1
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Humphries BS, Kinslow JC, Green D, Jones GA. Role of Quantum Information in HEOM Trajectories. J Chem Theory Comput 2024; 20:5383-5395. [PMID: 38889316 PMCID: PMC11238535 DOI: 10.1021/acs.jctc.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024]
Abstract
Open quantum systems often operate in the non-Markovian regime where a finite history of a trajectory is intrinsic to its evolution. The degree of non-Markovianity for a trajectory may be measured in terms of the amount of information flowing from the bath back into the system. In this study, we consider how information flows through the auxiliary density operators (ADOs) in the hierarchical equations of motion. We consider three cases for a range of baths, underdamped, intermediate, and overdamped. By understanding how information flows, we are able to determine the relative importance of different ADOs within the hierarchy. We show that ADOs sharing a common Matsubara axis behave similarly, while ADOs on different Matsubara axes behave differently. Using this knowledge, we are able to truncate hierarchies significantly, thus reducing the computation time, while obtaining qualitatively similar results. This is illustrated by comparing 2D electronic spectra for a molecule with an underdamped vibration subsumed into the bath spectral density.
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Affiliation(s)
- Ben S. Humphries
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Joshua C. Kinslow
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Dale Green
- Physics,
Faculty of Science, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Garth A. Jones
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
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2
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Rode AJ, Arpin PC, Turner DB. Theoretical model of femtosecond coherence spectroscopy of vibronic excitons in molecular aggregates. J Chem Phys 2024; 160:164101. [PMID: 38647298 DOI: 10.1063/5.0200570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
When used as pump pulses in transient absorption spectroscopy measurements, femtosecond laser pulses can produce oscillatory signals known as quantum beats. The quantum beats arise from coherent superpositions of the states of the sample and are best studied in the Fourier domain using Femtosecond Coherence Spectroscopy (FCS), which consists of one-dimensional amplitude and phase plots of a specified oscillation frequency as a function of the detection frequency. Prior works have shown ubiquitous amplitude nodes and π phase shifts in FCS from excited-state vibrational wavepackets in monomer samples. However, the FCS arising from vibronic-exciton states in molecular aggregates have not been studied theoretically. Here, we use a model of vibronic-exciton states in molecular dimers based on displaced harmonic oscillators to simulate FCS for dimers in two important cases. Simulations reveal distinct spectral signatures of excited-state vibronic-exciton coherences in molecular dimers that may be used to distinguish them from monomer vibrational coherences. A salient result is that, for certain relative orientations of the transition dipoles, the key resonance condition between the electronic coupling and the frequency of the vibrational mode may yield strong enhancement of the quantum-beat amplitude and, perhaps, also cause a significant decrease of the oscillation frequency to a value far lower than the vibrational frequency. Future studies using these results will lead to new insights into the excited-state coherences generated in photosynthetic pigment-protein complexes.
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Affiliation(s)
- Alexander J Rode
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul C Arpin
- Department of Physics, California State University, Chico, Chico, California 95929, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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3
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Zhu R, Li W, Zhen Z, Zou J, Liao G, Wang J, Wang Z, Chen H, Qin S, Weng Y. Quantum phase synchronization via exciton-vibrational energy dissipation sustains long-lived coherence in photosynthetic antennas. Nat Commun 2024; 15:3171. [PMID: 38609379 PMCID: PMC11015008 DOI: 10.1038/s41467-024-47560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The lifetime of electronic coherences found in photosynthetic antennas is known to be too short to match the energy transfer time, rendering the coherent energy transfer mechanism inactive. Exciton-vibrational coherence time in excitonic dimers which consist of two chromophores coupled by excitation transfer interaction, can however be much longer. Uncovering the mechanism for sustained coherences in a noisy biological environment is challenging, requiring the use of simpler model systems as proxies. Here, via two-dimensional electronic spectroscopy experiments, we present compelling evidence for longer exciton-vibrational coherence time in the allophycocyanin trimer, containing excitonic dimers, compared to isolated pigments. This is attributed to the quantum phase synchronization of the resonant vibrational collective modes of the dimer, where the anti-symmetric modes, coupled to excitonic states with fast dephasing, are dissipated. The decoupled symmetric counterparts are subject to slower energy dissipation. The resonant modes have a predicted nearly 50% reduction in the vibrational amplitudes, and almost zero amplitude in the corresponding dynamical Stokes shift spectrum compared to the isolated pigments. Our findings provide insights into the mechanisms for protecting coherences against the noisy environment.
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Affiliation(s)
- Ruidan Zhu
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Zhanghe Zhen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, P. R. China
| | - Jiading Zou
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Guohong Liao
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jiayu Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Zhuan Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Hailong Chen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
- Songshan Lake Materials Laboratory, Dongguan, 523808, Guangdong, P.R. China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
| | - Yuxiang Weng
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
- Songshan Lake Materials Laboratory, Dongguan, 523808, Guangdong, P.R. China.
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4
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Sorour MI, Marcus AH, Matsika S. Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer. J Phys Chem A 2023; 127:9530-9540. [PMID: 37934679 PMCID: PMC10774018 DOI: 10.1021/acs.jpca.3c06090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck-Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.
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Affiliation(s)
- Mohammed I Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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5
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Freytag E, Kreimendahl L, Holzapfel M, Petersen J, Lackinger H, Stolte M, Würthner F, Mitric R, Lambert C. Chiroptical Properties of Planar Benzobisthiazole-Bridged Squaraine Dimers. J Org Chem 2023. [PMID: 37487529 DOI: 10.1021/acs.joc.3c00821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Five chiral squaraine dimers were synthesized by fusing chiral indolenine semisquaraines with three different benzobisthiazole bridges. The thereby created squaraine dimers show a strong splitting of the lowest energy absorption bands caused by exciton coupling. The intensities of the two exciton transitions and the energetic splitting depend on the angle of the two squaraine moieties within the chromophore dimer. The electric circular dichroism spectra of the dimers show intense Cotton effects whose sign depends on the used squaraine chromophores. Sizable anisotropies gabs of up to 2.6 × 10-3 could be obtained. TD-DFT calculations were used to partition the rotational strength into the three Rosenfeld terms where the electric-magnetic coupling turned out to be the dominant contribution while the exciton chirality term is much smaller. This is because the chromophore dimers are essentially planar but the angle between the electric transition dipole moment of one squaraine and the magnetic transition dipole moment of the other squaraine strongly deviates from 90°, which makes the dot product between the two moment vectors and, thus, the rotational strength substantial.
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Affiliation(s)
- Emely Freytag
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lasse Kreimendahl
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Marco Holzapfel
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jens Petersen
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Heiko Lackinger
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthias Stolte
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roland Mitric
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christoph Lambert
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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6
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Chiriboga M, Green CM, Mathur D, Hastman DA, Melinger JS, Veneziano R, Medintz IL, Díaz SA. Structural and optical variation of pseudoisocyanine aggregates nucleated on DNA substrates. Methods Appl Fluoresc 2023; 11. [PMID: 36719011 PMCID: PMC10362908 DOI: 10.1088/2050-6120/acb2b4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/12/2023] [Indexed: 02/01/2023]
Abstract
Coherently coupled pseudoisocyanine (PIC) dye aggregates have demonstrated the ability to delocalize electronic excitations and ultimately migrate excitons with much higher efficiency than similar designs where excitations are isolated to individual chromophores. Here, we report initial evidence of a new type of PIC aggregate, formed through heterogeneous nucleation on DNA oligonucleotides, displaying photophysical properties that differ significantly from previously reported aggregates. This new aggregate, which we call the super aggregate (SA) due to the need for elevated dye excess to form it, is clearly differentiated from previously reported aggregates by spectroscopic and biophysical characterization. In emission spectra, the SA exhibits peak narrowing and, in some cases, significant quantum yield variation, indicative of stronger coupling in cyanine dyes. The SA was further characterized with circular dichroism and atomic force microscopy observing unique features depending on the DNA substrate. Then by integrating an AlexaFluorTM647 (AF) dye as an energy transfer acceptor into the system, we observed mixed energy transfer characteristics using the different DNA. For example, SA formed with a rigid DNA double crossover tile (DX-tile) substrate resulted in AF emission sensitization. While SA formed with more flexible non-DX-tile DNA (i.e. duplex and single strand DNA) resulted in AF emission quenching. These combined characterizations strongly imply that DNA-based PIC aggregate properties can be controlled through simple modifications to the DNA substrate's sequence and geometry. Ultimately, we aim to inform rational design principles for future device prototyping. For example, one key conclusion of the study is that the high absorbance cross-section and efficient energy transfer observed with rigid substrates made for better photonic antennae, compared to flexible DNA substrates.
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Affiliation(s)
- Matthew Chiriboga
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America.,Department of Bioengineering. College of Engineering and Computing, George Mason University, 4400 University Drive, Fairfax, VA 22030, United States of America
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America.,Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States of America
| | - David A Hastman
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Joseph S Melinger
- Electronics Sciences and Technology Division, U.S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Remi Veneziano
- Department of Bioengineering. College of Engineering and Computing, George Mason University, 4400 University Drive, Fairfax, VA 22030, United States of America
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, 4555 Overlook Ave. S.W. Washington, DC 20375, United States of America
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7
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Taher-Ghahramani F, Zheng F, Eisfeld A. Gaussian process regression for absorption spectra analysis of molecular dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121091. [PMID: 35306303 DOI: 10.1016/j.saa.2022.121091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/05/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
A common task is the determination of system parameters from spectroscopy, where one compares the experimental spectrum with calculated spectra, that depend on the desired parameters. Here we discuss an approach based on a machine learning technique, where the parameters for the numerical calculations are chosen from Gaussian Process Regression (GPR). This approach does not only quickly converge to an optimal parameter set, but in addition provides information about the complete parameter space, which allows for example to identify extended parameter regions where numerical spectra are consistent with the experimental one. We consider as example dimers of organic molecules and aim at extracting in particular the interaction between the monomers, and their mutual orientation. We find that indeed the GPR gives reliable results which are in agreement with direct calculations of these parameters using quantum chemical methods.
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Affiliation(s)
- Farhad Taher-Ghahramani
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str 38, Dresden, Germany.
| | - Fulu Zheng
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany.
| | - Alexander Eisfeld
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str 38, Dresden, Germany.
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8
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Sláma V, Cupellini L, Mennucci B. Excitonic Nature of Carotenoid–Phthalocyanine Dyads and Its Role in Transient Absorption Spectra. ACS PHYSICAL CHEMISTRY AU 2022; 2:206-215. [PMID: 35637783 PMCID: PMC9136948 DOI: 10.1021/acsphyschemau.1c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
![]()
Artificial carotenoid–tetrapyrrole
dyads have been extensively
used as model systems to understand the quenching mechanisms that
occur in light-harvesting complexes during nonphotochemical quenching.
In particular, dyads containing a carotenoid covalently linked to
a zinc phthalocyanine have been studied by transient absorption spectroscopy,
and the observed signals have been interpreted in terms of an excitonically
coupled state involving the lowest excited states of the two fragments.
If present, such excitonic delocalization would have significant implications
on the mechanism of nonphotochemical quenching. Here, we use quantum
chemical calculations to show that this delocalization is not needed
to reproduce the transient absorption spectra. On the contrary, the
observed signals can be explained through excitonic couplings in the
higher-energy manifold of states. We also argue that the covalent
linkage between the two fragments allows for electronic communications,
which complicates the analysis of the spectra based on two independent
but coupled moieties. These findings call for a more thorough reassessment
of the photophysics in these dyads and its implications in the context
of natural nonphotochemical quenching.
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Affiliation(s)
- Vladislav Sláma
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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9
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Humphries BS, Green D, Jones GA. The influence of a Hamiltonian vibration vs a bath vibration on the 2D electronic spectra of a homodimer. J Chem Phys 2022; 156:084103. [DOI: 10.1063/5.0077404] [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
We elucidate the influence of the system–bath boundary placement within an open quantum system, with emphasis on the two-dimensional electronic spectra, through the application of the hierarchical equations of motion formalism for an exciton system. We apply two different models, the Hamiltonian vibration model (HVM) and bath vibration model (BVM), to a monomer and a homodimer. In the HVM, we specifically include the vibronic states in the Hamiltonian capturing vibronic quenching, whereas in the BVM, all vibrational details are contained within the bath and described by an underdamped spectral density. The resultant spectra are analyzed in terms of energetic peak position and thermodynamic broadening precision in order to evaluate the efficacy of the two models. The HVM produces 2D spectra with accurate peak positional information, while the BVM is well suited to modeling dynamic peak broadening. For the monomer, both models produce equivalent spectra in the limit where additional damping associated with the underdamped vibration in the BVM approaches zero. This is supported by analytical results. However, for the homodimer, the BVM spectra are redshifted with respect to the HVM due to an absence of vibronic quenching in the BVM. The computational efficiency of the two models is also discussed in order to inform us of the most appropriate use of each method.
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Affiliation(s)
- Ben S. Humphries
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Dale Green
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Garth A. Jones
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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10
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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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11
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Bubilaitis V, Rancova O, Abramavicius D. Vibration-mediated energy transport in bacterial reaction center: Simulation study. J Chem Phys 2021; 154:214115. [PMID: 34240965 DOI: 10.1063/5.0048815] [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
Exciton energy relaxation in a bacterial Reaction Center (bRC) pigment-protein aggregate presumably involves emission of high energy vibrational quanta to cover wide energy gaps between excitons. Here, we assess this hypothesis utilizing vibronic two-particle theory in modeling of the excitation relaxation process in bRC. Specific high frequency molecular vibrational modes are included explicitly one at a time in order to check which high frequency vibrations are involved in the excitation relaxation process. The low frequency bath modes are treated perturbatively within Redfield relaxation theory. The analysis of the population relaxation rate data indicates energy flow pathways in bRC and suggests that specific vibrations may be responsible for the excitation relaxation process.
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Affiliation(s)
- Vytautas Bubilaitis
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius 10222, Lithuania
| | - Olga Rancova
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius 10222, Lithuania
| | - Darius Abramavicius
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius 10222, Lithuania
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12
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Arsenault EA, Schile AJ, Limmer DT, Fleming GR. Vibronic coupling in energy transfer dynamics and two-dimensional electronic-vibrational spectra. J Chem Phys 2021; 155:054201. [PMID: 34364357 DOI: 10.1063/5.0056477] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We introduce a heterodimer model in which multiple mechanisms of vibronic coupling and their impact on energy transfer can be explicitly studied. We consider vibronic coupling that arises through either Franck-Condon activity in which each site in the heterodimer has a local electron-phonon coupling or Herzberg-Teller activity in which the transition dipole moment coupling the sites has an explicit vibrational mode-dependence. We have computed two-dimensional electronic-vibrational (2DEV) spectra for this model while varying the magnitude of these two effects and find that 2DEV spectra contain static and dynamic signatures of both types of vibronic coupling. Franck-Condon activity emerges through a change in the observed excitonic structure, while Herzberg-Teller activity is evident in the appearance of significant side-band transitions that mimic the lower-energy excitonic structure. A comparison of quantum beating patterns obtained from analysis of the simulated 2DEV spectra shows that this technique can report on the mechanism of energy transfer, elucidating a means of experimentally determining the role of specific vibronic coupling mechanisms in such processes.
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Affiliation(s)
- Eric A Arsenault
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Addison J Schile
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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13
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Bialas D, Kirchner E, Röhr MIS, Würthner F. Perspectives in Dye Chemistry: A Rational Approach toward Functional Materials by Understanding the Aggregate State. J Am Chem Soc 2021; 143:4500-4518. [DOI: 10.1021/jacs.0c13245] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David Bialas
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eva Kirchner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Merle I. S. Röhr
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Frank Würthner
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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14
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Sláma V, Perlík V, Langhals H, Walter A, Mančal T, Hauer J, Šanda F. Anharmonic Molecular Motion Drives Resonance Energy Transfer in peri-Arylene Dyads. Front Chem 2020; 8:579166. [PMID: 33330367 PMCID: PMC7732524 DOI: 10.3389/fchem.2020.579166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Spectral and dynamical properties of molecular donor-acceptor systems strongly depend on the steric arrangement of the constituents with exciton coupling J as a key control parameter. In the present work we study two peri-arylene based dyads with orthogonal and parallel transition dipoles for donor and acceptor moieties, respectively. We show that the anharmonic multi-well character of the orthogonal dyad's intramolecular potential explains findings from both stationary and time-resolved absorption experiments. While for a parallel dyad, standard quantum chemical estimates of J at 0 K are in good agreement with experimental observations, J becomes vanishingly small for the orthogonal dyad, in contrast to its ultrafast experimental transfer times. This discrepancy is not resolved even by accounting for harmonic fluctuations along normal coordinates. We resolve this problem by supplementing quantum chemical approaches with dynamical sampling of fluctuating geometries. In contrast to the moderate Gaussian fluctuations of J for the parallel dyad, fluctuations for the orthogonal dyad are found to follow non-Gaussian statistics leading to significantly higher effective J in good agreement with experimental observations. In effort to apply a unified framework for treating the dynamics of optical coherence and excitonic populations of both dyads, we employ a vibronic approach treating electronic and selected vibrational degrees on an equal footing. This vibronic model is used to model absorption and fluorescence spectra as well as donor-acceptor transport dynamics and covers the more traditional categories of Förster and Redfield transport as limiting cases.
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Affiliation(s)
- Vladislav Sláma
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Václav Perlík
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Heinz Langhals
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Walter
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomáš Mančal
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Jürgen Hauer
- Professur für Dynamische Spektroskopien, Fakultät für Chemie, Technische Universität München, Munich, Germany
| | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
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15
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Seibt J, Kühn O. Exciton transfer using rates extracted from the “hierarchical equations of motion”. J Chem Phys 2020; 153:194112. [DOI: 10.1063/5.0027373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Joachim Seibt
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Oliver Kühn
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
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16
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Cunningham PD, Díaz SA, Yurke B, Medintz IL, Melinger JS. Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers. J Phys Chem B 2020; 124:8042-8049. [PMID: 32706583 DOI: 10.1021/acs.jpcb.0c06732] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.
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Affiliation(s)
- Paul D Cunningham
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Bernard Yurke
- Boise State University, Boise, Idaho 83725, United States
| | - Igor L Medintz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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17
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Sohail SH, Otto JP, Cunningham PD, Kim YC, Wood RE, Allodi MA, Higgins JS, Melinger JS, Engel GS. DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer. Chem Sci 2020; 11:8546-8557. [PMID: 34123114 PMCID: PMC8163443 DOI: 10.1039/d0sc01127d] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm−1 and 1545 cm−1 for the 0-bp dimer and 1100 cm−1 for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications. Dyes coupled to DNA display distance-dependent vibronic couplings that prolongs quantum coherences detected with 2D spectroscopy.![]()
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Affiliation(s)
- Sara H Sohail
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - John P Otto
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Paul D Cunningham
- U.S. Naval Research Laboratory 4555 Overlook Avenue SW Washington DC 20375 USA
| | - Young C Kim
- U.S. Naval Research Laboratory 4555 Overlook Avenue SW Washington DC 20375 USA
| | - Ryan E Wood
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Marco A Allodi
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Jacob S Higgins
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Joseph S Melinger
- U.S. Naval Research Laboratory 4555 Overlook Avenue SW Washington DC 20375 USA
| | - Gregory S Engel
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
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18
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Arsenault EA, Yoneda Y, Iwai M, Niyogi KK, Fleming GR. Vibronic mixing enables ultrafast energy flow in light-harvesting complex II. Nat Commun 2020; 11:1460. [PMID: 32193383 PMCID: PMC7081214 DOI: 10.1038/s41467-020-14970-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/12/2020] [Indexed: 11/09/2022] Open
Abstract
Since the discovery of quantum beats in the two-dimensional electronic spectra of photosynthetic pigment-protein complexes over a decade ago, the origin and mechanistic function of these beats in photosynthetic light-harvesting has been extensively debated. The current consensus is that these long-lived oscillatory features likely result from electronic-vibrational mixing, however, it remains uncertain if such mixing significantly influences energy transport. Here, we examine the interplay between the electronic and nuclear degrees of freedom (DoF) during the excitation energy transfer (EET) dynamics of light-harvesting complex II (LHCII) with two-dimensional electronic-vibrational spectroscopy. Particularly, we show the involvement of the nuclear DoF during EET through the participation of higher-lying vibronic chlorophyll states and assign observed oscillatory features to specific EET pathways, demonstrating a significant step in mapping evolution from energy to physical space. These frequencies correspond to known vibrational modes of chlorophyll, suggesting that electronic-vibrational mixing facilitates rapid EET over moderately size energy gaps.
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Affiliation(s)
- Eric A Arsenault
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Yoneda
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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19
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Zheng J, Peng J, Xie Y, Long Y, Ning X, Lan Z. Study of the exciton dynamics in perylene bisimide (PBI) aggregates with symmetrical quasiclassical dynamics based on the Meyer–Miller mapping Hamiltonian. Phys Chem Chem Phys 2020; 22:18192-18204. [DOI: 10.1039/d0cp00648c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The exciton dynamics in one-dimensional stacked PBI (Perylene Bisimide) aggregates was studied with SQC-MM dynamics (Symmetrical Quasiclassical Dynamics based on the Meyer–Miller mapping Hamiltonian).
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Affiliation(s)
- Jie Zheng
- Industrial Research Institute of Nonwovens & Technical Textiles
- Shandong Center for Engineered Nonwovens (SCEN)
- College of Textiles Clothing
- Qingdao University
- Qingdao 266071
| | - Jiawei Peng
- SCNU Environmental Research Institute
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment
- South China Normal University
- Guangzhou 510006
- China
| | - Yu Xie
- SCNU Environmental Research Institute
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment
- South China Normal University
- Guangzhou 510006
- China
| | - Yunze Long
- Industrial Research Institute of Nonwovens & Technical Textiles
- Shandong Center for Engineered Nonwovens (SCEN)
- College of Textiles Clothing
- Qingdao University
- Qingdao 266071
| | - Xin Ning
- Industrial Research Institute of Nonwovens & Technical Textiles
- Shandong Center for Engineered Nonwovens (SCEN)
- College of Textiles Clothing
- Qingdao University
- Qingdao 266071
| | - Zhenggang Lan
- SCNU Environmental Research Institute
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment
- South China Normal University
- Guangzhou 510006
- China
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20
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Heussman D, Kittell J, Kringle L, Tamimi A, von Hippel PH, Marcus AH. Measuring local conformations and conformational disorder of (Cy3) 2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy. Faraday Discuss 2019; 216:211-235. [PMID: 31038134 DOI: 10.1039/c8fd00245b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The sugar-phosphate backbone of DNA near single-stranded (ss)-double-stranded (ds) junctions likely fluctuates within a broad distribution of conformations to permit the proper binding of genome regulatory proteins that function at these sites. In this work we use absorbance, circular dichroism (CD), and two-dimensional fluorescence spectroscopy (2DFS) to study the local conformations and conformational disorder within chromophore-labeled DNA constructs. These constructs employ dimers of the fluorescent chromophore Cy3 that are site-specifically incorporated into the sugar-phosphate backbones of DNA strands at ss-ds DNA fork junctions. We show that these data can be analyzed to determine the local conformations of the (Cy3)2 dimer, and the degree of conformational disorder. Our analysis employs an essential-state Holstein-Frenkel Hamiltonian model, which takes into account the internal electronic-vibrational motions within each Cy3 chromophore, and the resonant electronic interaction that couples the two chromophores together. Our results suggest that this approach may be applied generally to understand local backbone conformation and conformational disorder at ss-ds DNA fork junctions.
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Affiliation(s)
- Dylan Heussman
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Justin Kittell
- Department of Physics, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA
| | - Loni Kringle
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Amr Tamimi
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA. and Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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21
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Wang L, Allodi MA, Engel GS. Quantum coherences reveal excited-state dynamics in biophysical systems. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0109-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Storm FE, Rasmussen MH, Mikkelsen KV, Hansen T. Computational construction of the electronic Hamiltonian for photoinduced electron transfer and Redfield propagation. Phys Chem Chem Phys 2019; 21:17366-17377. [DOI: 10.1039/c9cp03297e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The construction of open-system diabatic Hamiltonians relevant for the investigation of electron transfer processes is a computational challenge. Here all relevant parameters for Redfield propagations are extracted fromab initiocomputations.
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Affiliation(s)
- Freja E. Storm
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | | | - Kurt V. Mikkelsen
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Thorsten Hansen
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen
- Denmark
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23
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Kringle L, Sawaya NPD, Widom J, Adams C, Raymer MG, Aspuru-Guzik A, Marcus AH. Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA. J Chem Phys 2018; 148:085101. [PMID: 29495791 DOI: 10.1063/1.5020084] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.
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Affiliation(s)
- Loni Kringle
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Julia Widom
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Carson Adams
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Michael G Raymer
- Department of Physics, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
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24
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Cunningham PD, Kim YC, Díaz SA, Buckhout-White S, Mathur D, Medintz IL, Melinger JS. Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds. J Phys Chem B 2018; 122:5020-5029. [PMID: 29698610 DOI: 10.1021/acs.jpcb.8b02134] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We examine the effect of electronic coupling on the optical properties of Cy3 dimers attached to DNA duplexes as a function of base pair (bp) separation using steady-state and time-resolved spectroscopy. For close Cy3-Cy3 separations, 0 and 1 bp between dyes, intermediate to strong electronic coupling is revealed by modulation of the absorption and fluorescence properties including spectral band shape, peak wavelength, and excited-state lifetime. Using a vibronic exciton model, we estimate coupling strengths of 150 and 266 cm-1 for the 1 and 0 bp separations, respectively, which are comparable to those found in natural light-harvesting complexes. For the strongest electronic coupling (0 bp separation), we observe that the absorption band shape is strongly affected by the base pairs that surround the dyes, where more strongly hydrogen-bonded G-C pairs produce a red-shifted absorption spectrum consistent with a J-type dimer. This effect is studied theoretically using molecular dynamics simulation, which predicts an in-line dye configuration that is consistent with the experimental J-type spectrum. When the Cy3 dimers are in a standard aqueous buffer, the presence of relatively strong electronic coupling is accompanied by decreased fluorescence lifetime, suggesting that it promotes nonradiative relaxation in cyanine dyes. However, we show that the use of a viscous solvent can suppress this nonradiative recombination and thereby restore the dimer fluorescent emission. Ultrafast transient absorption measurements of Cy3 dimers in both standard aqueous buffer and viscous glycerol buffer suggest that sufficiently strong electronic coupling increases the probability of excited-state relaxation through a dark state that is related to Cy3 torsional motion.
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Affiliation(s)
| | | | | | | | - Divita Mathur
- College of Science , George Mason University , Fairfax , Virginia 22030 , United States
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25
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Hestand NJ, Spano FC. Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer. Chem Rev 2018; 118:7069-7163. [PMID: 29664617 DOI: 10.1021/acs.chemrev.7b00581] [Citation(s) in RCA: 719] [Impact Index Per Article: 119.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The electronic excited states of molecular aggregates and their photophysical signatures have long fascinated spectroscopists and theoreticians alike since the advent of Frenkel exciton theory almost 90 years ago. The influence of molecular packing on basic optical probes like absorption and photoluminescence was originally worked out by Kasha for aggregates dominated by Coulombic intermolecular interactions, eventually leading to the classification of J- and H-aggregates. This review outlines advances made in understanding the relationship between aggregate structure and photophysics when vibronic coupling and intermolecular charge transfer are incorporated. An assortment of packing geometries is considered from the humble molecular dimer to more exotic structures including linear and bent aggregates, two-dimensional herringbone and "HJ" aggregates, and chiral aggregates. The interplay between long-range Coulomb coupling and short-range charge-transfer-mediated coupling strongly depends on the aggregate architecture leading to a wide array of photophysical behaviors.
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Affiliation(s)
- Nicholas J Hestand
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Frank C Spano
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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26
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Cipolloni M, Fresch B, Occhiuto I, Rukin P, Komarova KG, Cecconello A, Willner I, Levine RD, Remacle F, Collini E. Coherent electronic and nuclear dynamics in a rhodamine heterodimer-DNA supramolecular complex. Phys Chem Chem Phys 2018; 19:23043-23051. [PMID: 28817145 DOI: 10.1039/c7cp01334e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Elucidating the role of quantum coherences in energy migration within biological and artificial multichromophoric antenna systems is the subject of an intense debate. It is also a practical matter because of the decisive implications for understanding the biological processes and engineering artificial materials for solar energy harvesting. A supramolecular rhodamine heterodimer on a DNA scaffold was suitably engineered to mimic the basic donor-acceptor unit of light-harvesting antennas. Ultrafast 2D electronic spectroscopic measurements allowed identifying clear features attributable to a coherent superposition of dimer electronic and vibrational states contributing to the coherent electronic charge beating between the donor and the acceptor. The frequency of electronic charge beating is found to be 970 cm-1 (34 fs) and can be observed for 150 fs. Through the support of high level ab initio TD-DFT computations of the entire dimer, we established that the vibrational modes preferentially optically accessed do not drive subsequent coupling between the electronic states on the 600 fs of the experiment. It was thereby possible to characterize the time scales of the early time femtosecond dynamics of the electronic coherence built by the optical excitation in a large rigid supramolecular system at a room temperature in solution.
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Affiliation(s)
- M Cipolloni
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
| | - B Fresch
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy. and Theoretical Physical Chemistry, University of Liège, Allée du 6 Aout 11, B4000 Liège, Belgium
| | - I Occhiuto
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
| | - P Rukin
- Theoretical Physical Chemistry, University of Liège, Allée du 6 Aout 11, B4000 Liège, Belgium
| | - K G Komarova
- Theoretical Physical Chemistry, University of Liège, Allée du 6 Aout 11, B4000 Liège, Belgium
| | - A Cecconello
- The Institute of Chemistry, Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - I Willner
- The Institute of Chemistry, Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - R D Levine
- The Institute of Chemistry, Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - F Remacle
- Theoretical Physical Chemistry, University of Liège, Allée du 6 Aout 11, B4000 Liège, Belgium
| | - E Collini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
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27
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Cannon BL, Kellis DL, Patten LK, Davis PH, Lee J, Graugnard E, Yurke B, Knowlton WB. Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System. J Phys Chem A 2017; 121:6905-6916. [PMID: 28813152 DOI: 10.1021/acs.jpca.7b04344] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.
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Affiliation(s)
- Brittany L Cannon
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Donald L Kellis
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Lance K Patten
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering, ‡Department of Chemistry & Biochemistry, and §Department of Electrical & Computer Engineering, Boise State University , Boise, Idaho 83725, United States
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28
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Perlík V, Šanda F. Vibrational relaxation beyond the linear damping limit in two-dimensional optical spectra of molecular aggregates. J Chem Phys 2017; 147:084104. [DOI: 10.1063/1.4999680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Václav Perlík
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
| | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
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29
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Cunningham PD, Bricker WP, Díaz SA, Medintz IL, Bathe M, Melinger JS. Optical determination of the electronic coupling and intercalation geometry of thiazole orange homodimer in DNA. J Chem Phys 2017; 147:055101. [DOI: 10.1063/1.4995431] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Paul D. Cunningham
- Electronics Science and Technology Division, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
| | - William P. Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Joseph S. Melinger
- Electronics Science and Technology Division, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
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30
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Fujimoto KJ, Balashov SP. Vibronic coupling effect on circular dichroism spectrum: Carotenoid–retinal interaction in xanthorhodopsin. J Chem Phys 2017. [DOI: 10.1063/1.4977045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Kazuhiro J. Fujimoto
- Faculty of Pharmaceutical Sciences, Hokuriku University, Ho-3 Kanagawa-machi, Kanazawa 920-1181, Japan
| | - Sergei P. Balashov
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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31
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Lee MH, Troisi A. Vibronic enhancement of excitation energy transport: Interplay between local and non-local exciton-phonon interactions. J Chem Phys 2017; 146:075101. [DOI: 10.1063/1.4976558] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Myeong H. Lee
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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32
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Schulze J, Shibl MF, Al-Marri MJ, Kühn O. Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex. J Chem Phys 2017; 144:185101. [PMID: 27179506 DOI: 10.1063/1.4948563] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motion and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.
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Affiliation(s)
- Jan Schulze
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Mohamed F Shibl
- Gas Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammed J Al-Marri
- Gas Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
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33
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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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34
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35
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Lee MH, Troisi A. Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach. J Chem Phys 2016; 144:214106. [DOI: 10.1063/1.4953043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Myeong H. Lee
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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36
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Singh VP, Westberg M, Wang C, Dahlberg PD, Gellen T, Gardiner AT, Cogdell RJ, Engel GS. Towards quantification of vibronic coupling in photosynthetic antenna complexes. J Chem Phys 2016; 142:212446. [PMID: 26049466 DOI: 10.1063/1.4921324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photosynthetic antenna complexes harvest sunlight and efficiently transport energy to the reaction center where charge separation powers biochemical energy storage. The discovery of existence of long lived quantum coherence during energy transfer has sparked the discussion on the role of quantum coherence on the energy transfer efficiency. Early works assigned observed coherences to electronic states, and theoretical studies showed that electronic coherences could affect energy transfer efficiency--by either enhancing or suppressing transfer. However, the nature of coherences has been fiercely debated as coherences only report the energy gap between the states that generate coherence signals. Recent works have suggested that either the coherences observed in photosynthetic antenna complexes arise from vibrational wave packets on the ground state or, alternatively, coherences arise from mixed electronic and vibrational states. Understanding origin of coherences is important for designing molecules for efficient light harvesting. Here, we give a direct experimental observation from a mutant of LH2, which does not have B800 chromophores, to distinguish between electronic, vibrational, and vibronic coherence. We also present a minimal theoretical model to characterize the coherences both in the two limiting cases of purely vibrational and purely electronic coherence as well as in the intermediate, vibronic regime.
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Affiliation(s)
- V P Singh
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - M Westberg
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - C Wang
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - P D Dahlberg
- Graduate Program in the Biophysical Sciences, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - T Gellen
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - A T Gardiner
- Department of Botany, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, Scotland
| | - R J Cogdell
- Department of Botany, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, Scotland
| | - G S Engel
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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37
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Tubasum S, Torbjörnsson M, Yadav D, Camacho R, Söderlind G, Scheblykin IG, Pullerits T. Protein Configuration Landscape Fluctuations Revealed by Exciton Transition Polarizations in Single Light Harvesting Complexes. J Phys Chem B 2016; 120:724-32. [PMID: 26741912 DOI: 10.1021/acs.jpcb.5b12466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein is a flexible material with broad distribution of conformations forming an energy landscape of quasi-stationary states. Disentangling the system dynamics along this landscape is the key for understanding the functioning of the protein. Here we studied a photosynthetic antenna pigment-protein complex LH2 with single molecule two-dimensional polarization imaging. Modeling based on the Redfield relaxation theory well describes the observed polarization properties of LH2 fluorescence and fluorescence excitation, strongly suggesting that at 77 K the conformational subspace of the LH2 is limited to about three configurations with relatively frequent switching among each other. At room temperature the next level of fluctuations determines the conformational dynamics. The results support the multitier model of the energy landscape of proteins and demonstrate the potential of the method for the studies of structural dynamics in proteins.
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Affiliation(s)
- Sumera Tubasum
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
| | - Magne Torbjörnsson
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
| | - Dheerendra Yadav
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
| | - Rafael Camacho
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
| | - Gustaf Söderlind
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
| | - Ivan G Scheblykin
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
| | - Tõnu Pullerits
- Division of Chemical Physics, Department of Chemistry, Lund University , Box 124, 22100 Lund, Sweden.,Division of Numerical Analysis, Centre for Mathematical Sciences, Lund University , Box 124, 22100 Lund, Sweden
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38
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Plötz PA, Polyutov SP, Ivanov SD, Fennel F, Wolter S, Niehaus T, Xie Z, Lochbrunner S, Würthner F, Kühn O. Biphasic aggregation of a perylene bisimide dye identified by exciton-vibrational spectra. Phys Chem Chem Phys 2016; 18:25110-25119. [DOI: 10.1039/c6cp04898f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The quantum efficiency of light emission supramolecular aggregates strongly depends on the intermolecular coupling. We present a molecule which demonstrates two different aggregated structures with high and low quantum efficiency. The spectral signatures can be understood by simulating the aggregated structures and the corresponding exciton-vibrational spectra.
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Affiliation(s)
- P.-A. Plötz
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
| | - S. P. Polyutov
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
- Laboratory for Nonlinear Optics and Spectroscopy
| | - S. D. Ivanov
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
| | - F. Fennel
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
| | - S. Wolter
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
| | - T. Niehaus
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622
- France
| | - Z. Xie
- Institut für Organische Chemie & Center for Nanosystems Chemistry
- Universität Würzburg
- 97074 Würzburg
- Germany
| | - S. Lochbrunner
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
| | - F. Würthner
- Institut für Organische Chemie & Center for Nanosystems Chemistry
- Universität Würzburg
- 97074 Würzburg
- Germany
| | - O. Kühn
- Institut für Physik
- Universität Rostock
- 18059 Rostock
- Germany
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39
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Song KH, Gu M, Kim MS, Kwon HJ, Rhee H, Han H, Cho M. Quantum Beats and Phase Shifts in Two-Dimensional Electronic Spectra of Zinc Naphthalocyanine Monomer and Aggregate. J Phys Chem Lett 2015; 6:4314-4318. [PMID: 26722967 DOI: 10.1021/acs.jpclett.5b02030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The origin of quantum coherence in two-dimensional (2D) electronic spectra of molecular aggregates and light-harvesting complexes still remains an open question. In particular, it could be challenging to distinguish between electronic and vibrational coherences for a coupled system, where both degrees of freedom can be simultaneously excited. In this Letter, we examine quantum beats in the 2D spectra of zinc naphthalocyanine (ZnNc) aggregate and monomer, and compare their characteristic features in terms of the frequency and relative phase of diagonal and off-diagonal amplitude oscillations. The long-lasting oscillating components (>1 ps) at 600-700 cm(-1) observed in both the aggregate and monomer are found to be attributed to the vibrational coherence. The wide phase variations of the 2D spectral amplitude oscillations are observed not just in the aggregate but also in the monomer state. This suggests that the unusual 90° phase shift may be attributed to neither quantum population-to-coherence transfer nor vibronic exciton coupling.
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Affiliation(s)
- Ki-Hee Song
- Space-Time Resolved Molecular Imaging Research Team, Korea Basic Science Institute (KBSI) , Seoul 136-713, Korea
| | - Munui Gu
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Min-Seok Kim
- Space-Time Resolved Molecular Imaging Research Team, Korea Basic Science Institute (KBSI) , Seoul 136-713, Korea
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 136-701, Republic of Korea
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Hanju Rhee
- Space-Time Resolved Molecular Imaging Research Team, Korea Basic Science Institute (KBSI) , Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 136-701, Republic of Korea
- Department of Chemistry, Korea University , Seoul 136-701, Korea
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40
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Lambert C, Koch F, Völker SF, Schmiedel A, Holzapfel M, Humeniuk A, Röhr MIS, Mitric R, Brixner T. Energy Transfer Between Squaraine Polymer Sections: From Helix to Zigzag and All the Way Back. J Am Chem Soc 2015; 137:7851-61. [DOI: 10.1021/jacs.5b03644] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Lambert
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Federico Koch
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sebastian F. Völker
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander Schmiedel
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Marco Holzapfel
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander Humeniuk
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Merle I. S. Röhr
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roland Mitric
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tobias Brixner
- Institut
für Organische Chemie, ‡Center for Nanosystems Chemistry
(CNC), and §Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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41
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Schulze J, Kühn O. Explicit correlated exciton-vibrational dynamics of the FMO complex. J Phys Chem B 2015; 119:6211-6. [PMID: 25927682 DOI: 10.1021/acs.jpcb.5b03928] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coupled exciton-vibrational dynamics of a three-site model of the Fenna-Matthews-Olson complex is investigated using the numerically exact multilayer multiconfiguration time-dependent Hartree approach. Thereby the specific coupling of the vibrational modes to local electronic transitions is adapted from a discretized experimental spectral density. The solution of the resulting time-dependent Schrödinger equation including three electronic and 450 vibrational degrees of freedom is analyzed in terms of excitonic populations and coherences. Emphasis is put onto the role of specific ranges of vibrational frequencies. It is observed that modes between 160 and 300 cm(-1) are responsible for the sub-picosecond population and coherence decay. Further, it is found that a mean-field approach with respect to the vibrational degrees of freedom is not applicable.
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Affiliation(s)
- J Schulze
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| | - O Kühn
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
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42
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Gelzinis A, Abramavicius D, Valkunas L. Absorption lineshapes of molecular aggregates revisited. J Chem Phys 2015; 142:154107. [DOI: 10.1063/1.4918343] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Andrius Gelzinis
- 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
| | - 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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43
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Dinh TC, Renger T. Towards an exact theory of linear absorbance and circular dichroism of pigment-protein complexes: Importance of non-secular contributions. J Chem Phys 2015; 142:034104. [DOI: 10.1063/1.4904928] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Thanh-Chung Dinh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
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44
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Sato Y, Doolittle B. Influence of intra-pigment vibrations on dynamics of photosynthetic exciton. J Chem Phys 2014; 141:185102. [DOI: 10.1063/1.4901056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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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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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46
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Sand AM, Liu C, Valentine AJS, Mazziotti DA. Modulating the electronic structure of chromophores by chemical substituents for efficient energy transfer: application to fluorone. J Phys Chem A 2014; 118:6085-91. [PMID: 25062094 DOI: 10.1021/jp503900m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strong electron correlation within a quasi-spin model of chromophores was recently shown to enhance exciton energy transfer significantly. Here we investigate how the modulation of the electronic structure of the chromophores by chemical substitution can enhance energy-transfer efficiency. Unlike previous work that does not consider the direct effect of the electronic structure on exciton dynamics, we add chemical substituents to the fluorone dimer to study the effect of electron-donating and electron-withdrawing substituents on exciton energy transfer. The exciton dynamics are studied from the solution of a quantum Liouville equation for an open system whose model Hamiltonian is derived from excited-state electronic structure calculations. Both van der Waals energies and coupling energies, arising from the Hellmann-Feynman force generated upon transferring the dimers from infinity to a finite separation, are built into the model Hamiltonian. Though these two effects are implicitly treated in dipole-based models, their explicit and separate treatment as discussed here is critical to forging the correct connection with the electronic structure calculations. We find that the addition of electron-donating substituents to the fluorone system results in an increase in exciton-transfer rates by factors ranging from 1.3-1.9. The computed oscillator strength is consistent with the recent experimental results on a larger heterodimer system containing fluorone. The oscillator strength increases with the addition of electron-donating substituents. Our results indicate that the study of chromophore networks via electronic structure will help in the future design of efficient synthetic light-harvesting systems.
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Affiliation(s)
- Andrew M Sand
- Department of Chemistry and The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
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47
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Bašinskaitė E, Butkus V, Abramavicius D, Valkunas L. Vibronic models for nonlinear spectroscopy simulations. PHOTOSYNTHESIS RESEARCH 2014; 121:95-106. [PMID: 24740300 DOI: 10.1007/s11120-014-0002-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
It is already well established that the high-frequency intramolecular vibrations are responsible for many observed dynamic phenomena in linear and nonlinear electronic spectroscopy such as the spectral lineshape formation, the transition dipole moment, the lifetime borrowing, and vibrational and mixed coherence beats. All these implications together with the vibronic enhancement of the energy and charge transfer can be explained by the vibronic molecular exciton theory and are highly relevant for the description of the spectral dynamics in photosynthetic pigment-protein complexes. In this paper, a few critical points of the vibronic theory application to linear and nonlinear signals are discussed. Models, which differ in the selection and truncation of molecular basis, are compared by analyzing the energy spectrum and exciton-vibrational dynamics in the presence of the energetic disorder. The limits of the widely used one-particle approximation are defined.
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Affiliation(s)
- Eglė Bašinskaitė
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222, Vilnius, Lithuania
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48
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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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Halpin A, Johnson PJM, Miller RJD. Comment on "Engineering coherence among excited states in synthetic heterodimer systems". Science 2014; 344:1099. [PMID: 24904149 DOI: 10.1126/science.1250926] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hayes et al. (Reports, 21 June 2013, p. 1431) used two-dimensional (2D) electronic spectroscopy to study molecular heterodimers and reported a general mechanism for the prolongation of electronic coherences, consistent with previous interpretations of 2D spectra for light-harvesting systems. We argue that the dynamics attributed to electronic coherences are inconclusive based on experimental inconsistencies arising from limited sample characterization and insufficient control measurements.
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Affiliation(s)
- Alexei Halpin
- Institute for Optical Sciences and Departments of Chemistry and Physics, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | - Philip J M Johnson
- Institute for Optical Sciences and Departments of Chemistry and Physics, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | - R J Dwayne Miller
- Institute for Optical Sciences and Departments of Chemistry and Physics, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada. Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany.
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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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