | | | | | | | | - Ewald A Terpetschnig
- SETA BioMedicals, LLC, 2014 Silver Court East, Urbana, Illinois 61801, United States
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12
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Khyasudeen MF, Nowakowski PJ, Tan HS. Measuring the Ultrafast Correlation Dynamics between the Qx and Qy Bands in Chlorophyll Molecules. J Phys Chem B 2019; 123:1359-1364. [DOI: 10.1021/acs.jpcb.9b00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- M. Faisal Khyasudeen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Paweł J. Nowakowski
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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13
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Rancova O, Jankowiak R, Abramavicius D. Role of Bath Fluctuations in the Double-Excitation Manifold in Shaping the 2DES of Bacterial Reaction Centers at Low Temperature. J Phys Chem B 2018; 122:1348-1366. [DOI: 10.1021/acs.jpcb.7b08905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Olga Rancova
- Institute
of Chemical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
| | - Ryszard Jankowiak
- Department
of Chemistry and Department of Physics, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506-0401, United States
| | - Darius Abramavicius
- Institute
of Chemical Physics, Vilnius University, Sauletekio al 9-III, 10222 Vilnius, Lithuania
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14
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Maiuri M, Scholes GD. 2D Spectroscopy Helps Visualize the Influence of Spectral Motion on Chromophore Response. Chem 2018. [DOI: 10.1016/j.chempr.2017.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Correlated Protein Environments Drive Quantum Coherence Lifetimes in Photosynthetic Pigment-Protein Complexes. Chem 2018. [DOI: 10.1016/j.chempr.2017.12.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Butkus V, Alster J, Bašinskaitė E, Augulis RN, Neuhaus P, Valkunas L, Anderson HL, Abramavicius D, Zigmantas D. Discrimination of Diverse Coherences Allows Identification of Electronic Transitions of a Molecular Nanoring. J Phys Chem Lett 2017; 8:2344-2349. [PMID: 28493708 DOI: 10.1021/acs.jpclett.7b00612] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The role of quantum coherence in photochemical functions of molecular systems such as photosynthetic complexes is a broadly debated topic. Coexistence and intermixing of electronic and vibrational coherences has been proposed to be responsible for the observed long-lived coherences and high energy transfer efficiency. However, clear experimental evidence of coherences with different origins operating at the same time has been elusive. In this work, multidimensional spectra obtained from a six-porphyrin nanoring system are analyzed in detail with support from theoretical modeling. We uncover a great diversity of separable electronic, vibrational, and mixed coherences and show their cooperation in shaping the spectroscopic response. The results permit direct assignment of electronic and vibronic states and characterization of the excitation dynamics. The clear disentanglement of coherences in molecules with extended π-conjugation opens up new avenues for exploring coherent phenomena and understanding their importance for the function of complex systems.
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Affiliation(s)
- Vytautas Butkus
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio Avenue 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology , Sauletekio Avenue 3, 10257 Vilnius, Lithuania
| | - Jan Alster
- Department of Chemical Physics, Lund University , P.O. Box 124, 22100 Lund, Sweden
| | - Eglė Bašinskaitė
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio Avenue 9-III, 10222 Vilnius, Lithuania
- Department of Chemical Physics, Lund University , P.O. Box 124, 22100 Lund, Sweden
| | - Ramu Nas Augulis
- Center for Physical Sciences and Technology , Sauletekio Avenue 3, 10257 Vilnius, Lithuania
- Department of Chemical Physics, Lund University , P.O. Box 124, 22100 Lund, Sweden
| | - Patrik Neuhaus
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory , Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio Avenue 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology , Sauletekio Avenue 3, 10257 Vilnius, Lithuania
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory , Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio Avenue 9-III, 10222 Vilnius, Lithuania
| | - Donatas Zigmantas
- Department of Chemical Physics, Lund University , P.O. Box 124, 22100 Lund, Sweden
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17
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18
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Lim J, Ing DJ, Rosskopf J, Jeske J, Cole JH, Huelga SF, Plenio MB. Signatures of spatially correlated noise and non-secular effects in two-dimensional electronic spectroscopy. J Chem Phys 2017; 146:024109. [DOI: 10.1063/1.4973975] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Abstract
![]()
The field of organic
photovoltaics has developed rapidly over the
last 2 decades, and small solar cells with power conversion efficiencies
of 13% have been demonstrated. Light absorbed in the organic layers
forms tightly bound excitons that are split into free electrons and
holes using heterojunctions of electron donor and acceptor materials,
which are then extracted at electrodes to give useful electrical power.
This review gives a concise description of the fundamental processes
in photovoltaic devices, with the main emphasis on the characterization
of energy transfer and its role in dictating device architecture,
including multilayer planar heterojunctions, and on the factors that
impact free carrier generation from dissociated excitons. We briefly
discuss harvesting of triplet excitons, which now attracts substantial
interest when used in conjunction with singlet fission. Finally, we
introduce the techniques used by researchers for characterization
and engineering of bulk heterojunctions to realize large photocurrents,
and examine the formed morphology in three prototypical blends.
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Affiliation(s)
- Gordon J Hedley
- Organic Semiconductor Centre, SUPA, School of Physics and Astronomy, University of St Andrews , North Haugh, St Andrews, Fife KY16 9SS, U.K
| | - Arvydas Ruseckas
- Organic Semiconductor Centre, SUPA, School of Physics and Astronomy, University of St Andrews , North Haugh, St Andrews, Fife KY16 9SS, U.K
| | - Ifor D W Samuel
- Organic Semiconductor Centre, SUPA, School of Physics and Astronomy, University of St Andrews , North Haugh, St Andrews, Fife KY16 9SS, U.K
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Higashi M, Saito S. Quantitative Evaluation of Site Energies and Their Fluctuations of Pigments in the Fenna–Matthews–Olson Complex with an Efficient Method for Generating a Potential Energy Surface. J Chem Theory Comput 2016; 12:4128-37. [DOI: 10.1021/acs.jctc.6b00516] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Masahiro Higashi
- Department
of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Shinji Saito
- Department
of Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585, Japan
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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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22
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Butkus V, Dong H, Fleming GR, Abramavicius D, Valkunas L. Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules. J Phys Chem Lett 2016; 7:277-282. [PMID: 26720834 DOI: 10.1021/acs.jpclett.5b02642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Quantum superposition of molecular electronic states is very fragile because of thermal energy fluctuations and the static conformational disorder induced by the intimate surrounding of constituent molecules of the system. However, the nature of the long-lived quantum beats, observed in time-resolved spectra of molecular aggregates at physiological conditions, is still being debated. We present our study of the conditions when long-lived electronic quantum coherences originating from recently proposed inhomogeneous broadening mechanism are enhanced and reflected in the two-dimensional electronic spectra of the excitonically coupled molecular dimer. We show that depending on the amount of inhomogeneous broadening, the excitonically coupled molecular system can establish long-lived electronic coherences, caused by a disordered subensemble, for which the dephasing due to static energy disorder becomes significantly reduced. On the basis of these considerations, we present explanations for why the electronic or vibrational coherences were or were not observed in a range of recent experiments.
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Affiliation(s)
- Vytautas Butkus
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
| | - Hui Dong
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Graham R Fleming
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Darius Abramavicius
- 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
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
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23
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Yan YA. Exciton interference revealed by energy dependent exciton transfer rate for ring-structured molecular systems. J Chem Phys 2016; 144:024305. [DOI: 10.1063/1.4939523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yun-An Yan
- Guizhou Provincial Key Laboratory of Computational Nanomaterial Science, Guizhou Education University, Guiyang, Guizhou 550018, China
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24
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Abramavicius D, Valkunas L. Role of coherent vibrations in energy transfer and conversion in photosynthetic pigment-protein complexes. PHOTOSYNTHESIS RESEARCH 2016; 127:33-47. [PMID: 25618783 DOI: 10.1007/s11120-015-0080-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Oscillatory features of two-dimensional spectra of photosynthetic pigment-protein complexes during few picoseconds after electronic excitations of chlorophylls in various pigment-proteins were recently related to the coherent nuclear vibrations. It has been also speculated that the vibrations may assist the excitonic energy transfer and charge separation, hence contributing to energy transport and energy conversion efficiency. Here, we consider three theoretical approaches usually used for characterization of the excitation dynamics and charge separation, namely Redfield, Förster, and Marcus model descriptions, regarding this question. We show that two out of the three mechanisms require explicit resonances of excitonic splittings and the nuclear vibration frequencies. However, the third one related to the electron transfer is in principle off resonant.
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Affiliation(s)
- Darius Abramavicius
- Department of Theoretical Physics, Vilnius University, Sauletekio al. 9-III, 10222, Vilnius, Lithuania.
| | - Leonas Valkunas
- Department of Theoretical Physics, Vilnius University, Sauletekio al. 9-III, 10222, Vilnius, Lithuania.
- Center for Physical Sciences and Technology, A. Gostauto 11, 01108, Vilnius, Lithuania.
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25
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Duan HG, Dijkstra AG, Nalbach P, Thorwart M. Efficient tool to calculate two-dimensional optical spectra for photoactive molecular complexes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042708. [PMID: 26565273 DOI: 10.1103/physreve.92.042708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 06/05/2023]
Abstract
We combine the coherent modified Redfield theory (CMRT) with the equation of motion-phase matching approach (PMA) to calculate two-dimensional photon-echo spectra for photoactive molecular complexes with an intermediate strength of the coupling to their environment. Both techniques are highly efficient, yet they involve approximations at different levels. By explicitly comparing with the numerically exact quasiadiabatic path integral approach, we show for the Fenna-Matthews-Olson complex that the CMRT describes the decay rates in the population dynamics well, but final stationary populations and the oscillation frequencies differ slightly. In addition, we use the combined CMRT+PMA to calculate two-dimensional photon-echo spectra for a simple dimer model. We find excellent agreement with the exact path integral calculations at short waiting times where the dynamics is still coherent. For long waiting times, differences occur due to different final stationary states, specifically for strong system-bath coupling. For weak to intermediate system-bath couplings, which is most important for natural photosynthetic complexes, the combined CMRT+PMA gives reasonable results with acceptable computational efforts.
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Affiliation(s)
- Hong-Guang Duan
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arend G Dijkstra
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Peter Nalbach
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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26
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Jeske J, Ing DJ, Plenio MB, Huelga SF, Cole JH. Bloch-Redfield equations for modeling light-harvesting complexes. J Chem Phys 2015; 142:064104. [DOI: 10.1063/1.4907370] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jan Jeske
- Chemical and Quantum Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia
| | - David J. Ing
- Chemical and Quantum Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia
| | - Martin B. Plenio
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm, Germany
| | - Susana F. Huelga
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm, Germany
| | - Jared H. Cole
- Chemical and Quantum Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia
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27
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Room-temperature exciton coherence and dephasing in two-dimensional nanostructures. Nat Commun 2015; 6:6086. [DOI: 10.1038/ncomms7086] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 12/11/2014] [Indexed: 11/09/2022] Open
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28
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Tempelaar R, Jansen TLC, Knoester J. Vibrational beatings conceal evidence of electronic coherence in the FMO light-harvesting complex. J Phys Chem B 2014; 118:12865-72. [PMID: 25321492 DOI: 10.1021/jp510074q] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In biological light harvesting, solar energy is captured by photosynthetic antennae for subsequent storage into chemical bonds. The remarkable efficiency reached in transferring the energy between the collection and storage events recently has been attributed to long-lived electronic coherence present in such antennae systems. We present numerical simulations indicating that the spectroscopic transients that supported this hypothesis are not induced by electronic coherence but instead are caused by vibrational (nuclear) motion in the electronic ground state potential. Besides emphasizing the significance of such nuclear modes, our findings stimulate a reconsideration of the role of electronic coherence in promoting energy transfer in natural photosynthesis. Furthermore, they require us to rethink how energy transfer efficiency is reflected in spectral signals.
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Affiliation(s)
- Roel Tempelaar
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Seibt J, Pullerits T. Combined treatment of relaxation and fluctuation dynamics in the calculation of two-dimensional electronic spectra. J Chem Phys 2014; 141:114106. [DOI: 10.1063/1.4895401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Joachim Seibt
- Department of Chemical Physics, Lund University, Box 124, SE-2100 Lund, Sweden
| | - Tõnu Pullerits
- Department of Chemical Physics, Lund University, Box 124, SE-2100 Lund, Sweden
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30
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Higashi M, Kosugi T, Hayashi S, Saito S. Theoretical study on excited states of bacteriochlorophyll a in solutions with density functional assessment. J Phys Chem B 2014; 118:10906-18. [PMID: 25153487 DOI: 10.1021/jp507259g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The excited-state properties of bacteriochlorophyll (BChl) a in triethylamine, 1-propanol, and methanol are investigated with the time-dependent density functional theory by using the quantum mechanical and molecular mechanical reweighting free energy self-consistant field method. It is found that no prevalent density functionals can reproduce the experimental excited-state properties, i.e., the absorption and reorganization energies, of BChl a in the solutions. The parameter μ in the range-separated hybrid functional is therefore optimized to reproduce the differences of the absorption energies in the solutions. We examine the origin of the differences of the absorption energies in the solutions and find that sensitive balance between contributions of structural changes and solute-solvent interactions determines the differences. The accurate description of the excitation with the density functional with the adjusted parameter is therefore essential to the understanding of the excited-state properties of BChl a in proteins and also the mechanism of the photosynthetic systems.
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Affiliation(s)
- Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus , 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
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31
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32
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Tay BA. Attenuation of excitation decay rate due to collective effect. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022142. [PMID: 25215723 DOI: 10.1103/physreve.90.022142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 06/03/2023]
Abstract
We study a series of N oscillators, each coupled to its nearest neighbors, and linearly to a phonon field through the oscillator's number operator. We show that the Hamiltonian of a pair of adjacent oscillators, or a dimer, within the series of oscillators can be transformed into a form in which they are collectively coupled to the phonon field as a composite unit. In the weak coupling and rotating-wave approximation, the system behaves effectively as the trilinear boson model in the one excitation subspace of the dimer subsystem. The reduced dynamics of the one excitation subspace of the dimer subsystem coupled weakly to a phonon bath is similar to that of a two-level system, with a metastable state against the vacuum. The decay constant of the subsystem is proportional to the dephasing rate of the individual oscillator in a phonon bath, attenuated by a factor that depends on site asymmetry, intersite coupling, and the resonance frequency between the transformed oscillator modes, or excitons. As a result of the collective effect, the excitation relaxation lifetime is prolonged over the dephasing lifetime of an individual oscillator coupled to the same bath.
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Affiliation(s)
- B A Tay
- Foundation Studies, Faculty of Engineering, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
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33
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Chenu A, Christensson N, Kauffmann HF, Mančal T. Enhancement of vibronic and ground-state vibrational coherences in 2D spectra of photosynthetic complexes. Sci Rep 2014; 3:2029. [PMID: 23778355 PMCID: PMC3693153 DOI: 10.1038/srep02029] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/14/2013] [Indexed: 01/04/2023] Open
Abstract
A vibronic-exciton model is applied to investigate the recently proposed mechanism of enhancement of coherent oscillations due to mixing of electronic and nuclear degrees of freedom. We study a dimer system to elucidate the role of resonance coupling, site energies, vibrational frequency and energy disorder in the enhancement of vibronic-exciton and ground-state vibrational coherences, and to identify regimes where this enhancement is significant. For a heterodimer representing two coupled bachteriochloropylls of the FMO complex, long-lived vibronic coherences are found to be generated only when the frequency of the mode is in the vicinity of the electronic energy difference. Although the vibronic-exciton coherences exhibit a larger initial amplitude compared to the ground-state vibrational coherences, we conclude that, due to the dephasing of the former, both type of coherences have a similar magnitude at longer population time.
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Affiliation(s)
- Aurélia Chenu
- Faculty of Mathematics and Physics, Charles University in Prague, Prague 2, Czech Republic
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34
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Abramavicius V, Abramavicius D. Excitation transfer pathways in excitonic aggregates revealed by the stochastic Schrödinger equation. J Chem Phys 2014; 140:065103. [DOI: 10.1063/1.4863968] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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35
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Butkus V, Valkunas L, Abramavicius D. Vibronic phenomena and exciton–vibrational interference in two-dimensional spectra of molecular aggregates. J Chem Phys 2014; 140:034306. [DOI: 10.1063/1.4861466] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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36
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Halpin A, Johnson PJM, Tempelaar R, Murphy RS, Knoester J, Jansen TLC, Miller RJD. Two-dimensional spectroscopy of a molecular dimer unveils the effects of vibronic coupling on exciton coherences. Nat Chem 2014; 6:196-201. [DOI: 10.1038/nchem.1834] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/22/2013] [Indexed: 12/31/2022]
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Fassioli F, Oblinsky DG, Scholes GD. Designs for molecular circuits that use electronic coherence. Faraday Discuss 2013; 163:341-51; discussion 393-432. [PMID: 24020210 DOI: 10.1039/c3fd00009e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The mounting evidence of recent years regarding long-lived coherent dynamics of electronic excitations in several light-harvesting antenna proteins suggests the possibility of realizing and exploiting light-initiated quantum dynamics in synthetic molecular devices based on electronic energy transfer. Inspired by the field of molecular logic, we focus this discussion on the prospect of using quantum coherence to control the direction of energy flow in a molecular circuit. As a prototype system we consider a circuit consisting of three chromophores that deliver energy to two trap chromophores. Our aim is to control to which trap the energy is more likely to be delivered. This is achieved by switching one of the circuit chromophores ON and OFF from the system, such that the direction of energy flow substantially changes from the ON and OFF states of the circuit. We find that quantum coherence can allow a significant ability to direct energy transfer in the circuit. However, when realistic levels of noise are added, quantum coherence only slightly improves the ability to direct electronic energy in comparison to a classical hopping mechanism.
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Affiliation(s)
- Francesca Fassioli
- Lash Miller Chemical Laboratories, Institute for Optical Sciences and Centre for Quantum Information and Quantum Control, University of Toronto, 80 St. George St., Toronto, Canada
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38
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Viani L, Curutchet C, Mennucci B. Spatial and Electronic Correlations in the PE545 Light-Harvesting Complex. J Phys Chem Lett 2013; 4:372-377. [PMID: 26281726 DOI: 10.1021/jz301987u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The recent discovery of long-lasting quantum coherence effects in photosynthetic pigment-protein complexes has challenged our view of the role that protein motions play in light-harvesting processes. Several groups have suggested that correlated fluctuations involving the pigments site energies and couplings could be at the origin of such unexpected behavior. Here we combine molecular dynamics simulations with quantum mechanics/molecular mechanics calculations to analyze the degree of correlated fluctuations in the PE545 complex of Rhodomonas sp. strain CS24. We find that correlations between the motions of the chromophores, which are significantly assisted by the water solvent, do not translate into appreciable site energy correlations but do lead to significant cross-correlations of energies and couplings. Such behavior, not observed in a recent study on the Fenna-Mathews-Olson complex, seems to provide phycobiliproteins with an additional fundamental mechanism to control quantum coherence and light-harvesting efficiency compared with chlorophyll-containing complexes.
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Affiliation(s)
- Lucas Viani
- †Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Carles Curutchet
- ‡Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- †Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
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39
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Beatings in electronic 2D spectroscopy suggest another role of vibrations in photosynthetic light harvesting. Proc Natl Acad Sci U S A 2013; 110:1148-9. [PMID: 23319614 DOI: 10.1073/pnas.1221058110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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40
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Renger T, Klinger A, Steinecker F, Schmidt am Busch M, Numata J, Müh F. Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons. J Phys Chem B 2012; 116:14565-80. [PMID: 23163520 PMCID: PMC3557933 DOI: 10.1021/jp3094935] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/19/2012] [Indexed: 11/29/2022]
Abstract
We report a method for the structure-based calculation of the spectral density of the pigment-protein coupling in light-harvesting complexes that combines normal-mode analysis with the charge density coupling (CDC) and transition charge from electrostatic potential (TrEsp) methods for the computation of site energies and excitonic couplings, respectively. The method is applied to the Fenna-Matthews-Olson (FMO) protein in order to investigate the influence of the different parts of the spectral density as well as correlations among these contributions on the energy transfer dynamics and on the temperature-dependent decay of coherences. The fluctuations and correlations in excitonic couplings as well as the correlations between coupling and site energy fluctuations are found to be 1 order of magnitude smaller in amplitude than the site energy fluctuations. Despite considerable amplitudes of that part of the spectral density which contains correlations in site energy fluctuations, the effect of these correlations on the exciton population dynamics and dephasing of coherences is negligible. The inhomogeneous charge distribution of the protein, which causes variations in local pigment-protein coupling constants of the normal modes, is responsible for this effect. It is seen thereby that the same building principle that is used by nature to create an excitation energy funnel in the FMO protein also allows for efficient dissipation of the excitons' excess energy.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
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41
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42
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Westenhoff S, Palec̆ek D, Edlund P, Smith P, Zigmantas D. Coherent Picosecond Exciton Dynamics in a Photosynthetic Reaction Center. J Am Chem Soc 2012; 134:16484-7. [DOI: 10.1021/ja3065478] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Westenhoff
- Department of Chemistry and
Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - David Palec̆ek
- Department of Chemical Physics, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Petra Edlund
- Department of Chemistry and
Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Philip Smith
- Department of Chemistry and
Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Donatas Zigmantas
- Department of Chemical Physics, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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43
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Christensson N, Kauffmann HF, Pullerits T, Mančal T. Origin of long-lived coherences in light-harvesting complexes. J Phys Chem B 2012; 116:7449-54. [PMID: 22642682 PMCID: PMC3789255 DOI: 10.1021/jp304649c] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A vibronic exciton model is applied to explain the long-lived oscillatory features in the two-dimensional (2D) electronic spectra of the Fenna-Matthews-Olson (FMO) complex. Using experimentally determined parameters and uncorrelated site energy fluctuations, the model predicts oscillations with dephasing times of 1.3 ps at 77 K, which is in a good agreement with the experimental results. These long-lived oscillations originate from the coherent superposition of vibronic exciton states with dominant contributions from vibrational excitations on the same pigment. The oscillations obtain a large amplitude due to excitonic intensity borrowing, which gives transitions with strong vibronic character a significant intensity despite the small Huang-Rhys factor. Purely electronic coherences are found to decay on a 200 fs time scale.
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Affiliation(s)
- Niklas Christensson
- Faculty of Physics, University of Vienna, Strudlhofgasse 4, 1090 Vienna, Austria
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44
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Huo P, Coker DF. Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems. J Chem Phys 2012; 136:115102. [DOI: 10.1063/1.3693019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Abramavicius D, Nemeth A, Milota F, Sperling J, Mukamel S, Kauffmann HF. Weak exciton scattering in molecular nanotubes revealed by double-quantum two-dimensional electronic spectroscopy. PHYSICAL REVIEW LETTERS 2012; 108:067401. [PMID: 22401120 PMCID: PMC3721760 DOI: 10.1103/physrevlett.108.067401] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Indexed: 05/03/2023]
Abstract
The two-exciton manifold of a double-wall cylindrical molecular aggregate is studied using a coherent third order optical technique. Experiments reveal the anharmonic character of the exciton bands. Atomistic simulations of the exciton-exciton scattering show that the excitons can be treated as weakly coupled hard-core bosons. The weak coupling stems from the extended exciton delocalization made possible by the nanotube geometry.
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Affiliation(s)
- Darius Abramavicius
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
- Department of Theoretical Physics, Vilnius University, Saulėtekio al. 9-III, LT-10222 Vilnius, Lithuania
| | | | - Franz Milota
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
| | | | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - Harald F. Kauffmann
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
- Faculty of Physics, Vienna University of Technology, 1040 Vienna, Austria
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46
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Shim S, Rebentrost P, Valleau S, Aspuru-Guzik A. Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex. Biophys J 2012; 102:649-60. [PMID: 22325289 PMCID: PMC3274801 DOI: 10.1016/j.bpj.2011.12.021] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 11/08/2011] [Accepted: 12/05/2011] [Indexed: 12/16/2022] Open
Abstract
A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear, and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents, to our knowledge, one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.
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Affiliation(s)
| | | | | | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
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47
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Vlaming SM, Silbey RJ. Correlated intermolecular coupling fluctuations in photosynthetic complexes. J Chem Phys 2012; 136:055102. [DOI: 10.1063/1.3682988] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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48
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Gelin MF, Sharp LZ, Egorova D, Domcke W. Bath-induced correlations and relaxation of vibronic dimers. J Chem Phys 2012; 136:034507. [DOI: 10.1063/1.3676063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Gelin MF, Egorova D, Domcke W. Exact quantum master equation for a molecular aggregate coupled to a harmonic bath. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041139. [PMID: 22181119 DOI: 10.1103/physreve.84.041139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/04/2011] [Indexed: 05/31/2023]
Abstract
We consider a molecular aggregate consisting of N identical monomers. Each monomer comprises two electronic levels and a single harmonic mode. The monomers interact with each other via dipole-dipole forces. The monomer vibrational modes are bilinearly coupled to a bath of harmonic oscillators. This is a prototypical model for the description of coherent exciton transport, from quantum dots to photosynthetic antennae. We derive an exact quantum master equation for such systems. Computationally, the master equation may be useful for the testing of various approximations employed in theories of quantum transport. Physically, it offers a plausible explanation of the origins of long-lived coherent optical responses of molecular aggregates in dissipative environments.
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Affiliation(s)
- Maxim F Gelin
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
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50
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Olbrich C, Jansen TLC, Liebers J, Aghtar M, Strümpfer J, Schulten K, Knoester J, Kleinekathöfer U. From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex. J Phys Chem B 2011; 115:8609-21. [PMID: 21635010 PMCID: PMC3140161 DOI: 10.1021/jp202619a] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The experimental observation of long-lived quantum coherences in the Fenna-Matthews-Olson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search of explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings is analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian, linear and two-dimensional spectra are determined. The thus-obtained linear absorption line shape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.
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