51
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Besaw JE, Miller RJD. Addressing high excitation conditions in time-resolved X-ray diffraction experiments and issues of biological relevance. Curr Opin Struct Biol 2023; 81:102624. [PMID: 37331203 DOI: 10.1016/j.sbi.2023.102624] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
One of the most important fundamental questions connecting chemistry to biology is how chemistry scales in complexity up to biological systems where there are innumerable possible pathways and competing processes. With the development of ultrabright electron and x-ray sources, it has been possible to literally light up atomic motions to directly observe the reduction in dimensionality in the barrier crossing region to a few key reaction modes. How do these chemical processes further couple to the surrounding protein or macromolecular assembly to drive biological functions? Optical methods to trigger photoactive biological processes are needed to probe this issue on the relevant timescales. However, the excitation conditions have been in the highly nonlinear regime, which questions the biological relevance of the observed structural dynamics.
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Affiliation(s)
- Jessica E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
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52
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Li Q, Orcutt K, Cook RL, Sabines-Chesterking J, Tong AL, Schlau-Cohen GS, Zhang X, Fleming GR, Whaley KB. Single-photon absorption and emission from a natural photosynthetic complex. Nature 2023; 619:300-304. [PMID: 37316658 PMCID: PMC10338339 DOI: 10.1038/s41586-023-06121-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/24/2023] [Indexed: 06/16/2023]
Abstract
Photosynthesis is generally assumed to be initiated by a single photon1-3 from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre squared per second within a chlorophyll absorption band1. Yet much experimental and theoretical work over the past 40 years has explored the events during photosynthesis subsequent to absorption of light from intense, ultrashort laser pulses2-15. Here, we use single photons to excite under ambient conditions the light-harvesting 2 (LH2) complex of the purple bacterium Rhodobacter sphaeroides, comprising B800 and B850 rings that contain 9 and 18 bacteriochlorophyll molecules, respectively. Excitation of the B800 ring leads to electronic energy transfer to the B850 ring in approximately 0.7 ps, followed by rapid B850-to-B850 energy transfer on an approximately 100-fs timescale and light emission at 850-875 nm (refs. 16-19). Using a heralded single-photon source20,21 along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons. We also find that the probability distribution of the number of heralds per detected fluorescence photon supports the view that a single photon can upon absorption drive the subsequent energy transfer and fluorescence emission and hence, by extension, the primary charge separation of photosynthesis. An analytical stochastic model and a Monte Carlo numerical model capture the data, further confirming that absorption of single photons is correlated with emission of single photons in a natural light-harvesting complex.
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Affiliation(s)
- Quanwei Li
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, USA
| | - Kaydren Orcutt
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert L Cook
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, USA
| | - Javier Sabines-Chesterking
- Joint Quantum Institute, National Institute of Standards and Technology and University of Maryland, Gaithersburg, MD, USA
| | - Ashley L Tong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Xiang Zhang
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, USA
- Nanoscale Science and Engineering Center, University of California, Berkeley, CA, USA
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - K Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, USA.
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53
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Kumar S, Dunn IS, Deng S, Zhu T, Zhao Q, Williams OF, Tempelaar R, Huang L. Exciton annihilation in molecular aggregates suppressed through qu antum interference. Nat Chem 2023:10.1038/s41557-023-01233-x. [PMID: 37337112 DOI: 10.1038/s41557-023-01233-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/05/2023] [Indexed: 06/21/2023]
Abstract
Exciton-exciton annihilation (EEA), an important loss channel in optoelectronic devices and photosynthetic complexes, has conventionally been assumed to be an incoherent, diffusion-limited process. Here we challenge this assumption by experimentally demonstrating the ability to control EEA in molecular aggregates using the quantum phase relationships of excitons. We employed time-resolved photoluminescence microscopy to independently determine exciton diffusion constants and annihilation rates in two substituted perylene diimide aggregates featuring contrasting excitonic phase envelopes. Low-temperature EEA rates were found to differ by more than two orders of magnitude for the two compounds, despite comparable diffusion constants. Simulated rates based on a microscopic theory, in excellent agreement with experiments, rationalize this EEA behaviour based on quantum interference arising from the presence or absence of spatial phase oscillations of delocalized excitons. These results offer an approach for designing molecular materials using quantum interference where low annihilation can coexist with high exciton concentrations and mobilities.
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Affiliation(s)
- Sarath Kumar
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Ian S Dunn
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Shibin Deng
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Tong Zhu
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Qiuchen Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Roel Tempelaar
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Libai Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
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54
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Hansen T, Bezriadina T, Popova-Gorelova D. Theoretical Description of Attosecond X-ray Absorption Spectroscopy of Frenkel Exciton Dynamics. Molecules 2023; 28:molecules28114502. [PMID: 37298978 DOI: 10.3390/molecules28114502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Frenkel excitons are responsible for the transport of light energy in many molecular systems. Coherent electron dynamics govern the initial stage of Frenkel-exciton transfer. Capability to follow coherent exciton dynamics in real time will help to reveal their actual contribution to the efficiency of light-harvesting. Attosecond X-ray pulses are the tool with the necessary temporal resolution to resolve pure electronic processes with atomic sensitivity. We describe how attosecond X-ray pulses can probe coherent electronic processes during Frenkel-exciton transport in molecular aggregates. We analyze time-resolved absorption cross section taking broad spectral bandwidth of an attosecond pulse into account. We demonstrate that attosecond X-ray absorption spectra can reveal delocalization degree of coherent exciton transfer dynamics.
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Affiliation(s)
- Tim Hansen
- I. Institute for Theoretical Physics, Universität Hamburg, Notkestr. 9, 22607 Hamburg, Germany
| | - Tatiana Bezriadina
- I. Institute for Theoretical Physics, Universität Hamburg, Notkestr. 9, 22607 Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
| | - Daria Popova-Gorelova
- I. Institute for Theoretical Physics, Universität Hamburg, Notkestr. 9, 22607 Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
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55
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Cartwright JHE. Quantum noise may limit the mechanosensory sensitivity of cilia in the left-right organizer of the vertebrate bodyplan. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:83-86. [PMID: 37137357 DOI: 10.1016/j.pbiomolbio.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Could nature be harnessing quantum mechanics in cilia to optimize the sensitivity of the mechanism of left-right symmetry breaking during development in vertebrates? I evaluate whether mechanosensing - i.e., the detection of a left-right asymmetric signal through mechanical stimulation of sensory cilia, as opposed to biochemical signalling - might be functioning in the embryonic left-right organizer of the vertebrate bodyplan through quantum mechanics. I conclude that there is a possible role for quantum biology in mechanosensing in cilia. The system may not be limited by classical thermal noise, but instead by quantum noise, with an amplification process providing active cooling.
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Affiliation(s)
- Julyan H E Cartwright
- Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, 18100, Armilla, Granada, Spain; Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, 18071, Granada, Spain.
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56
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Dani R, Kundu S, Makri N. Coherence Maps and Flow of Excitation Energy in the Bacterial Light Harvesting Complex 2. J Phys Chem Lett 2023; 14:3835-3843. [PMID: 37067041 DOI: 10.1021/acs.jpclett.3c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
We present and analyze coherence maps [ J. Phys. Chem. B 2022, 126, 9361-9375] to investigate the quantum coherences that are created, sustained, and damped by vibrational modes during the transfer of excitation energy from the B800 (outer) to the B850 (inner) ring of the light harvesting complex 2 (LH2) of purple bacteria with a variety of initial conditions. The reduced density matrix of the 24-pigment complex, where the ground and excited electronic states of each bacteriochlorophyll are explicitly coupled to 50 intramolecular vibrations at room temperature, is obtained from fully quantum-mechanical small matrix path integral (SMatPI) calculations. The coherence maps show a very rapid localization within the outer ring, accompanied by the formation of inter-ring quantum superpositions that evolve to a partial quantum delocalization at equilibrium, and quantify in state-to-state detail the flow of energy within the complex.
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Affiliation(s)
- Reshmi Dani
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Sohang Kundu
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Nancy Makri
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
- Illinois Quantum Information Science and Technology Center, University of Illinois, Urbana, Illinois 61801, United States
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57
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Maity S, Kleinekathöfer U. Recent progress in atomistic modeling of light-harvesting complexes: a mini review. PHOTOSYNTHESIS RESEARCH 2023; 156:147-162. [PMID: 36207489 PMCID: PMC10070314 DOI: 10.1007/s11120-022-00969-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany.
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58
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Cina JA. Dynamics of an excitation-transfer trimer: Interference, coherence, Berry's phase development, and vibrational control of non-adiabaticity. J Chem Phys 2023; 158:124307. [PMID: 37003733 DOI: 10.1063/5.0139174] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
We detail several interesting features in the dynamics of an equilaterally shaped electronic excitation-transfer (EET) trimer with distance-dependent intermonomer excitation-transfer couplings. In the absence of electronic-vibrational coupling, symmetric and antisymmetric superpositions of two single-monomer excitations are shown to exhibit purely constructive, oscillatory, and purely destructive interference in the EET to the third monomer, respectively. In the former case, the transfer is modulated by motion in the symmetrical framework-expansion vibration induced by the Franck-Condon excitation. Distortions in the shape of the triangular framework degrade that coherent EET while activating excitation transfer in the latter case of an antisymmetric initial state. In its symmetrical configuration, two of the three single-exciton states of the trimer are degenerate. This degeneracy is broken by the Jahn-Teller-active framework distortions. The calculations illustrate closed, approximately circular pseudo-rotational wave-packet dynamics on both the lower and the upper adiabatic potential energy surfaces of the degenerate manifold, which lead to the acquisition after one cycle of physically meaningful geometric (Berry) phases of π. Another manifestation of Berry-phase development is seen in the evolution of the vibrational probability density of a wave packet on the lower Jahn-Teller adiabatic potential comprising a superposition of clockwise and counterclockwise circular motions. The circular pseudo-rotation on the upper cone is shown to stabilize the adiabatic electronic state against non-adiabatic internal conversion via the conical intersection, a dynamical process analogous to Slonczewski resonance. Strategies for initiating and monitoring these various dynamical processes experimentally using pre-resonant impulsive Raman excitation, short-pulse absorption, and multi-dimensional wave-packet interferometry are outlined in brief.
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Affiliation(s)
- Jeffrey A Cina
- Department of Chemistry and Biochemistry, Oregon Center for Optical, Molecular, and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
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59
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Malpathak S, Ananth N. Non-linear correlation functions and zero-point energy flow in mixed quantum-classical semiclassical dynamics. J Chem Phys 2023; 158:104106. [PMID: 36922136 DOI: 10.1063/5.0133222] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Mixed quantum classical (MQC)-initial value representation (IVR) is a recently introduced semiclassical framework that allows for selective quantization of the modes of a complex system. In the quantum limit, MQC reproduces the semiclassical Double Herman-Kluk IVR results, accurately capturing nuclear quantum coherences and conserving zero-point energy. However, in the classical limit, although MQC mimics the Husimi-IVR for real-time correlation functions with linear operators, it is significantly less accurate for non-linear correlation functions with errors even at time zero. Here, we identify the origin of this discrepancy in the MQC formulation and propose a modification. We analytically show that the modified MQC approach is exact for all correlation functions at time zero, and in a study of zero-point energy (ZPE) flow, we numerically demonstrate that it correctly obtains the quantum and classical limits as a function of time. Interestingly, although classical-limit MQC simulations show the expected, unphysical ZPE leakage, we find that it is possible to predict and even modify the direction of ZPE flow through selective quantization of the system, with the quantum-limit modes accepting energy but preserving the minimum quantum mechanically required energy.
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Affiliation(s)
- Shreyas Malpathak
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
| | - Nandini Ananth
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
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60
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Zaragoza JPT, Offenbacher AR, Hu S, Gee CL, Firestein ZM, Minnetian N, Deng Z, Fan F, Iavarone AT, Klinman JP. Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase. Proc Natl Acad Sci U S A 2023; 120:e2211630120. [PMID: 36867685 PMCID: PMC10013837 DOI: 10.1073/pnas.2211630120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen-deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein-solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation (Ea) for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.
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Affiliation(s)
- Jan Paulo T. Zaragoza
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Adam R. Offenbacher
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, East Carolina University, Greenville, NC27858
| | - Shenshen Hu
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
| | | | - Natalie Minnetian
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Zhenyu Deng
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Flora Fan
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
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61
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Brosseau P, Seiler H, Palato S, Sonnichsen C, Baker H, Socie E, Strandell D, Kambhampati P. Perturbed free induction decay obscures early time dynamics in two-dimensional electronic spectroscopy: The case of semiconductor nanocrystals. J Chem Phys 2023; 158:084201. [PMID: 36859087 DOI: 10.1063/5.0138252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Two-dimensional electronic spectroscopy (2DES) has recently been gaining popularity as an alternative to the more common transient absorption spectroscopy due to the combination of high frequency and time resolution of 2DES. In order to advance the reliable analysis of population dynamics and to optimize the time resolution of the method, one has to understand the numerous field matter interactions that take place at an early and negative time. These interactions have historically been discussed in one-dimensional spectroscopy as coherent artifacts and have been assigned to both resonant and non-resonant system responses during or before the pulse overlap. These coherent artifacts have also been described in 2DES but remain less well-understood due to the complexity of 2DES and the relative novelty of the method. Here, we present 2DES results in two model nanocrystal samples, CdSe and CsPbI3. We demonstrate non-resonant signals due to solvent response during the pulse overlap and resonant signals, which we assign to perturbed free induction decay (PFID), both before and during the pulse overlap. The simulations of the 2DES response functions at early and negative time delays reinforce the assignment of the negative time delay signals to PFID. Modeling reveals that the PFID signals will severely distort the initial picture of the resonant population dynamics. By including these effects in models of 2DES spectra, one is able to push forward the extraction of early time dynamics in 2DES.
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Affiliation(s)
- Patrick Brosseau
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Hélène Seiler
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Samuel Palato
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Colin Sonnichsen
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Harry Baker
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Etienne Socie
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Dallas Strandell
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
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62
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Zhang C, Gruebele M, Logan D, Wolynes P. Surface crossing and energy flow in many-dimensional quantum systems. Proc Natl Acad Sci U S A 2023; 120:e2221690120. [PMID: 36821585 PMCID: PMC9992837 DOI: 10.1073/pnas.2221690120] [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: 12/21/2022] [Accepted: 01/19/2023] [Indexed: 02/24/2023] Open
Abstract
Energy flow in molecules, like the dynamics of other many-dimensional finite systems, involves quantum transport across a dense network of near-resonant states. For molecules in their electronic ground state, the network is ordinarily provided by anharmonic vibrational Fermi resonances. Surface crossing between different electronic states provides another route to chaotic motion and energy redistribution. We show that nonadiabatic coupling between electronic energy surfaces facilitates vibrational energy flow and, conversely, anharmonic vibrational couplings facilitate nonadiabatic electronic state mixing. A generalization of the Logan-Wolynes theory of quantum energy flow in many-dimensional Fermi resonance systems to the two-surface case gives a phase diagram describing the boundary between localized quantum dynamics and global energy flow. We explore these predictions and test them using a model inspired by the problem of electronic excitation energy transfer in the photosynthetic reaction center. Using an explicit numerical solution of the time-dependent Schrödinger equation for this ten-dimensional model, we find quite good agreement with the expectations from the approximate analytical theory.
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Affiliation(s)
- Chenghao Zhang
- Department of Physics, University of Illinois at Urbana-Champaign, IL61801
| | - Martin Gruebele
- Department of Physics, University of Illinois at Urbana-Champaign, IL61801
- Department of Chemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL61801
| | - David E. Logan
- Physical and Theoretical Chemistry, Oxford University, OxfordOX1 3QZ, United Kingdom
| | - Peter G. Wolynes
- Department of Chemistry Rice University, Houston, TX77251
- Department of Physics, Rice University, Houston, TX77251
- Center for Theoretical Biological Physics, Rice University, Houston, TX77251
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63
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Goudarzi H, Koutsokeras L, Balawi AH, Sun C, Manolis GK, Gasparini N, Peisen Y, Antoniou G, Athanasopoulos S, Tselios CC, Falaras P, Varotsis C, Laquai F, Cabanillas-González J, Keivanidis PE. Microstructure-driven annihilation effects and dispersive excited state dynamics in solid-state films of a model sensitizer for photon energy up-conversion applications. Chem Sci 2023; 14:2009-2023. [PMID: 36845913 PMCID: PMC9945257 DOI: 10.1039/d2sc06426j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/25/2023] [Indexed: 01/26/2023] Open
Abstract
Bimolecular processes involving exciton spin-state interactions gain attention for their deployment as wavelength-shifting tools. Particularly triplet-triplet annihilation induced photon energy up-conversion (TTA-UC) holds promise to enhance the performance of solar cell and photodetection technologies. Despite the progress noted, a correlation between the solid-state microstructure of photoactuating TTA-UC organic composites and their photophysical properties is missing. This lack of knowledge impedes the effective integration of functional TTA-UC interlayers as ancillary components in operating devices. We here investigate a solution-processed model green-to-blue TTA-UC binary composite. Solid-state films of a 9,10 diphenyl anthracene (DPA) blue-emitting activator blended with a (2,3,7,8,12,13,17,18-octaethyl-porphyrinato) PtII (PtOEP) green-absorbing sensitizer are prepared with a range of compositions and examined by a set of complementary characterization techniques. Grazing incidence X-ray diffractometry (GIXRD) measurements identify three PtOEP composition regions wherein the DPA:PtOEP composite microstructure varies due to changes in the packing motifs of the DPA and PtOEP phases. In Region 1 (≤2 wt%) DPA is semicrystalline and PtOEP is amorphous, in Region 2 (between 2 and 10 wt%) both DPA and PtOEP phases are amorphous, and in Region 3 (≥10 wt%) DPA remains amorphous and PtOEP is semicrystalline. GIXRD further reveals the metastable DPA-β polymorph species as the dominant DPA phase in Region 1. Composition dependent UV-vis and FT-IR measurements identify physical PtOEP dimers, irrespective of the structural order in the PtOEP phase. Time-gated photoluminescence (PL) spectroscopy and scanning electron microscopy imaging confirm the presence of PtOEP aggregates, even after dispersing DPA:PtOEP in amorphous poly(styrene). When arrested in Regions 1 and 2, DPA:PtOEP exhibits delayed PtOEP fluorescence at 580 nm that follows a power-law decay on the ns time scale. The origin of PtOEP delayed fluorescence is unraveled by temperature- and fluence-dependent PL experiments. Triplet PtOEP excitations undergo dispersive diffusion and enable TTA reactions that activate the first singlet-excited (S1) PtOEP state. The effect is reproduced when PtOEP is mixed with a poly(fluorene-2-octyl) (PFO) derivative. Transient absorption measurements on PFO:PtOEP films find that selective PtOEP photoexcitation activates the S1 of PFO within ∼100 fs through an up-converted 3(d, d*) PtII-centered state.
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Affiliation(s)
- Hossein Goudarzi
- Centre for Nano Science and Technology @PoliMi, Fondazione Istituto Italiano di Tecnologia 20133 Milano Italy
| | - Loukas Koutsokeras
- Device Technology and Chemical Physics Laboratory, Department of Mechanical Engineering and Materials Science and Engineering, Cyprus University of Technology 3041 Limassol Cyprus
| | - Ahmed H Balawi
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE) 23955-6900 Thuwal Kingdom of Saudi Arabia
| | - Chen Sun
- IMDEA Nanoscience, Ciudad Universitaria de Cantoblanco Calle Faraday 9 ES 28049 Madrid Spain
| | - Giorgos K Manolis
- Institute of Nanoscience and Nanotechnology, NCSR "Demokritos" 15341 Agia Paraskevi Athens Greece
| | - Nicola Gasparini
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE) 23955-6900 Thuwal Kingdom of Saudi Arabia
- Department of Chemistry, Centre for Processable Electronics, Imperial College London W120BZ UK
| | - Yuan Peisen
- Device Technology and Chemical Physics Laboratory, Department of Mechanical Engineering and Materials Science and Engineering, Cyprus University of Technology 3041 Limassol Cyprus
| | - Giannis Antoniou
- Device Technology and Chemical Physics Laboratory, Department of Mechanical Engineering and Materials Science and Engineering, Cyprus University of Technology 3041 Limassol Cyprus
| | | | - Charalampos C Tselios
- Environmental Biocatalysis and Biotechnology Laboratory, Department of Chemical Engineering, Cyprus University of Technology 3603 Limassol Cyprus
| | - Polycarpos Falaras
- Institute of Nanoscience and Nanotechnology, NCSR "Demokritos" 15341 Agia Paraskevi Athens Greece
| | - Constantinos Varotsis
- Environmental Biocatalysis and Biotechnology Laboratory, Department of Chemical Engineering, Cyprus University of Technology 3603 Limassol Cyprus
| | - Frédéric Laquai
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE) 23955-6900 Thuwal Kingdom of Saudi Arabia
| | | | - Panagiotis E Keivanidis
- Device Technology and Chemical Physics Laboratory, Department of Mechanical Engineering and Materials Science and Engineering, Cyprus University of Technology 3041 Limassol Cyprus
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64
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Calderón LF, Chuang C, Brumer P. Electronic-Vibrational Resonance Does Not Significantly Alter Steady-State Transport in Natural Light-Harvesting Systems. J Phys Chem Lett 2023; 14:1436-1444. [PMID: 36734680 DOI: 10.1021/acs.jpclett.2c03842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Oscillations in time-dependent two-dimensional electronic spectra appear as evidence of quantum coherence in light-harvesting systems related to electronic-vibrational resonant interactions. Nature, however, takes place in a non-equilibrium steady-state; therefore, the relevance of these arguments to the natural process is unclear. Here, we examine the role of intramolecular vibrations in the non-equilibrium steady-state of photosynthetic dimers in the natural scenario of incoherent light excitation. Specifically, we analyze the PEB dimer in the cryptophyte algae PE545 antenna protein. It is found that vibrations resonant with the energy difference between exciton states only marginally increase the quantum yield and the imaginary part of the intersite coherence that is relevant for transport compared to non-resonant vibrations in the natural non-equilibrium steady-state. That is, the electronic-vibrational resonance interaction does not significantly enhance energy transport under natural incoherent light excitation conditions.
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Affiliation(s)
- Leonardo F Calderón
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Grupo de Física Computacional en Materia Condensada, Escuela de Física, Facultad de Ciencias, Universidad Industrial de Santander, Carrera 27 Calle 9, Bucaramanga, Santander 680002, Colombia
| | - Chern Chuang
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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65
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Tsubouchi M, Ishii N, Kagotani Y, Shimizu R, Fujita T, Adachi M, Itakura R. Beat-frequency-resolved two-dimensional electronic spectroscopy: disentangling vibrational coherences in artificial fluorescent proteins with sub-10-fs visible laser pulses. OPTICS EXPRESS 2023; 31:6890-6906. [PMID: 36823935 DOI: 10.1364/oe.480505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
We perform a beat-frequency-resolved analysis for two-dimensional electronic spectroscopy using a high-speed and stable 2D electronic spectrometer and few-cycle visible laser pulses to disentangle the vibrational coherences in an artificial fluorescent protein. We develop a highly stable ultrashort light source that generates 5.3-fs visible pulses with a pulse energy of 4.7 µJ at a repetition rate of 10 kHz using multi-plate pulse compression and laser filamentation in a gas cell. The above-5.3-fs laser pulses together with a high-speed multichannel detector enable us to measure a series of 2D electronic spectra, which are resolved in terms of beat frequency related to vibrational coherence. We successfully extract the discrete vibrational peaks behind the inhomogeneous broadening in the absorption spectra and the vibrational quantum beats of the excited electronic state behind the strong incoherent population background in the typical 2D electronic spectra.
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66
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Leng X, Yan Y, Zhu R, Zou J, Zhang W, Shi Q. Revealing Intermolecular Electronic and Vibronic Coherence with Polarization-Dependent Two-Dimensional Beating Maps. J Phys Chem Lett 2023; 14:838-845. [PMID: 36656105 DOI: 10.1021/acs.jpclett.2c03413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Two-dimensional electronic spectroscopy (2DES) has been widely employed as an efficient tool to reveal the impact of intermolecular electronic and/or vibronic quantum coherence on excitation energy transfer in light-harvesting complexes. However, intramolecular vibrational coherence would also contribute to oscillating signals in 2D spectra, along with the intermolecular coherence signals that are directly related to energy transfer. In this work, the possibility of screening the vibrational coherence signals is explored through polarization-dependent 2DES. The all-parallel (AP) and double-crossed (DC) polarization-dependent two-dimensional rephasing spectra (2DRS) are simulated for a minimalist heterodimer model with vibrational coupling. By combining the DC-2DRS and the 2D beating maps, we demonstrate that the population and vibrational coherence signals can be largely suppressed, resulting in highlighted intermolecular electronic and vibronic coherence signals. Moreover, the AP- and DC-2DBMs show rather different patterns at the vibrational frequency, indicating a possible way to identify pure vibrational coherence.
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Affiliation(s)
- Xuan Leng
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Ruidan Zhu
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiading Zou
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzhao Zhang
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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67
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Xie H, Lyratzakis A, Khera R, Koutantou M, Welsch S, Michel H, Tsiotis G. Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum. Proc Natl Acad Sci U S A 2023; 120:e2216734120. [PMID: 36693097 PMCID: PMC9945994 DOI: 10.1073/pnas.2216734120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/27/2022] [Indexed: 01/25/2023] Open
Abstract
Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the Fenna-Matthews-Olson (FMO) proteins to a homodimeric reaction center (RC). Here, we report the cryogenic electron microscopic structure of the intact FMO-RC apparatus from Chlorobaculum tepidum at 2.5 Å resolution. The FMO-RC apparatus presents an asymmetric architecture and contains two FMO trimers that show different interaction patterns with the RC core. Furthermore, the two permanently bound transmembrane subunits PscC, which donate electrons to the special pair, interact only with the two large PscA subunits. This structure fills an important gap in our understanding of the transfer of energy from antenna to the electron transport chain of this RC and the transfer of electrons from reduced sulfur compounds to the special pair.
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Affiliation(s)
- Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | | | - Radhika Khera
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Myrto Koutantou
- Department of Chemistry, University of Crete, Voutes HeraklionGR-70013, Greece
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Georgios Tsiotis
- Department of Chemistry, University of Crete, Voutes HeraklionGR-70013, Greece
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68
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Barclay MS, Chowdhury AU, Biaggne A, Huff JS, Wright ND, Davis PH, Li L, Knowlton WB, Yurke B, Pensack RD, Turner DB. Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye. J Chem Phys 2023; 158:035101. [PMID: 36681650 DOI: 10.1063/5.0131795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.
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Affiliation(s)
- Matthew S Barclay
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Azhad U Chowdhury
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Austin Biaggne
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jonathan S Huff
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas D Wright
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul H Davis
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Lan Li
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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69
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Jing H, Magdaong NCM, Diers JR, Kirmaier C, Bocian DF, Holten D, Lindsey JS. Dyads with tunable near-infrared donor-acceptor excited-state energy gaps: molecular design and Förster analysis for ultrafast energy transfer. Phys Chem Chem Phys 2023; 25:1827-1847. [PMID: 36601996 DOI: 10.1039/d2cp04689j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacteriochlorophylls, nature's near-infrared absorbers, play an essential role in energy transfer in photosynthetic antennas and reaction centers. To probe energy-transfer processes akin to those in photosynthetic systems, nine synthetic bacteriochlorin-bacteriochlorin dyads have been prepared wherein the constituent pigments are joined at the meso-positions by a phenylethyne linker. The phenylethyne linker is an unsymmetric auxochrome, which differentially shifts the excited-state energies of the phenyl- or ethynyl-attached bacteriochlorin constituents in the dyad. Molecular designs utilized known effects of macrocycle substituents to engineer bacteriochlorins with S0 → S1 (Qy) transitions spanning 725-788 nm. The design-predicted donor-acceptor excited-state energy gaps in the dyads agree well with those obtained from time dependent density functional theory calculations and with the measured range of 197-1089 cm-1. Similar trends with donor-acceptor excited-state energy gaps are found for (1) the measured ultrafast energy-transfer rates of (0.3-1.7 ps)-1, (2) the spectral overlap integral (J) in Förster energy-transfer theory, and (3) donor-acceptor electronic mixing manifested in the natural transition orbitals for the S0 → S1 transition. Subtle outcomes include the near orthogonal orientation of the π-planes of the bacteriochlorin macrocycles, and the substituent-induced shift in transition-dipole moment from the typical coincidence with the NH-NH axis; the two features together afforded the Förster orientation term κ2 ranging from 0.55-1.53 across the nine dyads, a value supportive of efficient excited-state energy transfer. The molecular design and collective insights on the dyads are valuable for studies relevant to artificial photosynthesis and other processes requiring ultrafast energy transfer.
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Affiliation(s)
- Haoyu Jing
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA.
| | | | - James R Diers
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA.
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4889, USA.
| | - David F Bocian
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA.
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4889, USA.
| | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA.
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70
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Martyn JM, Liu Y, Chin ZE, Chuang IL. Efficient fully-coherent quantum signal processing algorithms for real-time dynamics simulation. J Chem Phys 2023; 158:024106. [PMID: 36641381 DOI: 10.1063/5.0124385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the simulation of electronic dynamics, which plays an essential role in chemical reactions, non-equilibrium dynamics, and material design. These systems are time-dependent, which requires that the corresponding simulation algorithm can be successfully concatenated with itself over different time intervals to reproduce the overall coherent quantum dynamics of the system. In this paper, we quantify such simulation algorithms by the property of being fully-coherent: the algorithm succeeds with arbitrarily high success probability 1 - δ while only requiring a single copy of the initial state. We subsequently develop fully-coherent simulation algorithms based on quantum signal processing (QSP), including a novel algorithm that circumvents the use of amplitude amplification while also achieving a query complexity additive in time t, ln(1/δ), and ln(1/ϵ) for error tolerance ϵ: Θ‖H‖|t|+ln(1/ϵ)+ln(1/δ). Furthermore, we numerically analyze these algorithms by applying them to the simulation of the spin dynamics of the Heisenberg model and the correlated electronic dynamics of an H2 molecule. Since any electronic Hamiltonian can be mapped to a spin Hamiltonian, our algorithm can efficiently simulate time-dependent ab initio electronic dynamics in the circuit model of quantum computation. Accordingly, it is also our hope that the present work serves as a bridge between QSP-based quantum algorithms and chemical dynamics, stimulating a cross-fertilization between these exciting fields.
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Affiliation(s)
- John M Martyn
- Department of Physics, Center for Theoretical Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yuan Liu
- Department of Physics, Co-Design Center for Quantum Advantage, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Zachary E Chin
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Isaac L Chuang
- Department of Physics, Co-Design Center for Quantum Advantage, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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71
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Sahu A, Bhat VN, Patra S, Tiwari V. High-sensitivity fluorescence-detected multidimensional electronic spectroscopy through continuous pump-probe delay scan. J Chem Phys 2023; 158:024201. [PMID: 36641398 DOI: 10.1063/5.0130887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Fluorescence-detected multidimensional electronic spectroscopy (fMES) promises high sensitivity compared to conventional approaches and is an emerging spectroscopic approach toward combining the advantages of MES with the spatial resolution of a microscope. Here, we present a visible white light continuum-based fMES spectrometer and systematically explore the sensitivity enhancement expected from fluorescence detection. As a demonstration of sensitivity, we report room temperature two-dimensional coherence maps of vibrational quantum coherences in a laser dye at optical densities of ∼2-3 orders of magnitude lower than conventional approaches. This high sensitivity is enabled by a combination of biased sampling along the optical coherence time axes and a rapid scan of the pump-probe waiting time T at each sample. A combination of this approach with acousto-optic phase modulation and phase-sensitive lock-in detection enables measurements of room temperature vibrational wavepackets even at the lowest ODs. Alternative faster data collection schemes, which are enabled by the flexibility of choosing a non-uniform undersampled grid in the continuous T scanning approach, are also demonstrated.
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Affiliation(s)
- Amitav Sahu
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Vivek N Bhat
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Sanjoy Patra
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Vivek Tiwari
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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72
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Shu Y, Truhlar DG. Decoherence and Its Role in Electronically Nonadiabatic Dynamics. J Chem Theory Comput 2023; 19:380-395. [PMID: 36622843 PMCID: PMC9878713 DOI: 10.1021/acs.jctc.2c00988] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 01/10/2023]
Abstract
Decoherence is the tendency of a time-evolved reduced density matrix for a subsystem to assume a form corresponding to a statistical ensemble of states rather than a coherent combination of pure-state wave functions. When a molecular process involves changes in the electronic state and the coordinates of the nuclei, as in ultraviolet or visible light photochemistry or electronically inelastic collisions, the reduced density matrix of the electronic subsystem suffers decoherence, due to its interaction with the nuclear subsystem. We present the background necessary to conceptualize this decoherence; in particular, we discuss the density matrix description of pure states and mixed states, and we discuss pointer states and decoherence time. We then discuss how decoherence is treated in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry,
Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry,
Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota55455-0431, United States
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73
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Jayachandran A, Mueller S, Brixner T. Fluorescence-Detected Two-Quantum Photon Echoes via Cogwheel Phase Cycling. J Phys Chem Lett 2022; 13:11710-11719. [PMID: 36512681 DOI: 10.1021/acs.jpclett.2c03372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Two-dimensional (2D) electronic spectroscopy can separate homogeneous and inhomogeneous broadening. While established methods usually probe a photon-echo signal, i.e., a third-order response, to access the homogeneous line width of singly excited states, the homogeneous line width of doubly excited states remained spectroscopically inaccessible. Here we demonstrate the acquisition of two-quantum (2Q) photon echoes using fluorescence-detected 2D spectroscopy. In these eighth-order signals, 2Q coherences are rephased with themselves, leading to line-narrowed 2Q-2Q 2D spectra. By using cogwheel phase cycling, adapted from nuclear magnetic resonance spectroscopy, we isolate the 2Q-2Q 2D spectra of a squaraine dimer and a squaraine polymer and verify the same selectivity of cogwheel phase cycling compared to traditional "nested" phase cycling. The observed difference, between the two systems, in the homogeneous line width of the biexciton can be rationalized as a signature of the interplay of exciton-exciton annihilation, exciton diffusion, and exciton delocalization.
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Affiliation(s)
- Ajay Jayachandran
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefan Mueller
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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74
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Sindhu A, Jain A. Coherence and Efficient Energy Transfer in Molecular Wires: Insights from Surface Hopping Simulations. Chemphyschem 2022; 23:e202200392. [PMID: 35944188 DOI: 10.1002/cphc.202200392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/09/2022] [Indexed: 01/04/2023]
Abstract
Understanding the dynamics of electronic energy transfer through a molecular wire is essential to understand the working of natural processes like photosynthesis. We investigate simpler 2 and 3-site model Hamiltonians in this work to understand the importance of coherence to efficient energy transfer. We compare the results of surface hopping simulation with that of numerically exact results and rate theories. Different parameters are analyzed, motivated by a photosynthetic molecular wire - the FMO complex. A comparison of results from different theories shows that coherence can play an important role towards efficient energy transfer for certain parameters. When these coherences are important, even small couplings (of the order of 5 cm-1 ) in the Hamiltonian can significantly affect rates. Surface hopping simulations capture all the results correctly qualitatively. Rate theories, on the other hand, can differ significantly from numerically exact results when coherences become important. The results of this work should provide design guidelines for efficient energy transfer in molecular wires.
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75
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Wu JY, Hu XY, Zhu HY, Deng RQ, Ai Q. A Bionic Compass Based on Multiradicals. J Phys Chem B 2022; 126:10327-10334. [PMID: 36448780 DOI: 10.1021/acs.jpcb.2c02711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The underlying chemical and physical mechanism of avian navigation is an important issue of broad interest. One of the most famous candidates is the radical-pair mechanism, which shows that the magnetoreception is achieved by detecting the amount of chemical-reaction product from the singlet state. In the hypothesis, the surrounding nuclear spins play an important role as inducing the coherent transition between the singlet and triplet states. Recently, it was suggested that a multiradical model beyond two radicals can also realize magnetoreception without the assistance of nuclear spins. Inspired by this discovery, we explore the amount of the singlet recombination product in a multiradical model, with a radical bath described by the Lipkin-Meshkov-Glick (LMG) model, which was originally proposed for quantum phase transition (QPT). We show that the sensitivity of the bionic compass can be improved at the critical point. Our results may pave the way for the exploration of the design principle of the bionic compass.
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Affiliation(s)
- Jia-Yi Wu
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing100875, China
| | - Xin-Yuan Hu
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing100875, China
| | - Hai-Yuan Zhu
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing100875, China
| | - Ru-Qiong Deng
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing100875, China
| | - Qing Ai
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing100875, China
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76
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Liang D, Savio Rodriguez L, Zhou H, Zhu Y, Li H. Optical two-dimensional coherent spectroscopy of cold atoms. OPTICS LETTERS 2022; 47:6452-6455. [PMID: 36538460 DOI: 10.1364/ol.478793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
We report an experimental demonstration of optical two-dimensional coherent spectroscopy (2DCS) in cold atoms. The experiment integrates a collinear 2DCS setup with a magneto-optical trap (MOT), in which cold rubidium (Rb) atoms are prepared at a temperature of approximately 200 µK and a number density of 1010 cm-3. With a sequence of femtosecond laser pulses, we first obtain one-dimensional second- and fourth-order nonlinear signals and then acquire both one-quantum and zero-quantum 2D spectra of cold Rb atoms. The capability of performing optical 2DCS in cold atoms is an important step toward optical 2DCS study of many-body physics in cold atoms and ultimately in atom arrays and trapped ions. Optical 2DCS in cold atoms/molecules can also be a new avenue to probe chemical reaction dynamics in cold molecules.
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77
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Quantum coherent energy transport in the Fenna-Matthews-Olson complex at low temperature. Proc Natl Acad Sci U S A 2022; 119:e2212630119. [PMID: 36442134 PMCID: PMC9894199 DOI: 10.1073/pnas.2212630119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In the primary step of natural light harvesting, the solar photon energy is captured in a photoexcited electron-hole pair, or an exciton, in chlorophyll. Its conversion to chemical potential occurs in the special pair reaction center, which is reached by downhill ultrafast excited-state energy transport through a network of chromophores. Being inherently quantum, transport could in principle occur via a matter wave, with vast implications for efficiency. How long a matter wave remains coherent is determined by the intensity by which the exciton is disturbed by the noisy biological environment. The stronger this is, the stronger the electronic coupling between chromophores must be to overcome the fluctuations and phase shifts. The current consensus is that under physiological conditions, quantum coherence vanishes on the 10-fs time scale, rendering it irrelevant for the observed picosecond transfer. Yet, at low-enough temperature, quantum coherence should in principle be present. Here, we reveal the onset of longer-lived electronic coherence at extremely low temperatures of ∼20 K. Using two-dimensional electronic spectroscopy, we determine the exciton coherence times in the Fenna-Matthew-Olson complex over an extensive temperature range. At 20 K, coherence persists out to 200 fs (close to the antenna) and marginally up to 500 fs at the reaction center. It decays markedly faster with modest increases in temperature to become irrelevant above 150 K. At low temperature, the fragile electronic coherence can be separated from the robust vibrational coherence, using a rigorous theoretical analysis. We believe that by this generic principle, light harvesting becomes robust against otherwise fragile quantum effects.
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78
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Cao J. Generalized Resonance Energy Transfer Theory: Applications to Vibrational Energy Flow in Optical Cavities. J Phys Chem Lett 2022; 13:10943-10951. [PMID: 36408925 DOI: 10.1021/acs.jpclett.2c02707] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A general rate theory for resonance energy transfer (gRET) is formulated to incorporate any degrees of freedom (e.g., rotation, vibration, exciton, and polariton) as well as coherently coupled composite donor or acceptor states. The compact rate expression allows us to establish useful relationships: (i) detailed balance condition when the donor and acceptor are at the same temperature; (ii) proportionality to the product of dipole correlation tensors, which is not necessarily equivalent to spectral overlap; (iii) scaling with the effective coherent size, i.e., the number of coherently coupled molecules or modes; (iv) decomposition of collective rate in homogeneous systems into the monomer and coherence contributions such that the ratio of the two defines the quantum enhancement factor F; (v) spatial and orientational dependences as derived from the interaction potential. For the special case of exciton transfer, the general rate formalism reduces to FRET or its multichromophoric extension. When applied to cavity-assisted vibrational energy transfer between molecules or within a molecule, the general rate expression provides an intuitive explanation of intriguing phenomena such as cooperativity, resonance, and nonlinearity in the collective vibrational strong coupling (VSC) regime, as demonstrated in recent simulations. The relevance of gRET to cavity-catalyzed reactions and intramolecular vibrational redistribution is discussed and will lead to further theoretical developments.
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Affiliation(s)
- Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
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79
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Westenhoff S, Meszaros P, Schmidt M. Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins. Curr Opin Struct Biol 2022; 77:102481. [PMID: 36252455 DOI: 10.1016/j.sbi.2022.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
Proteins are dynamic objects and undergo conformational changes when functioning. These changes range from interconversion between states in equilibrium to ultrafast and coherent structural motions within one perturbed state. Time-resolved serial femtosecond crystallography at free-electron X-ray lasers can unravel structural changes with atomic resolution and down to femtosecond time scales. In this review, we summarize recent advances on detecting structural changes for phytochrome photosensor proteins and a bacterial photosynthetic reaction center. In the phytochrome structural changes are extensive and involve major rearrangements of many amino acids and water molecules, accompanying the regulation of its biochemical activity, whereas in the photosynthetic reaction center protein the structural changes are smaller, more localized, and are optimized to facilitate electron transfer along the chromophores. The detected structural motions underpin the proteins' function, providing a showcase for the importance of detecting ultrafast protein structural dynamics.
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Affiliation(s)
- Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden.
| | - Petra Meszaros
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, Physic, University of Wisconsin-Milwaukee, 3134 N. Maryland Ave., Milwaukee, WI 53211, United States
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80
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Hu Z, Liu Z, Sun X. Effects of Heterogeneous Protein Environment on Excitation Energy Transfer Dynamics in the Fenna-Matthews-Olson Complex. J Phys Chem B 2022; 126:9271-9287. [PMID: 36327977 DOI: 10.1021/acs.jpcb.2c06605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Fenna-Matthews-Olson (FMO) complex of green sulfur bacteria has been serving as a prototypical light-harvesting protein for studying excitation energy transfer (EET) dynamics in photosynthesis. The most widely used Frenkel exciton model for FMO complex assumes that each excited bacteriochlorophyll site couples to an identical and isolated harmonic bath, which does not account for the heterogeneous local protein environment. To better describe the realistic environment, we propose to use the recently developed multistate harmonic (MSH) model, which contains a globally shared bath that couples to the different pigment sites according to the atomistic quantum mechanics/molecular mechanics simulations with explicit protein scaffold and solvent. In this work, the effects of heterogeneous protein environment on EET in FMO complexes from Prosthecochloris aestuarii and Chlorobium tepidum, specifically including realistic spectral density, site-dependent reorganization energies, and system-bath couplings are investigated. Semiclassical and mixed quantum-classical mapping dynamics were applied to obtain the nonadiabatic EET dynamics in several models ranging from the Frenkel exciton model to the MSH model and their variants. The MSH model with realistic spectral density and site-dependent system-bath couplings displays slower EET dynamics than the Frenkel exciton model. Our comparative study shows that larger average reorganization energy, heterogeneity in spectral densities, and low-frequency modes could facilitate energy dissipation, which is insensitive to the static disorder in reorganization energies. The effects of the spectral densities and system-bath couplings along with the MSH model can be used to optimize EET dynamics for artificial light-harvesting systems.
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Affiliation(s)
- Zhubin Hu
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zengkui Liu
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
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81
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Dodson EJ, Werren N, Paltiel Y, Gauger EM, Keren N. Large-scale FRET simulations reveal the control parameters of phycobilisome light-harvesting complexes. J R Soc Interface 2022; 19:20220580. [PMID: 36448289 PMCID: PMC9709516 DOI: 10.1098/rsif.2022.0580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Phycobilisomes (PBS) are massive structures that absorb and transfer light energy to photochemical reaction centres. Among the range of light harvesting systems, PBS are considered to be excellent solutions for absorption cross-sections but relatively inefficient energy transferring systems. This is due to the combination of a large number of chromophores with intermediate coupling distances. Nevertheless, PBS systems persisted from the origin of oxygenic photosynthesis to present-day cyanobacteria and red algae, organisms that account for approximately half of the primary productivity in the ocean. In this study, we modelled energy transfer through subsets of PBS structures, using a comprehensive dynamic Hamiltonian model. Our approach was applied, initially, to pairs of phycobilin hexamers and then extended to short rods. By manipulating the distances and angles between the structures, we could probe the dynamics of exciton transfer. These simulations suggest that the PBS chromophore network enhances energy distribution over the entire PBS structure-both horizontally and vertically to the rod axis. Furthermore, energy transfer was found to be relatively immune to the effects of distances or rotations, within the range of intermediate coupling distances. Therefore, we suggest that the PBS provides unique advantages and flexibility to aquatic photosynthesis.
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Affiliation(s)
- Emma Joy Dodson
- Department of Plant and Environmental Science, The Alexander Silberman Institute of Life Sciences, The Hebrew University in Jerusalem, Jerusalem, Israel
| | - Nicholas Werren
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Yossi Paltiel
- Department of Applied Physics, The Hebrew University in Jerusalem, Jerusalem, Israel
| | - Erik M. Gauger
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Nir Keren
- Department of Plant and Environmental Science, The Alexander Silberman Institute of Life Sciences, The Hebrew University in Jerusalem, Jerusalem, Israel
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82
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Maroudas‐Sklare N, Kolodny Y, Yochelis S, Keren N, Paltiel Y. Controlling photosynthetic energy conversion by small conformational changes. PHYSIOLOGIA PLANTARUM 2022; 174:e13802. [PMID: 36259916 PMCID: PMC9828261 DOI: 10.1111/ppl.13802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Control phenomena in biology usually refer to changes in gene expression and protein translation and modification. In this paper, another mode of regulation is highlighted; we propose that photosynthetic organisms can harness the interplay between localization and delocalization of energy transfer by utilizing small conformational changes in the structure of light-harvesting complexes. We examine the mechanism of energy transfer in photosynthetic pigment-protein complexes, first through the scope of theoretical work and then by in vitro studies of these complexes. Next, the biological relevance to evolutionary fitness of this localization-delocalization switch is explored by in vivo experiments on desert crust and marine cyanobacteria, which are both exposed to rapidly changing environmental conditions. These examples demonstrate the flexibility and low energy cost of this mechanism, making it a competitive survival strategy.
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Affiliation(s)
- Naama Maroudas‐Sklare
- Department of Applied PhysicsHebrew University of JerusalemJerusalemIsrael
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life SciencesHebrew University of JerusalemJerusalemIsrael
| | - Yuval Kolodny
- Department of Applied PhysicsHebrew University of JerusalemJerusalemIsrael
| | - Shira Yochelis
- Department of Applied PhysicsHebrew University of JerusalemJerusalemIsrael
| | - Nir Keren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life SciencesHebrew University of JerusalemJerusalemIsrael
| | - Yossi Paltiel
- Department of Applied PhysicsHebrew University of JerusalemJerusalemIsrael
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83
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Kundu S, Dani R, Makri N. Tight inner ring architecture and quantum motion of nuclei enable efficient energy transfer in bacterial light harvesting. SCIENCE ADVANCES 2022; 8:eadd0023. [PMID: 36288310 PMCID: PMC9604522 DOI: 10.1126/sciadv.add0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
The efficient, directional transfer of absorbed solar energy between photosynthetic light-harvesting complexes continues to pose intriguing questions. In this work, we identify the pathways of energy flow between the B800 and B850 rings in the LH2 complex of Rhodopseudomonas molischianum using fully quantum mechanical path integral methods to simulate the excited-state dynamics of the 24 bacteriochlorophyll molecules and their coupling to 50 normal mode vibrations in each chromophore. While all pigments are identical, the tighter packing of the inner B850 ring is responsible for the thermodynamic stabilization of the inner ring. Molecular vibrations enable the 1-ps flow of energy to the B850 states, which would otherwise be kinetically inaccessible. A classical treatment of the vibrations leads to uniform equilibrium distribution of the excitation, with only 67% transferred to the inner ring. However, spontaneous fluctuations associated with the quantum motion of the nuclei increase the transfer efficiency to 90%.
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Affiliation(s)
- Sohang Kundu
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Reshmi Dani
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Nancy Makri
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
- Department of Physics, University of Illinois, Urbana, IL 61801, USA
- Illinois Quantum Information Science and Technology Center, University of Illinois, Urbana, IL 61801, USA
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84
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Doležal J, Canola S, Hapala P, de Campos Ferreira RC, Merino P, Švec M. Evidence of exciton-libron coupling in chirally adsorbed single molecules. Nat Commun 2022; 13:6008. [PMID: 36224183 PMCID: PMC9556530 DOI: 10.1038/s41467-022-33653-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022] Open
Abstract
Interplay between motion of nuclei and excitations has an important role in molecular photophysics of natural and artificial structures. Here we provide a detailed analysis of coupling between quantized librational modes (librons) and charged excited states (trions) on single phthalocyanine dyes adsorbed on a surface. By means of tip-induced electroluminescence performed with a scanning probe microscope, we identify libronic signatures in spectra of chirally adsorbed phthalocyanines and find that these signatures are absent from spectra of symmetrically adsorbed species. We create a model of the libronic coupling based on the Franck-Condon principle to simulate the spectral features. Experimentally measured librational spectra match very well the theoretically calculated librational eigenenergies and peak intensities (Franck-Condon factors). Moreover, the comparison reveals an unexpected depopulation channel for the zero libron of the excited state that can be effectively controlled by tuning the size of the nanocavity. Our results showcase the possibility of characterizing the dynamics of molecules by their low-energy molecular modes using µeV-resolved tip-enhanced spectroscopy. Vibronic coupling in molecules plays an essential role in photophysics. Here, the authors observe optical fingerprints of the coupling between librational states and charged excited states in a single phthalocyanine molecule chirally absorbed on a surface.
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Affiliation(s)
- Jiří Doležal
- Institute of Physics, Czech Academy of Sciences, CZ16200, Praha 6, Czech Republic. .,Faculty of Mathematics and Physics, Charles University, CZ12116, Praha 2, Czech Republic.
| | - Sofia Canola
- Institute of Physics, Czech Academy of Sciences, CZ16200, Praha 6, Czech Republic
| | - Prokop Hapala
- Institute of Physics, Czech Academy of Sciences, CZ16200, Praha 6, Czech Republic
| | | | - Pablo Merino
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, E08193, Barcelona, Spain.,Instituto de Ciencia de Materiales de Madrid; CSIC, E28049, Madrid, Spain
| | - Martin Švec
- Institute of Physics, Czech Academy of Sciences, CZ16200, Praha 6, Czech Republic. .,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, CZ16000, Praha 6, Czech Republic.
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85
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Kernbach S, Kernbach O. Environment-dependent fluctuations of potentiometric pH dynamics in geomagnetic field. Electromagn Biol Med 2022; 41:409-418. [PMID: 36200513 DOI: 10.1080/15368378.2022.2125527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This work explores fluctuations of potentiometric pH dynamics in environments with different configurations of geomagnetic fields. High-resolution pH measurements of test liquids are conducted in electromagnetically shielded and thermally stabilized conditions. External measurement environment in two laboratories is modulated by non-conducting/non-magnetic objects of organic and inorganic origins. Totally, 88 experiments in three groups have been conducted during 4 months. The affected pH dynamics at the level of 10-2-10-5 pH is detected in 93.5%, 82.2% and 74.4% depending on dielectric permittivity of environmental objects. Reaction of potentiometric system has a typical delay of 30-180 minutes. Experiments in both laboratories demonstrated 19% difference of reproducibility rate caused by different background fluctuations. To explain the obtained results, the paper discusses the effects of the Earth's electric and magnetic fields in the form of magnetospheric Poynting vectors or spin-spin forces in geomagnetic field, which affects the productivity of ionic and free-radical reactions. Since the pH level of aqueous solutions controls various biochemical reactions, this mechanism can explain several biological effects with non-contact signal transmission observed in environmental biology and electromagnetic biophysics.
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Affiliation(s)
- S Kernbach
- Research Center of Advanced Robotics and Environmental Science, CYBRES GmbH, Stuttgart, Germany
| | - O Kernbach
- Research Center of Advanced Robotics and Environmental Science, CYBRES GmbH, Stuttgart, Germany
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86
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Koyu S, Tscherbul TV. Long-lived quantum coherent dynamics of a Λ-system driven by a thermal environment. J Chem Phys 2022; 157:124302. [PMID: 36182443 DOI: 10.1063/5.0102808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a theoretical study of quantum coherent dynamics of a three-level Λ-system driven by a thermal environment (such as blackbody radiation), which serves as an essential building block of photosynthetic light-harvesting models and quantum heat engines. By solving nonsecular Bloch-Redfield master equations, we obtain analytical results for the ground-state population and coherence dynamics and classify the dynamical regimes of the incoherently driven Λ-system as underdamped and overdamped depending on whether the ratio Δ/[rf(p)] is greater or less than one, where Δ is the ground-state energy splitting, r is the incoherent pumping rate, and f(p) is a function of the transition dipole alignment parameter p. In the underdamped regime, we observe long-lived coherent dynamics that lasts for τc ≃ 1/r, even though the initial state of the Λ-system contains no coherences in the energy basis. In the overdamped regime for p = 1, we observe the emergence of coherent quasi-steady states with the lifetime τc = 1.34(r/Δ2), which have a low von Neumann entropy compared to conventional thermal states. We propose an experimental scenario for observing noise-induced coherent dynamics in metastable He* atoms driven by x-polarized incoherent light. Our results suggest that thermal excitations can generate experimentally observable long-lived quantum coherent dynamics in the ground-state subspace of atomic and molecular Λ-systems in the absence of coherent driving.
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Affiliation(s)
- Suyesh Koyu
- Department of Physics, University of Nevada, Reno, Nevada 89557, USA
| | - Timur V Tscherbul
- Department of Physics, University of Nevada, Reno, Nevada 89557, USA
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87
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Magdaong NCM, Jing H, Diers JR, Kirmaier C, Lindsey JS, Bocian DF, Holten D. Probing the Effects of Electronic-Vibrational Resonance on the Rate of Excited-State Energy Transfer in Bacteriochlorin Dyads. J Phys Chem Lett 2022; 13:7906-7910. [PMID: 35980198 DOI: 10.1021/acs.jpclett.2c02154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The impact of vibrational-electronic resonances on the rate of excited-state energy transfer is examined in a set of bacteriochlorin dyads that employ the same phenylethyne linker. The donor/acceptor excited-state energy gap is tuned from ∼200 to ∼1100 cm-1 using peripheral substituents on the donor and acceptor bacteriochlorin macrocycles. Ultrafast energy transfer is observed with rate constants of (0.3 ps)-1 to (1.7 ps)-1, which agree with those predicted by Förster theory to within a factor of 2. Furthermore, the measured rates follow a trend-line with only small deviations that do not correlate with the density of vibrations at the donor/acceptor excited-state energy gap. Thus, if vibrational-electronic resonances occur in any of these dyads, which seems likely, the impact on the rate of energy transfer is small.
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Affiliation(s)
- Nikki Cecil M Magdaong
- Department of Chemistry, Washington University, St. Louis, Missouri63130-4889, United States
| | - Haoyu Jing
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina27695-8204, United States
| | - James R Diers
- Department of Chemistry, University of California, Riverside, Riverside, California92521-0403, United States
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, Missouri63130-4889, United States
| | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina27695-8204, United States
| | - David F Bocian
- Department of Chemistry, University of California, Riverside, Riverside, California92521-0403, United States
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, Missouri63130-4889, United States
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88
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Chen L, Bennett DIG, Eisfeld A. Calculating non-linear response functions for multi-dimensional electronic spectroscopy using dyadic non-Markovian quantum state diffusion. J Chem Phys 2022; 157:114104. [DOI: 10.1063/5.0107925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a methodology for simulating multi-dimensional electronic spectra of molecular aggregates with coupling of electronic excitation to a structured environment using the stochastic non-Markovian quantum state diffusion (NMQSD) method in combination with perturbation theory for the response functions. A crucial aspect of our approach is that we propagate the NMQSD equation in a doubled system Hilbert space, but with the same noise. We demonstrate that our approach shows fast convergence with respect to the number of stochastic trajectories, providing a promising technique for numerical calculation of two-dimensional electronic spectra of large molecular aggregates.
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Affiliation(s)
- Lipeng Chen
- Department of Chemistry, Max-Planck-Institute for the Physics of Complex Systems, Germany
| | - Doran I. G Bennett
- Chemistry, Southern Methodist University Department of Chemistry, United States of America
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89
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Pedram A, Çakmak B, Müstecaplıoğlu ÖE. Environment-Assisted Modulation of Heat Flux in a Bio-Inspired System Based on Collision Model. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1162. [PMID: 36010826 PMCID: PMC9407596 DOI: 10.3390/e24081162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
The high energy transfer efficiency of photosynthetic complexes has been a topic of research across many disciplines. Several attempts have been made in order to explain this energy transfer enhancement in terms of quantum mechanical resources such as energetic and vibration coherence and constructive effects of environmental noise. The developments in this line of research have inspired various biomimetic works aiming to use the underlying mechanisms in biological light harvesting complexes for the improvement of synthetic systems. In this article, we explore the effect of an auxiliary hierarchically structured environment interacting with a system on the steady-state heat transport across the system. The cold and hot baths are modeled by a series of identically prepared qubits in their respective thermal states, and we use a collision model to simulate the open quantum dynamics of the system. We investigate the effects of system-environment, inter-environment couplings and coherence of the structured environment on the steady state heat flux and find that such a coupling enhances the energy transfer. Our calculations reveal that there exists a non-monotonic and non-trivial relationship between the steady-state heat flux and the mentioned parameters.
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Affiliation(s)
- Ali Pedram
- Department of Physics, Koç University, Sarıyer, Istanbul 34450, Türkiye
| | - Barış Çakmak
- College of Engineering and Natural Sciences, Bahçeşehir University, Beşiktaş, Istanbul 34353, Türkiye
| | - Özgür E. Müstecaplıoğlu
- Department of Physics, Koç University, Sarıyer, Istanbul 34450, Türkiye
- TÜBİTAK Research Institute for Fundamental Sciences, Gebze 41470, Türkiye
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90
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Parker KA, Schultz JD, Singh N, Wasielewski MR, Beratan DN. Mapping Simulated Two-Dimensional Spectra to Molecular Models Using Machine Learning. J Phys Chem Lett 2022; 13:7454-7461. [PMID: 35930790 DOI: 10.1021/acs.jpclett.2c01913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two-dimensional (2D) spectroscopy encodes molecular properties and dynamics into expansive spectral data sets. Translating these data into meaningful chemical insights is challenging because of the many ways chemical properties can influence the spectra. To address the task of extracting chemical information from 2D spectroscopy, we study the capacity of simple feedforward neural networks (NNs) to map simulated 2D electronic spectra to underlying physical Hamiltonians. We examined hundreds of simulated 2D spectra corresponding to monomers and dimers with varied Franck-Condon active vibrations and monomer-monomer electronic couplings. We find the NNs are able to correctly characterize most Hamiltonian parameters in this study with an accuracy above 90%. Our results demonstrate that NNs can aid in interpreting 2D spectra, leading from spectroscopic features to underlying effective Hamiltonians.
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Affiliation(s)
- Kelsey A Parker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jonathan D Schultz
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael R Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
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91
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Fang J, Chen ZH, Su Y, Zhu ZF, Wang Y, Xu RX, Yan Y. Coherent excitation energy transfer in model photosynthetic reaction center: Effects of non-Markovian quantum environment. J Chem Phys 2022; 157:084119. [DOI: 10.1063/5.0104641] [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
Excitation energy transfer (EET) and electron transfer (ET) are crucially involved in photosynthetic processes. In reality, the photosynthetic reaction center constitutes an open quantum system of EET and ET, which manifests an interplay of pigments, solar light and phonon baths. So far theoretical studies have been mainly based on master equation approaches in the Markovian condition. The non-Markovian environmental effect, which may play a crucial role, has not been sufficiently considered. In this work, we propose a mixed dynamic approach to investigate this open system. The influence of phonon bath is treated via the exact dissipaton equation of motion (DEOM) while that of photon bath is via the Lindblad master equation. Specifically, we explore the effect of non-Markovian quantum phonon bath on the coherent transfer dynamics and its manipulation on the current--voltage behavior. Distinguished from the results of completely Markovian Lindblad equation and those adopting classical environment description, the mixed DEOM--Lindblad simulations exhibittransfer coherence up to a few hundreds femtosecondsand the related environmental manipulation effect on current.These non-Markovian quantum coherent effects may be extended tomore complex and realistic systems and be helpful to thedesign of organic photovoltaic devices.
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Affiliation(s)
- Jie Fang
- University of Science and Technology of China, China
| | - Zi-Hao Chen
- University of Science and Technology of China, China
| | - Yu Su
- Department of Chemical Physics, University of Science and Technology of China, China
| | - Zi-Fan Zhu
- University of Science and Technology of China, China
| | - Yao Wang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, China
| | - Rui-Xue Xu
- University of Science and Technology of China, China
| | - YiJing Yan
- Department of Chemical Physics, USTC, China
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92
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Zadeh-Haghighi H, Simon C. Magnetic field effects in biology from the perspective of the radical pair mechanism. J R Soc Interface 2022; 19:20220325. [PMID: 35919980 PMCID: PMC9346374 DOI: 10.1098/rsif.2022.0325] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/14/2022] [Indexed: 04/07/2023] Open
Abstract
Hundreds of studies have found that weak magnetic fields can significantly influence various biological systems. However, the underlying mechanisms behind these phenomena remain elusive. Remarkably, the magnetic energies implicated in these effects are much smaller than thermal energies. Here, we review these observations, and we suggest an explanation based on the radical pair mechanism, which involves the quantum dynamics of the electron and nuclear spins of transient radical molecules. While the radical pair mechanism has been studied in detail in the context of avian magnetoreception, the studies reviewed here show that magnetosensitivity is widespread throughout biology. We review magnetic field effects on various physiological functions, discussing static, hypomagnetic and oscillating magnetic fields, as well as isotope effects. We then review the radical pair mechanism as a potential unifying model for the described magnetic field effects, and we discuss plausible candidate molecules for the radical pairs. We review recent studies proposing that the radical pair mechanism provides explanations for isotope effects in xenon anaesthesia and lithium treatment of hyperactivity, magnetic field effects on the circadian clock, and hypomagnetic field effects on neurogenesis and microtubule assembly. We conclude by discussing future lines of investigation in this exciting new area of quantum biology.
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Affiliation(s)
- Hadi Zadeh-Haghighi
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Institute for Quantum Science and Technology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Christoph Simon
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Institute for Quantum Science and Technology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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93
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Kessing RK, Yang PY, Manmana SR, Cao J. Long-Range Nonequilibrium Coherent Tunneling Induced by Fractional Vibronic Resonances. J Phys Chem Lett 2022; 13:6831-6838. [PMID: 35857895 DOI: 10.1021/acs.jpclett.2c01455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We study the influence of a linear energy bias on a nonequilibrium excitation on a chain of molecules coupled to local vibrations (a tilted Holstein model) using both a random-walk rate kernel theory and a nonperturbative, massively parallelized adaptive-basis algorithm. We uncover structured and discrete vibronic resonance behavior fundamentally different from both linear response theory and homogeneous polaron dynamics. Remarkably, resonance between the phonon energy ℏω and the bias δϵ occurs not only at integer but also fractional ratios δϵ/(ℏω) = m/n, which effect long-range n-bond m-phonon tunneling. These observations are reproduced in a model calculation of a recently demonstrated Cy3 system, and the effect of dipole-dipole-type non-nearest-neighbor coupling and vibrationally relaxed initial states is also considered. Potential applications range from molecular electronics to optical lattices and artificial light harvesting via vibronic engineering of coherent quantum transport.
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Affiliation(s)
- R Kevin Kessing
- Institut für Theoretische Physik, Universität Ulm, Ulm, 89069, Germany
- Institut für Theoretische Physik, Georg-August-Universität Göttingen, Göttingen, 37077, Germany
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Pei-Yun Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Physics, National Taiwan University, Taipei, 10617, Taiwan (R.O.C.)
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Salvatore R Manmana
- Institut für Theoretische Physik, Georg-August-Universität Göttingen, Göttingen, 37077, Germany
- Fachbereich Physik, Philipps-Universität Marburg, Marburg, 35032, Germany
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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94
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Sneyd A, Beljonne D, Rao A. A New Frontier in Exciton Transport: Transient Delocalization. J Phys Chem Lett 2022; 13:6820-6830. [PMID: 35857739 PMCID: PMC9340810 DOI: 10.1021/acs.jpclett.2c01133] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/18/2022] [Indexed: 05/20/2023]
Abstract
Efficient exciton transport is crucial to the application of organic semiconductors (OSCs) in light-harvesting devices. While the physics of exciton transport in highly disordered media is well-explored, the description of transport in structurally and energetically ordered OSCs is less established, despite such materials being favorable for devices. In this Perspective we describe and highlight recent research pointing toward a highly efficient exciton transport mechanism which occurs in ordered OSCs, transient delocalization. Here, exciton-phonon couplings play a critical role in allowing localized exciton states to temporarily access higher-energy delocalized states whereupon they move large distances. The mechanism shows great promise for facilitating long-range exciton transport and may allow for improved device efficiencies and new device architectures. However, many fundamental questions on transient delocalization remain to be answered. These questions and suggested next steps are summarized.
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Affiliation(s)
- Alexander
J. Sneyd
- Department
of Physics, Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - David Beljonne
- Laboratory
for Chemistry of Novel Materials, University
of Mons, Mons 7000, Belgium
| | - Akshay Rao
- Department
of Physics, Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
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95
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Sokolov B, Rossi MAC, García-Pérez G, Maniscalco S. Emergent entanglement structures and self-similarity in quantum spin chains. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200421. [PMID: 35599560 DOI: 10.1098/rsta.2020.0421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localized communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding and description of new physical phenomena even in models studied for decades. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Boris Sokolov
- QTF Centre of Excellence, Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland
- Algorithmiq Ltd, Kanavakatu 3C, Helsinki 00160, Finland
- InstituteQ - the Finnish Quantum Institute, University of Helsinki, Finland
| | - Matteo A C Rossi
- Algorithmiq Ltd, Kanavakatu 3C, Helsinki 00160, Finland
- QTF Centre of Excellence, Center for Quantum Engineering, Department of Applied Physics, Aalto University School of Science, Aalto 00076, Finland
- InstituteQ - the Finnish Quantum Institute, Aalto University, Finland
| | - Guillermo García-Pérez
- QTF Centre of Excellence, Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland
- Algorithmiq Ltd, Kanavakatu 3C, Helsinki 00160, Finland
- InstituteQ - the Finnish Quantum Institute, University of Helsinki, Finland
- Complex Systems Research Group, Department of Mathematics and Statistics, University of Turku, Turun Yliopisto 20014, Finland
| | - Sabrina Maniscalco
- QTF Centre of Excellence, Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland
- Algorithmiq Ltd, Kanavakatu 3C, Helsinki 00160, Finland
- InstituteQ - the Finnish Quantum Institute, University of Helsinki, Finland
- QTF Centre of Excellence, Center for Quantum Engineering, Department of Applied Physics, Aalto University School of Science, Aalto 00076, Finland
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96
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Kundu S, Dani R, Makri N. B800-to-B850 relaxation of excitation energy in bacterial light harvesting: All-state, all-mode path integral simulations. J Chem Phys 2022; 157:015101. [DOI: 10.1063/5.0093828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report fully quantum mechanical simulations of excitation energy transfer within the peripheral light harvesting complex (LH2) of Rhodopseudomonas molischianum at room temperature. The exciton–vibration Hamiltonian comprises the 16 singly excited bacteriochlorophyll states of the B850 (inner) ring and the 8 states of the B800 (outer) ring with all available electronic couplings. The electronic states of each chromophore couple to 50 intramolecular vibrational modes with spectroscopically determined Huang–Rhys factors and to a weakly dissipative bath that models the biomolecular environment. Simulations of the excitation energy transfer following photoexcitation of various electronic eigenstates are performed using the numerically exact small matrix decomposition of the quasiadiabatic propagator path integral. We find that the energy relaxation process in the 24-state system is highly nontrivial. When the photoexcited state comprises primarily B800 pigments, a rapid intra-band redistribution of the energy sharply transitions to a significantly slower relaxation component that transfers 90% of the excitation energy to the B850 ring. The mixed character B850* state lacks the slow component and equilibrates very rapidly, providing an alternative energy transfer channel. This (and also another partially mixed) state has an anomalously large equilibrium population, suggesting a shift to lower energy by virtue of exciton–vibration coupling. The spread of the vibrationally dressed states is smaller than that of the eigenstates of the bare electronic Hamiltonian. The total population of the B800 band is found to decay exponentially with a 1/ e time of 0.5 ps, which is in good agreement with experimental results.
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Affiliation(s)
- Sohang Kundu
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
| | - Reshmi Dani
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
| | - Nancy Makri
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
- Illinois Quantum Information Science and Technology Center, University of Illinois, Urbana, Illinois 61801, USA
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97
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Fay TP. A simple improved low temperature correction for the hierarchical equations of motion. J Chem Phys 2022; 157:054108. [DOI: 10.1063/5.0100365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The study of open system quantum dynamics has been transformed by the hierarchical equations of motion (HEOM) method, which gives the exact dynamics for a system coupled to a harmonic bath at arbitrary temperature and system-bath coupling strength. However in its standard form the method is only consistent with the weak-coupling quantum master equation at all temperatures when many auxiliary density operators are included in the hierarchy, even when low temperature corrections are included. Here we propose a new low temperature correction scheme for the termination of the hierarchy based on Zwanzig projection which alleviates this problem, and restores consistency with the weak-coupling master equation with a minimal hierarchy. The utility of the new correction scheme is demonstrated on a range of model systems, including the Fenna-Metthews-Olson complex. The new closure is found to improve convergence of the HEOM even beyond the weak-coupling limit and is very straightforward to implement in existing HEOM codes.
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Affiliation(s)
- Thomas Patrick Fay
- Department of Chemistry, University of California Berkeley Department of Chemistry, United States of America
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98
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Kong FF, Tian XJ, Zhang Y, Zhang Y, Chen G, Yu YJ, Jing SH, Gao HY, Luo Y, Yang JL, Dong ZC, Hou JG. Wavelike electronic energy transfer in donor-acceptor molecular systems through quantum coherence. NATURE NANOTECHNOLOGY 2022; 17:729-736. [PMID: 35668169 DOI: 10.1038/s41565-022-01142-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Quantum-coherent intermolecular energy transfer is believed to play a key role in light harvesting in photosynthesis and photovoltaics. So far, a direct, real-space demonstration of quantum coherence in donor-acceptor systems has been lacking because of the fragile quantum coherence in lossy molecular systems. Here, we precisely control the separations in well-defined donor-acceptor model systems and unveil a transition from incoherent to coherent electronic energy transfer. We monitor the fluorescence from the heterodimers with subnanometre resolution through scanning tunnelling microscopy induced luminescence. With decreasing intermolecular distance, the dipole coupling strength increases and two new emission peaks emerge: a low-intensity peak blueshifted from the donor emission, and an intense peak redshifted from the acceptor emission. Spatially resolved spectroscopic images of the redshifted emission exhibit a σ antibonding-like pattern and thus indicate a delocalized nature of the excitonic state over the whole heterodimer due to the in-phase superposition of molecular excited states. These observations suggest that the exciton can travel coherently through the whole heterodimer as a quantum-mechanical wavepacket. In our model system, the wavelike quantum-coherent transfer channel is three times more efficient than the incoherent channel.
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Affiliation(s)
- Fan-Fang Kong
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Xiao-Jun Tian
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Yang Zhang
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
- School of Physics and Department of Chemical Physics, University of Science and Technology of China, Hefei, China.
- Hefei National Laboratory, Hefei, China.
| | - Yao Zhang
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
- School of Physics and Department of Chemical Physics, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory, Hefei, China
| | - Gong Chen
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Yun-Jie Yu
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Shi-Hao Jing
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Hong-Ying Gao
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yi Luo
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
- School of Physics and Department of Chemical Physics, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory, Hefei, China
| | - Jin-Long Yang
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
- School of Physics and Department of Chemical Physics, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory, Hefei, China
| | - Zhen-Chao Dong
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
- School of Physics and Department of Chemical Physics, University of Science and Technology of China, Hefei, China.
- Hefei National Laboratory, Hefei, China.
| | - J G Hou
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
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99
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Sidhardh GL, Ajith A, Sebastian E, Hariharan M, Shaji A. Local Phonon Environment as a Design Element for Long-Lived Excitonic Coherence: Dithia-anthracenophane Revisited. J Phys Chem A 2022; 126:3765-3773. [PMID: 35666186 DOI: 10.1021/acs.jpca.2c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to investigate the role of a structured immediate phonon environment in determining the exciton dynamics and the possibility of using it as an optimal design element. Through the case study of dithia-anthracenophane, a bichromophore using the Hierarchical Equations Of Motion formalism, we show that the experimentally observed coherent exciton dynamics can be reproduced only by considering the actual structure of the phonon environment. While the slow dephasing of quantum coherence in dithia-anthracenophane can be attributed to strong vibronic coupling to high-frequency modes, vibronic quenching is the source of long oscillation periods in population transfer. This study sheds light on the crucial role of the structure of the immediate phonon environment in determining the exciton dynamics. We conclude by proposing some design principles for sustaining long-lived coherence in molecular systems.
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Affiliation(s)
- Govind Lal Sidhardh
- School of Physics, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Adithi Ajith
- School of Physics, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Ebin Sebastian
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Anil Shaji
- School of Physics, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala 695551, India
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100
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High-resolution two-dimensional electronic spectroscopy reveals the homogeneous line profile of chromophores solvated in nanoclusters. Nat Commun 2022; 13:3350. [PMID: 35688839 PMCID: PMC9187667 DOI: 10.1038/s41467-022-31021-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Doped clusters in the gas phase provide nanoconfined model systems for the study of system-bath interactions. To gain insight into interaction mechanisms between chromophores and their environment, the ensemble inhomogeneity has to be lifted and the homogeneous line profile must be accessed. However, such measurements are very challenging at the low particle densities and low signal levels in cluster beam experiments. Here, we dope cryogenic rare-gas clusters with phthalocyanine molecules and apply action-detected two-dimensional electronic spectroscopy to gain insight into the local molecule-cluster environment for solid and superfluid cluster species. The high-resolution homogeneous linewidth analysis provides a benchmark for the theoretical modelling of binding configurations and shows a promising route for high-resolution molecular two-dimensional spectroscopy. Understanding the interaction of single chromophores with nanoparticles remains a challenging task in nanoscience. Here the authors provide insight into the interaction between isolated base-free phthalocyanine molecules and He and Ne nanoclusters in the gas phase using high-resolution two-dimensional spectroscopy.
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