1
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Green D, Bressan G, Heisler IA, Meech SR, Jones GA. Vibrational coherences in half-broadband 2D electronic spectroscopy: Spectral filtering to identify excited state displacements. J Chem Phys 2024; 160:234104. [PMID: 38884412 DOI: 10.1063/5.0214023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/03/2024] [Indexed: 06/18/2024] Open
Abstract
Vibrational coherences in ultrafast pump-probe (PP) and 2D electronic spectroscopy (2DES) provide insights into the excited state dynamics of molecules. Femtosecond coherence spectra and 2D beat maps yield information about displacements of excited state surfaces for key vibrational modes. Half-broadband 2DES uses a PP configuration with a white light continuum probe to extend the detection range and resolve vibrational coherences in the excited state absorption (ESA). However, the interpretation of these spectra is difficult as they are strongly dependent on the spectrum of the pump laser and the relative displacement of the excited states along the vibrational coordinates. We demonstrate the impact of these convoluting factors for a model based upon cresyl violet. A careful consideration of the position of the pump spectrum can be a powerful tool in resolving the ESA coherences to gain insights into excited state displacements. This paper also highlights the need for caution in considering the spectral window of the pulse when interpreting these spectra.
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Affiliation(s)
- Dale Green
- Physics, Faculty of Science, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Giovanni Bressan
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Ismael A Heisler
- Instituto de Física, Universidade Federal do Rio Grande do Sul, 91509-900 Porto Alegre, RS, Brazil
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Garth A Jones
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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2
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Nath A, Sharma A, Singh SK, Sundaram S. Assessing the Impact of Hexavalent Chromium (Cr VI) at Varied Concentrations on Spirulina platensis for Growth, Metal Sorption, and Photosynthetic Responses. Curr Microbiol 2024; 81:231. [PMID: 38896297 DOI: 10.1007/s00284-024-03743-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/19/2024] [Indexed: 06/21/2024]
Abstract
Spirulina platensis, a photosynthetic cyanobacterium, has garnered attention for its potential role in environmental remediation due to its ability to absorb and metabolize toxic heavy metals. Understanding its response toward toxicity of one of the most common contaminants, Cr(VI) is crucial for assessing its efficacy in bioremediation efforts. This study aims to investigate the physiological and biochemical responses of Spirulina platensis to varying concentrations of Cr(VI) from 0.5 to 5 ppm, shedding light on its potential as a bioindicator for environmental contamination and its suitability for bioremediation purposes. The impact of Cr(VI) on cell density, biosorption, pigment levels, nutrient content, fluorescence response, and photosynthetic efficiency was examined. The study revealed a gradual reduction in cell density, biomass production, and biosorption efficiency with increasing Cr(VI) concentrations. Pigment levels, carbohydrate, protein, and lipid content showed significant decreases, indicating physiological stress. Fluorescence response and photosynthetic efficiency were also adversely affected, suggesting alterations in electron transfer dynamics. A threshold for chromium toxicity was observed at 0.5 ppm, beyond which significant physiological disturbances occurred. This investigation highlights the sensitivity of Spirulina platensis to Cr(VI) toxicity and its potential as a bioindicator for heavy metal contamination. Metal sorption was highest in 0.5 ppm Cr(VI) with 56.56% removal. Notably, at lower concentrations, Cr(VI) acted as an intermediate electron acceptor, enhancing the electron transport chain and potentially increasing biomass under controlled conditions. The findings underscore the importance of understanding the mechanisms underlying heavy metal stress in microalgae for effective environmental remediation strategies. The research highlights the dual role of chromium(VI) in influencing S. platensis, depending on the concentration, and underscores the importance of understanding metal ion interactions with photosynthetic organisms for potential applications in bioremediation.
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Affiliation(s)
- Adi Nath
- Department of Botany, Nehru Gram Bharati Deemed to University, Prayagraj, 221505, India.
| | - Abhijeet Sharma
- Centre of Biotechnology, University of Allahabad, Prayagraj, 211002, India
| | | | - Shanthy Sundaram
- Centre of Biotechnology, University of Allahabad, Prayagraj, 211002, India
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3
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Dietert RR, Dietert JM. Examining Sound, Light, and Vibrations as Tools to Manage Microbes and Support Holobionts, Ecosystems, and Technologies. Microorganisms 2024; 12:905. [PMID: 38792734 PMCID: PMC11123986 DOI: 10.3390/microorganisms12050905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
The vast array of interconnected microorganisms across Earth's ecosystems and within holobionts has been called the "Internet of Microbes." Bacteria and archaea are masters of energy and information collection, storage, transformation, and dissemination using both "wired" and wireless (at a distance) functions. Specific tools affecting microbial energy and information functions offer effective strategies for managing microbial populations within, between, and beyond holobionts. This narrative review focuses on microbial management using a subset of physical modifiers of microbes: sound and light (as well as related vibrations). These are examined as follows: (1) as tools for managing microbial populations, (2) as tools to support new technologies, (3) as tools for healing humans and other holobionts, and (4) as potential safety dangers for microbial populations and their holobionts. Given microbial sensitivity to sound, light, and vibrations, it is critical that we assign a higher priority to the effects of these physical factors on microbial populations and microbe-laden holobionts. We conclude that specific sound, light, and/or vibrational conditions are significant therapeutic tools that can help support useful microbial populations and help to address the ongoing challenges of holobiont disease. We also caution that inappropriate sound, light, and/or vibration exposure can represent significant hazards that require greater recognition.
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Affiliation(s)
- Rodney R. Dietert
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
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4
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Bruschi M, Gallina F, Fresch B. A Quantum Algorithm from Response Theory: Digital Quantum Simulation of Two-Dimensional Electronic Spectroscopy. J Phys Chem Lett 2024; 15:1484-1492. [PMID: 38295347 DOI: 10.1021/acs.jpclett.3c03499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Multidimensional optical spectroscopies are powerful techniques to investigate energy transfer pathways in natural and artificial systems. Because of the high information content of the spectra, numerical simulations of the optical response are of primary importance to assist the interpretation of spectral features. However, the increasing complexity of the investigated systems and their quantum dynamics call for the development of novel simulation strategies. In this work, we consider using digital quantum computers. By combining quantum dynamical simulation and nonlinear response theory, we present a quantum algorithm for computing the optical response of molecular systems. The quantum advantage stems from the efficient quantum simulation of the dynamics governed by the molecular Hamiltonian, and it is demonstrated by explicitly considering exciton-vibrational coupling. The protocol is tested on a near-term quantum device, providing the digital quantum simulation of the linear and nonlinear response of simple molecular models.
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Affiliation(s)
- Matteo Bruschi
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, Padua 35131, Italy
| | - Federico Gallina
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, Padua 35131, Italy
| | - Barbara Fresch
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, Padua 35131, Italy
- Padua Quantum Technologies Research Center, Università degli Studi di Padova, via Gradenigo 6/A, Padua 35131, Italy
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5
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Zerah Harush E, Dubi Y. Signature of Quantum Coherence in the Exciton Energy Pathways of the LH2 Photosynthetic Complex. ACS OMEGA 2023; 8:38871-38878. [PMID: 37901547 PMCID: PMC10601065 DOI: 10.1021/acsomega.3c02676] [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: 04/19/2023] [Accepted: 06/15/2023] [Indexed: 10/31/2023]
Abstract
Unraveling the energy transfer pathways in photosynthetic complexes is an important step toward understanding their structure-function interplay. Here, we use an open quantum systems approach to investigate energy transfer within the LH2 photosynthetic apparatus and its dependence on environmental conditions. We find that energy transfer pathways strongly depend on the environment-induced dephasing time. A comparison between the computational results and experiments performed on similar systems demonstrates that quantum coherences are present in these systems under physiological conditions and have an important role in shaping the energy transfer pathways. Moreover, our calculations indicate that relatively simple spectroscopy experiments can be used to detect traces of quantum coherence. Finally, our results suggest that quantum coherence may play a role in photosynthesis, but not in enhancing the efficiency as was previously suggested.
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Affiliation(s)
- Elinor Zerah Harush
- Department of Chemistry and
Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yonatan Dubi
- Department of Chemistry and
Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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6
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Humphries BS, Green D, Borgh MO, Jones GA. Phonon Signatures in Photon Correlations. PHYSICAL REVIEW LETTERS 2023; 131:143601. [PMID: 37862651 DOI: 10.1103/physrevlett.131.143601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/21/2023] [Indexed: 10/22/2023]
Abstract
We show that the second-order, two-time correlation functions for phonons and photons emitted from a vibronic molecule in a thermal bath result in bunching and antibunching (a purely quantum effect), respectively. Signatures relating to phonon exchange with the environment are revealed in photon-photon correlations. We demonstrate that cross-correlation functions have a strong dependence on the order of detection giving insight into how phonon dynamics influences the emission of light. This work offers new opportunities to investigate quantum effects in condensed-phase molecular systems.
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Affiliation(s)
- Ben S Humphries
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Dale Green
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Magnus O Borgh
- Physics, Faculty of Science, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Garth A Jones
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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7
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Yang J, Gelin MF, Chen L, Šanda F, Thyrhaug E, Hauer J. Two-dimensional fluorescence excitation spectroscopy: A novel technique for monitoring excited-state photophysics of molecular species with high time and frequency resolution. J Chem Phys 2023; 159:074201. [PMID: 37581414 DOI: 10.1063/5.0156297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
We propose a novel UV/Vis femtosecond spectroscopic technique, two-dimensional fluorescence-excitation (2D-FLEX) spectroscopy, which combines spectral resolution during the excitation process with exclusive monitoring of the excited-state system dynamics at high time and frequency resolution. We discuss the experimental feasibility and realizability of 2D-FLEX, develop the necessary theoretical framework, and demonstrate the high information content of this technique by simulating the 2D-FLEX spectra of a model four-level system and the Fenna-Matthews-Olson antenna complex. We show that the evolution of 2D-FLEX spectra with population time directly monitors energy transfer dynamics and can thus yield direct qualitative insight into the investigated system. This makes 2D-FLEX a highly efficient instrument for real-time monitoring of photophysical processes in polyatomic molecules and molecular aggregates.
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Affiliation(s)
- Jianmin Yang
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | | | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, 12116 Prague, Czech Republic
| | - Erling Thyrhaug
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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8
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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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9
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Rammler T, Wackenhut F, Rapp J, zur Oven-Krockhaus S, Forchhammer K, Meixner AJ, Harter K. Analysis of Fast Fluorescence Kinetics of a Single Cyanobacterium Trapped in an Optical Microcavity. PLANTS (BASEL, SWITZERLAND) 2023; 12:607. [PMID: 36771691 PMCID: PMC9919002 DOI: 10.3390/plants12030607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Photosynthesis is one the most important biological processes on earth, producing life-giving oxygen, and is the basis for a large variety of plant products. Measurable properties of photosynthesis provide information about its biophysical state, and in turn, the physiological conditions of a photoautotrophic organism. For instance, the chlorophyll fluorescence intensity of an intact photosystem is not constant as in the case of a single fluorescent dye in solution but shows temporal changes related to the quantum yield of the photosystem. Commercial photosystem analyzers already use the fluorescence kinetics characteristics of photosystems to infer the viability of organisms under investigation. Here, we provide a novel approach based on an optical Fabry-Pérot microcavity that enables the readout of photosynthetic properties and activity for an individual cyanobacterium. This approach offers a completely new dimension of information, which would normally be lost due to averaging in ensemble measurements obtained from a large population of bacteria.
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Affiliation(s)
- Tim Rammler
- Institute for Physical and Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Frank Wackenhut
- Institute for Physical and Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Sven zur Oven-Krockhaus
- Institute for Physical and Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Alfred J. Meixner
- Institute for Physical and Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
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10
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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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11
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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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12
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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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13
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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: 0] [Impact Index Per Article: 0] [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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14
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Policht VR, Niedringhaus A, Willow R, Laible PD, Bocian DF, Kirmaier C, Holten D, Mančal T, Ogilvie JP. Hidden vibronic and excitonic structure and vibronic coherence transfer in the bacterial reaction center. SCIENCE ADVANCES 2022; 8:eabk0953. [PMID: 34985947 PMCID: PMC8730630 DOI: 10.1126/sciadv.abk0953] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We report two-dimensional electronic spectroscopy (2DES) experiments on the bacterial reaction center (BRC) from purple bacteria, revealing hidden vibronic and excitonic structure. Through analysis of the coherent dynamics of the BRC, we identify multiple quasi-resonances between pigment vibrations and excitonic energy gaps, and vibronic coherence transfer processes that are typically neglected in standard models of photosynthetic energy transfer and charge separation. We support our assignment with control experiments on bacteriochlorophyll and simulations of the coherent dynamics using a reduced excitonic model of the BRC. We find that specific vibronic coherence processes can readily reveal weak exciton transitions. While the functional relevance of such processes is unclear, they provide a spectroscopic tool that uses vibrations as a window for observing excited state structure and dynamics elsewhere in the BRC via vibronic coupling. Vibronic coherence transfer reveals the upper exciton of the “special pair” that was weakly visible in previous 2DES experiments.
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Affiliation(s)
- Veronica R. Policht
- Department of Physics, University of Michigan, 450 Church St, Ann Arbor, MI 48109, USA
| | - Andrew Niedringhaus
- Department of Physics, University of Michigan, 450 Church St, Ann Arbor, MI 48109, USA
| | - Rhiannon Willow
- Department of Physics, University of Michigan, 450 Church St, Ann Arbor, MI 48109, USA
| | - Philip D. Laible
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - David F. Bocian
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Tomáš Mančal
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
| | - Jennifer P. Ogilvie
- Department of Physics, University of Michigan, 450 Church St, Ann Arbor, MI 48109, USA
- Corresponding author.
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15
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Breuil G, Mangaud E, Lasorne B, Atabek O, Desouter-Lecomte M. Funneling dynamics in a phenylacetylene trimer: Coherent excitation of donor excitonic states and their superposition. J Chem Phys 2021; 155:034303. [PMID: 34293889 DOI: 10.1063/5.0056351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Funneling dynamics in conjugated dendrimers has raised great interest in the context of artificial light-harvesting processes. Photoinduced relaxation has been explored by time-resolved spectroscopy and simulations, mainly by semiclassical approaches or referring to open quantum systems methods, within the Redfield approximation. Here, we take the benefit of an ab initio investigation of a phenylacetylene trimer, and in the spirit of a divide-and-conquer approach, we focus on the early dynamics of the hierarchy of interactions. We build a simplified but realistic model by retaining only bright electronic states and selecting the vibrational domain expected to play the dominant role for timescales shorter than 500 fs. We specifically analyze the role of the in-plane high-frequency skeletal vibrational modes involving the triple bonds. Open quantum system non-adiabatic dynamics involving conical intersections is conducted by separating the electronic subsystem from the high-frequency tuning and coupling vibrational baths. This partition is implemented within a robust non-perturbative and non-Markovian method, here the hierarchical equations of motion. We will more precisely analyze the coherent preparation of donor states or of their superposition by short laser pulses with different polarizations. In particular, we extend the π-pulse strategy for the creation of a superposition to a V-type system. We study the relaxation induced by the high-frequency vibrational collective modes and the transitory dissymmetry, which results from the creation of a superposition of electronic donor states.
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Affiliation(s)
- Gabriel Breuil
- ICGM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Etienne Mangaud
- MSME, Université Gustave Eiffel, UPEC, CNRS, F-77454 Marne-La-Vallée, France
| | | | - Osman Atabek
- Institut des Sciences Moléculaires, Université Paris-Saclay-CNRS, UMR8214, F-91400 Orsay, France
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16
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Gelin MF, Borrelli R. Simulation of Nonlinear Femtosecond Signals at Finite Temperature via a Thermo Field Dynamics-Tensor Train Method: General Theory and Application to Time- and Frequency-Resolved Fluorescence of the Fenna-Matthews-Olson Complex. J Chem Theory Comput 2021; 17:4316-4331. [PMID: 34076412 DOI: 10.1021/acs.jctc.1c00158] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Addressing needs of contemporary nonlinear femtosecond optical spectroscopy, we have developed a fully quantum, numerically accurate wave function-based approach for the calculation of third-order spectroscopic signals of polyatomic molecules and molecular aggregates at finite temperature. The systems are described by multimode nonadiabatic vibronic-coupling Hamiltonians, in which diagonal terms are treated in harmonic approximation, while off-diagonal interstate couplings are assumed to be coordinate independent. The approach is based on the Thermo Field Dynamics (TFD) representation of quantum mechanics and tensor-train (TT) machinery for efficient numerical simulation of quantum evolution of systems with many degrees of freedom. The developed TFD-TT approach is applied to the calculation of time- and frequency-resolved fluorescence spectra of the Fenna-Matthews-Olson (FMO) antenna complex at room temperature taking into account finite time-frequency resolution in fluorescence detection, orientational averaging, and static disorder.
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Affiliation(s)
- Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
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17
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Janković V, Mančal T. Nonequilibrium steady-state picture of incoherent light-induced excitation harvesting. J Chem Phys 2020; 153:244110. [PMID: 33380098 DOI: 10.1063/5.0029918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We formulate a comprehensive theoretical description of excitation harvesting in molecular aggregates photoexcited by weak incoherent radiation. An efficient numerical scheme that respects the continuity equation for excitation fluxes is developed to compute the nonequilibrium steady state (NESS) arising from the interplay between excitation generation, excitation relaxation, dephasing, trapping at the load, and recombination. The NESS is most conveniently described in the so-called preferred basis in which the steady-state excitonic density matrix is diagonal. The NESS properties are examined by relating the preferred-basis description to the descriptions in the site or excitonic bases. Focusing on a model photosynthetic dimer, we find that the NESS in the limit of long trapping time is quite similar to the excited-state equilibrium in which the stationary coherences originate from the excitation-environment entanglement. For shorter trapping times, we demonstrate how the properties of the NESS can be extracted from the time-dependent description of an incoherently driven but unloaded dimer. This relation between stationary and time-dependent pictures is valid, provided that the trapping time is longer than the decay time of dynamic coherences accessible in femtosecond spectroscopy experiments.
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Affiliation(s)
- Veljko Janković
- Scientific Computing Laboratory, Center for the Study of Complex Systems, Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - Tomáš Mančal
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
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18
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Sun K, Xie W, Chen L, Domcke W, Gelin MF. Multi-faceted spectroscopic mapping of ultrafast nonadiabatic dynamics near conical intersections: A computational study. J Chem Phys 2020; 153:174111. [DOI: 10.1063/5.0024148] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kewei Sun
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Weiwei Xie
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Lipeng Chen
- Max Planck Institute for the Physics of Complex Systems, 38 Nöethnitzer Str., Dresden, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - Maxim F. Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
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19
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Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.
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20
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Green D, Jones GA, Salam A. Polariton mediated resonance energy transfer in a fluid. J Chem Phys 2020; 153:034111. [PMID: 32716175 DOI: 10.1063/5.0011562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The focus of this work is on a microscopic quantum electrodynamical understanding of cumulative quantum effects in resonance energy transfer occurring in an isotropic and disordered medium. In particular, we consider quantum coherence, defined in terms of interferences between Feynman pathways, and analyze pure-amplitude and phase cross terms that appear in the Fermi golden rule rate equation that results from squaring the matrix element for mediated energy transfer. It is shown that pure-amplitude terms dominate in the near-zone when chromophores are close in proximity to one another (within a few nanometers), and phase cross terms dominate toward the far-zone when phase differences between different Feynman pathways begin to emerge. This can be understood in terms of physical attributes of the mediating photon, whose character becomes more real at long distances, coinciding with vanishing longitudinal components of the field, as transverse components begin to dominate.
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Affiliation(s)
- Dale Green
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Garth A Jones
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - A Salam
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
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21
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Ikeda T, Scholes GD. Generalization of the hierarchical equations of motion theory for efficient calculations with arbitrary correlation functions. J Chem Phys 2020; 152:204101. [DOI: 10.1063/5.0007327] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tatsushi Ikeda
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544, USA
| | - Gregory D. Scholes
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544, USA
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