1
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Grechishnikova G, Wat JH, de Cordoba N, Miyake E, Phadkule A, Srivastava A, Savikhin S, Slipchenko L, Huang L, Reppert M. Controlling Vibronic Coupling in Chlorophyll Proteins: The Effects of Excitonic Delocalization and Vibrational Localization. J Phys Chem Lett 2024; 15:9456-9465. [PMID: 39250712 DOI: 10.1021/acs.jpclett.4c01826] [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: 09/11/2024]
Abstract
Vibrational-electronic (vibronic) coupling plays a critical role in excitation energy transfer in molecular aggregates and pigment-protein complexes (PPCs). But the interplay between excitonic delocalization and vibronic interactions is complex, often leaving even qualitative questions as to what conceptual framework (e.g., Redfield versus Förster theory) should be used to interpret experimental results. To shed light on this issue, we report here on the interplay between excitonic delocalization and vibronic coupling in site-directed mutants of the water-soluble chlorophyll protein (WSCP), as reflected in 77 K fluorescence spectra. Experimentally, we find that in PPCs where excitonic delocalization is disrupted (either by mutagenesis or heterodimer formation), the relative intensity of the vibrational sideband (VSB) in fluorescence spectra is suppressed by up to 37% compared to that of the native protein. Numerical simulations reveal that this effect results from the localization of high-frequency vibrations in the coupled system; while excitonic delocalization suppresses the purely electronic transition due to H-aggregate-like dipole-dipole interference, high-frequency vibrations are unaffected, leading to a relative enhancement of the VSB. By comparing VSB intensities of PPCs both in the presence and absence of excitonic delocalization, we extract a set of "local" Huang-Rhys (HR) factors for Chl a in WSCP. More generally, our results suggest a significant role for geometric effects in controlling energy-transfer rates (which depend sensitively on absorption/fluorescence line shapes) in molecular aggregates and PPCs.
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Affiliation(s)
- Galina Grechishnikova
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nicolas de Cordoba
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ethan Miyake
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Libai Huang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Sheng Z, Jiang T, Li W, Shuai Z. TD-DMRG Study of Exciton Dynamics with both Thermal and Static Disorders for Fenna-Matthews-Olson Complex. J Chem Theory Comput 2024. [PMID: 39087905 DOI: 10.1021/acs.jctc.4c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Photosynthesis is a fundamental process that converts solar energy into chemical energy. Understanding the microscopic mechanisms of energy transfer in photosynthetic systems is crucial for the development of novel optoelectronic materials. Simulating these processes poses significant challenges due to the intricate interactions between electrons and phonons, compounded by static disorder. In this work, we present a numerically nearly exact study using the time-dependent density matrix renormalization group (TD-DMRG) method to simulate the quantum dynamics of the Fenna-Matthews-Olson (FMO) complex considering an eight-site model with both thermal and static disorders. We employ the thermo-field dynamics formalism for temperature effects. We merge all electronic interactions into one large matrix product state (MPS) site, boosting accuracy efficiently without increasing complexity. Previous combined experimental and computational studies indicated that the static disorders range from 30 to 90 cm-1 for different FMO sites. We employ a Gaussian distribution and the auxiliary bosonic operator approach to consider the static disorder in our TD-DMRG algorithm. We investigate the impact of different initial excitation sites, temperatures, and degrees of static disorder on the exciton dynamics and temporal coherence. It is found that under the influence of the experimentally determined static disorder strength, the exciton population evolution shows a non-negligible difference at zero temperature, while it is hardly affected at room temperature.
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Affiliation(s)
- Zirui Sheng
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, P. R. China
| | - Tong Jiang
- MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, 100084 Beijing, P. R. China
| | - Weitang Li
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, P. R. China
| | - Zhigang Shuai
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, P. R. China
- MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, 100084 Beijing, P. R. China
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3
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Myers CA, Lu SY, Shedge S, Pyuskulyan A, Donahoe K, Khanna A, Shi L, Isborn CM. Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol. J Phys Chem B 2024; 128:5685-5699. [PMID: 38832562 DOI: 10.1021/acs.jpcb.4c01401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. The strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.
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Affiliation(s)
- Christopher A Myers
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Sapana Shedge
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Arthur Pyuskulyan
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Katherine Donahoe
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Ajay Khanna
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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4
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Hunter KE, Mao Y, Chin AW, Zuehlsdorff TJ. Environmentally Driven Symmetry Breaking Quenches Dual Fluorescence in Proflavine. J Phys Chem Lett 2024; 15:4623-4632. [PMID: 38647005 DOI: 10.1021/acs.jpclett.4c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Nonadiabatic couplings between several electronic excited states are ubiquitous in many organic chromophores and can significantly influence optical properties. A recent experimental study demonstrated that the proflavine molecule exhibits surprising dual fluorescence in the gas phase, which is suppressed in polar solvent environments. Here, we uncover the origin of this phenomenon by parametrizing a linear-vibronic coupling Hamiltonian from spectral densities of system-bath coupling constructed along molecular dynamics trajectories, fully accounting for interactions with the condensed-phase environment. The finite-temperature absorption, steady-state emission, and time-resolved emission spectra are then computed using powerful, numerically exact tensor network approaches. We find that the dual fluorescence in vacuum is driven by a single well-defined coupling mode but is quenched in solution due to dynamic solvent-driven symmetry breaking that mixes the two low-lying electronic states. We expect the computational framework developed here to be widely applicable to the study of non-Condon effects in complex condensed-phase environments.
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Affiliation(s)
- Kye E Hunter
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Alex W Chin
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, 4 place Jussieu, Paris 75005, France
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
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5
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Allan L, Zuehlsdorff TJ. Taming the third order cumulant approximation to linear optical spectroscopy. J Chem Phys 2024; 160:074108. [PMID: 38380749 DOI: 10.1063/5.0182745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
The second order cumulant method offers a promising pathway to predicting optical properties in condensed phase systems. It allows for the computation of linear absorption spectra from excitation energy fluctuations sampled along molecular dynamics (MD) trajectories, fully accounting for vibronic effects, direct solute-solvent interactions, and environmental polarization effects. However, the second order cumulant approximation only guarantees accurate line shapes for energy gap fluctuations obeying Gaussian statistics. A third order correction has recently been derived but often yields unphysical spectra or divergent line shapes for moderately non-Gaussian fluctuations due to the neglect of higher order terms in the cumulant expansion. In this work, we develop a corrected cumulant approach, where the collective effect of neglected higher order contributions is approximately accounted for through a dampening factor applied to the third order cumulant term. We show that this dampening factor can be expressed as a function of the skewness and kurtosis of energy gap fluctuations and can be parameterized from a large set of randomly sampled model Hamiltonians for which exact spectral line shapes are known. This approach is shown to systematically remove unphysical contributions in the form of negative absorbances from cumulant spectra in both model Hamiltonians and condensed phase systems sampled from MD and dramatically improves over the second order cumulant method in describing systems exhibiting Duschinsky mode mixing effects. We successfully apply the approach to the coumarin-153 dye in toluene, obtaining excellent agreement with experiment.
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Affiliation(s)
- Lucas Allan
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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6
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Gustin I, Kim CW, McCamant DW, Franco I. Mapping electronic decoherence pathways in molecules. Proc Natl Acad Sci U S A 2023; 120:e2309987120. [PMID: 38015846 PMCID: PMC10710033 DOI: 10.1073/pnas.2309987120] [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: 06/13/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.
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Affiliation(s)
- Ignacio Gustin
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Chang Woo Kim
- Department of Chemistry, Chonnam National University, Gwangju61186, South Korea
| | - David W. McCamant
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Physics, University of Rochester, Rochester, NY14627
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7
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Kang DH, Cho KH, Kim J, Eun HJ, Rhee YM, Kim SK. Electron-Binding Dynamics of the Dipole-Bound State: Correlation Effect on the Autodetachment Dynamics. J Am Chem Soc 2023; 145:25824-25833. [PMID: 37972034 DOI: 10.1021/jacs.3c10099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The nature of the electron-binding forces in the dipole-bound states (DBS) of anions is interrogated through experimental and theoretical means by investigating the autodetachment dynamics from DBS Feshbach resonances of ortho-, meta-, and para-bromophenoxide (BrPhO-). Though the charge-dipole electrostatic potential has been widely regarded to be mainly responsible for the electron binding in DBS, the effect of nonclassical electron correlation has been conceived to be quite significant in terms of its static and/or dynamic contributions toward the binding of the excess electron to the neutral core. State-specific real-time autodetachment dynamics observed by picosecond time-resolved photoelectron velocity-map imaging spectroscopy reveal that the autodetachment processes from the DBS Feshbach resonances of BrPhO- anions cannot indeed be rationalized by the conventional charge-dipole potential. Specifically, the autodetachment lifetime is drastically lengthened depending on differently positioned Br-substitution, and this rate change cannot be explained within the framework of Fermi's golden rule based on the charge-dipole assumption. High-level ab initio quantum chemical calculations with EOM-EA-CCSD, which intrinsically takes into account electron correlations, generate more reasonable predictions on the binding energies than density functional theory (DFT) calculations, and semiclassical quantum dynamics simulations based on the EOM-EA-CCSD data excellently predict the trend in the autodetachment rates. These findings illustrate that static and dynamic properties of the excess electron in the DBS are strongly influenced by correlation interactions among electrons in the nonvalence orbital of the dipole-bound electron and highly polarizable valence orbitals of the bromine atom, which, in turn, dictate the interesting chemical fate of exotic anion species.
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Affiliation(s)
- Do Hyung Kang
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Kwang Hyun Cho
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Jinwoo Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Han Jun Eun
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Young Min Rhee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
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8
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Bose A, Walters PL. Impact of Spatial Inhomogeneity on Excitation Energy Transport in the Fenna-Matthews-Olson Complex. J Phys Chem B 2023; 127:7663-7673. [PMID: 37647510 DOI: 10.1021/acs.jpcb.3c03062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The dynamics of the excitation energy transfer (EET) in photosynthetic complexes is an interesting question both from the perspective of fundamental understanding and the research in artificial photosynthesis. Over the past decade, very accurate spectral densities have been developed to capture spatial inhomogeneities in the Fenna-Matthews-Olson (FMO) complex. However, challenges persist in numerically simulating these systems, both in terms of parameterizing them and following their dynamics over long periods of time because of long non-Markovian memories. We investigate the dynamics of FMO with the exact treatment of various theoretical spectral densities using the new tensor network path integral-based methods, which are uniquely capable of addressing the difficulty of long memory length and incoherent Förster theory. It is also important to be able to analyze the pathway of EET flow, which can be difficult to identify given the non-trivial structure of connections between bacteriochlorophyll molecules in FMO. We use the recently introduced ideas of relating coherence to population derivatives to analyze the transport process and reveal some new routes of transport. The combination of exact and approximate methods sheds light on the role of coherences in affecting the fine details of the transport and promises to be a powerful toolbox for future exploration of other open systems with quantum transport.
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Affiliation(s)
- Amartya Bose
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Peter L Walters
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Miller Institute for Basic Research in Science, University of California Berkeley, Berkeley, California 94720, United States
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9
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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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10
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Feighan O, Manby FR, Bourne-Worster S. An efficient protocol for excited states of large biochromophores. J Chem Phys 2023; 158:024107. [PMID: 36641400 DOI: 10.1063/5.0132417] [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
Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Qy transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory's accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies.
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Affiliation(s)
- Oliver Feighan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Susannah Bourne-Worster
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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11
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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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12
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Bose A, Walters PL. Tensor Network Path Integral Study of Dynamics in B850 LH2 Ring with Atomistically Derived Vibrations. J Chem Theory Comput 2022; 18:4095-4108. [PMID: 35732015 DOI: 10.1021/acs.jctc.2c00163] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently introduced multisite tensor network path integral (MS-TNPI) allows simulation of extended quantum systems coupled to dissipative media. We use MS-TNPI to simulate the exciton transport and the absorption spectrum of a B850 bacteriochlorophyll (BChl) ring. The MS-TNPI network is extended to account for the ring topology of the B850 system. Accurate molecular-dynamics-based description of the molecular vibrations and the protein scaffold is incorporated through the framework of Feynman-Vernon influence functional. To relate the present work with the excitonic picture, an exploration of the absorption spectrum is done by simulating it using approximate and topologically consistent transition dipole moment vectors. Comparison of these numerically exact MS-TNPI absorption spectra are shown with second-order cumulant approximations. The effect of temperature on both the exact and the approximate spectra is also explored.
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Affiliation(s)
- Amartya Bose
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Peter L Walters
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Miller Institute for Basic Research in Science, University of California Berkeley, Berkeley, California 94720, United States
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13
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Sarngadharan P, Maity S, Kleinekathöfer U. Spectral densities and absorption spectra of the core antenna complex CP43 from photosystem II. J Chem Phys 2022; 156:215101. [DOI: 10.1063/5.0091005] [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
Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities, and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system along with the computed site-dependent spectral densities was used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained, which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areas of molecular dynamics simulations, quantum chemistry, and open quantum systems, it is possible to obtain first-principle results for photosynthetic complexes, which are in accord with experimental findings.
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Affiliation(s)
- Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - 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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14
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ZHU ZHE, Higashi M, Saito S. Excited states of chlorophyll a and b in solution by time-dependent density functional theory. J Chem Phys 2022; 156:124111. [DOI: 10.1063/5.0083395] [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
The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in functionals. Here, we optimize the range-separated parameter, µ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of µ for Chl a and Chl b are smaller than the default value of µ and that for bacteriochlorophyll a, indicating the change in electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.
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Affiliation(s)
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
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15
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Nakamura K, Tanimura Y. Open quantum dynamics theory for a complex subenvironment system with a quantum thermostat: Application to a spin heat bath. J Chem Phys 2021; 155:244109. [PMID: 34972367 DOI: 10.1063/5.0074047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Complex environments, such as molecular matrices and biological material, play a fundamental role in many important dynamic processes in condensed phases. Because it is extremely difficult to conduct full quantum dynamics simulations on such environments due to their many degrees of freedom, here, we treat in detail the environment only around the main system of interest (the subenvironment), while the other degrees of freedom needed to maintain the equilibrium temperature are described by a simple harmonic bath, which we call a quantum thermostat. The noise generated by the subenvironment is spatially non-local and non-Gaussian and cannot be characterized by the fluctuation-dissipation theorem. We describe this model by simulating the dynamics of a two-level system (TLS) that interacts with a subenvironment consisting of a one-dimensional XXZ spin chain. The hierarchical Schrödinger equations of motion are employed to describe the quantum thermostat, allowing for time-irreversible simulations of the dynamics at arbitrary temperature. To see the effects of a quantum phase transition of the subenvironment, we investigate the decoherence and relaxation processes of the TLS at zero and finite temperatures for various values of the spin anisotropy. We observed the decoherence of the TLS at finite temperature even when the anisotropy of the XXZ model is enormous. We also found that the population-relaxation dynamics of the TLS changed in a complex manner with the change in the anisotropy and the ferromagnetic or antiferromagnetic orders of spins.
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Affiliation(s)
- Kiyoto Nakamura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
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16
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Cho KH, Rhee YM. Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes. Phys Chem Chem Phys 2021; 23:26623-26639. [PMID: 34842245 DOI: 10.1039/d1cp04615b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes.
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Affiliation(s)
- Kwang Hyun Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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17
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Lu SY, Zuehlsdorff TJ, Hong H, Aguirre VP, Isborn CM, Shi L. The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy. J Phys Chem B 2021; 125:12214-12227. [PMID: 34726915 DOI: 10.1021/acs.jpcb.1c05914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The environment surrounding a chromophore can dramatically affect the energy absorption and relaxation process, as manifested in optical spectra. Simulations of nonlinear optical spectroscopy, such as two-dimensional electronic spectroscopy (2DES) and transient absorption (TA), will be influenced by the computational model of the environment. We here compare a fixed point charge molecular mechanics model and a quantum mechanical (QM) model of the environment in computed 2DES and TA spectra of Nile red in water and the chromophore of photoactive yellow protein (PYP) in water and protein environments. In addition to simulating these nonlinear optical spectra, we directly juxtapose the computed excitation energy correlation function to the dynamic Stokes shift function often used to analyze environment dynamics. Overall, we find that for the three systems studied here the mutual electronic polarization provided by the QM environment manifests in broader 2DES signals, as well as a larger reorganization energy and a larger static Stokes shift due to stronger coupling between the chromophore and the environment.
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Affiliation(s)
- Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hanbo Hong
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Vincent P Aguirre
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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18
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Cui X, Yan Y, Wei J. Role of Pigment-Protein Coupling in the Energy Transport Dynamics in the Fenna-Matthews-Olson Complex. J Phys Chem B 2021; 125:11884-11892. [PMID: 34669415 DOI: 10.1021/acs.jpcb.1c06844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of pigment-protein coupling in the dynamics of photosynthetic energy transport in chromophoric complexes has not been fully understood. The excitation energy transfer in the photosynthetic system is tremendously efficient. In particular, we investigate the excitation energy transport in the Fenna-Matthews-Olson (FMO) complex. The exciton dynamics and excitation energy transfer (EET) depend on the interaction between the excited chromophores and their environment. Most theoretical models believe that all bacteriochlorophyll-a (BChla) sites are surrounded by the same local protein environment, which is contradicted by the structural analysis of the FMO complex. Based on different values of pigment-protein coupling for different sites, measured in the adiabatic limit, we have theoretically investigated the effect of the heterogeneous local protein environment on the EET process. By the realistic and site-dependent model of the system-bath couplings, the results show that this interaction may have a critical value for the coherent energy-transfer process. Furthermore, we verify that the two transport pathways are coherent and stable to the important parameter reorganization energy of environmental interactions. The quantum dynamical simulations show that the correlation fluctuation keeps the oscillation of the coherent excitation on a long timescale. In addition, due to the inhomogeneous pigment-protein coupling, different BChl sites have asymmetric excitation oscillation timescales.
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Affiliation(s)
- XueYan Cui
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
| | - YiJing Yan
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - JianHua Wei
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
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19
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Srivastava A, Ahad S, Wat JH, Reppert M. Accurate prediction of mutation-induced frequency shifts in chlorophyll proteins with a simple electrostatic model. J Chem Phys 2021; 155:151102. [PMID: 34686046 DOI: 10.1063/5.0064567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photosynthetic pigment-protein complexes control local chlorophyll (Chl) transition frequencies through a variety of electrostatic and steric forces. Site-directed mutations can modify this local spectroscopic tuning, providing critical insight into native photosynthetic functions and offering the tantalizing prospect of creating rationally designed Chl proteins with customized optical properties. Unfortunately, at present, no proven methods exist for reliably predicting mutation-induced frequency shifts in advance, limiting the method's utility for quantitative applications. Here, we address this challenge by constructing a series of point mutants in the water-soluble chlorophyll protein of Lepidium virginicum and using them to test the reliability of a simple computational protocol for mutation-induced site energy shifts. The protocol uses molecular dynamics to prepare mutant protein structures and the charge density coupling model of Adolphs et al. [Photosynth. Res. 95, 197-209 (2008)] for site energy prediction; a graphical interface that implements the protocol automatically is published online at http://nanohub.org/tools/pigmenthunter. With the exception of a single outlier (presumably due to unexpected structural changes), we find that the calculated frequency shifts match the experiment remarkably well, with an average error of 1.6 nm over a 9 nm spread in wavelengths. We anticipate that the accuracy of the method can be improved in the future with more advanced sampling of mutant protein structures.
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Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Safa Ahad
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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20
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Dunnett AJ, Gowland D, Isborn CM, Chin AW, Zuehlsdorff TJ. Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue. J Chem Phys 2021; 155:144112. [PMID: 34654312 DOI: 10.1063/5.0062950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute-solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute-solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.
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Affiliation(s)
- Angus J Dunnett
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, 4 place Jussieu, 75005 Paris, France
| | - Duncan Gowland
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Alex W Chin
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, 4 place Jussieu, 75005 Paris, France
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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21
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Brian D, Sun X. Generalized quantum master equation: A tutorial review and recent advances. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2109157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Dominikus Brian
- Division of Arts and Sciences, NYU Shanghai, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York 10003, USA
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York 10003, USA
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
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22
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Maity S, Sarngadharan P, Daskalakis V, Kleinekathöfer U. Time-dependent atomistic simulations of the CP29 light-harvesting complex. J Chem Phys 2021; 155:055103. [PMID: 34364345 DOI: 10.1063/5.0053259] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II, which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional-based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results, the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, time-dependent and time-independent excitonic Hamiltonians of the system have been constructed and applied to the determination of absorption spectra as well as exciton dynamics.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str. 3603, Limassol, Cyprus
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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23
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Kumar M, Provazza J, Coker DF. Influence of solution phase environmental heterogeneity and fluctuations on vibronic spectra: Perylene diimide molecular chromophore complexes in solution. J Chem Phys 2021; 154:224109. [PMID: 34241200 DOI: 10.1063/5.0054377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ensembles of ab initio parameterized Frenkel-exciton model Hamiltonians for different perylene diimide dimer systems are used, together with various dissipative quantum dynamics approaches, to study the influence of the solvation environment and fluctuations in chromophore relative orientation and packing on the vibronic spectra of two different dimer systems: a π-stacked dimer in aqueous solution in which the relative chromophore geometry is strongly confined by a phosphate bridge and a side-by-side dimer in dichloromethane involving a more flexible alkyne bridge that allows quasi-free rotation of the chromophores relative to one another. These entirely first-principles calculations are found to accurately reproduce the main features of the experimental absorption spectra, providing a detailed mechanistic understanding of how the structural fluctuations and environmental interactions influence the vibronic dynamics and spectroscopy of solutions of these multi-chromophore complexes.
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Affiliation(s)
- Manav Kumar
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Justin Provazza
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - David F Coker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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24
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Timpmann K, Rätsep M, Kangur L, Lehtmets A, Wang-Otomo ZY, Freiberg A. Exciton Origin of Color-Tuning in Ca 2+-Binding Photosynthetic Bacteria. Int J Mol Sci 2021; 22:ijms22147338. [PMID: 34298960 PMCID: PMC8303132 DOI: 10.3390/ijms22147338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
Flexible color adaptation to available ecological niches is vital for the photosynthetic organisms to thrive. Hence, most purple bacteria living in the shade of green plants and algae apply bacteriochlorophyll a pigments to harvest near infra-red light around 850–875 nm. Exceptions are some Ca2+-containing species fit to utilize much redder quanta. The physical basis of such anomalous absorbance shift equivalent to ~5.5 kT at ambient temperature remains unsettled so far. Here, by applying several sophisticated spectroscopic techniques, we show that the Ca2+ ions bound to the structure of LH1 core light-harvesting pigment–protein complex significantly increase the couplings between the bacteriochlorophyll pigments. We thus establish the Ca-facilitated enhancement of exciton couplings as the main mechanism of the record spectral red-shift. The changes in specific interactions such as pigment–protein hydrogen bonding, although present, turned out to be secondary in this regard. Apart from solving the two-decade-old conundrum, these results complement the list of physical principles applicable for efficient spectral tuning of photo-sensitive molecular nano-systems, native or synthetic.
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Affiliation(s)
- Kõu Timpmann
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | - Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | - Liina Kangur
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | - Alexandra Lehtmets
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
| | | | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411 Tartu, Estonia; (K.T.); (M.R.); (L.K.); (A.L.)
- Correspondence:
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25
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Du M, Qin M, Cui H, Wang C, Xu Y, Ma X, Yi X. Role of Spatially Correlated Fluctuations in Photosynthetic Excitation Energy Transfer with an Equilibrium and a Nonequilibrium Initial Bath. J Phys Chem B 2021; 125:6417-6430. [PMID: 34105973 DOI: 10.1021/acs.jpcb.1c02041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of excitation energy in photosynthetic light-harvesting complexes has inspired growing interest for its scientific and engineering significance. Recent experimental findings have suggested that spatially correlated environmental fluctuations may account for the existence of long-lived quantum coherent energy transfer observed even at physiological temperature. In this paper, we investigate the effects of spatial correlations on the excitation energy transfer dynamics by including a nonequilibrium initial bath in a simulated donor-acceptor model. The initial bath state, which is assumed to be either equilibrium or nonequilibrium, is expanded in powers of coupling strength within the polaron formalism of a quantum master equation. The spatial correlations of bath fluctuations strongly influence the decay of coherence in the dynamics. The role of a nonequilibrium initial bath is also influenced by spatial correlations and becomes the most conspicuous for certain degrees of spatial correlations from which we propose a picture that the spatial correlations of bath fluctuations open up new energy transfer pathways, playing a role of protecting coherence. Besides, we apply the polaron master equation approach to study the dynamics in a two-site subsystem of the FMO complex and provide a practical example that shows the versatility of this approach.
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Affiliation(s)
- Min Du
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Ming Qin
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Haitao Cui
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China.,Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
| | - Chunyang Wang
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Yuqing Xu
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xiaoguang Ma
- College of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Xuexi Yi
- Center for Quantum Sciences and School of Physics, Northeast Normal University, Changchun 130024, China
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26
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Ueno S, Tanimura Y. Modeling and Simulating the Excited-State Dynamics of a System with Condensed Phases: A Machine Learning Approach. J Chem Theory Comput 2021; 17:3618-3628. [PMID: 33999606 DOI: 10.1021/acs.jctc.1c00104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Simulating the irreversible quantum dynamics of exciton- and electron-transfer problems poses a nontrivial challenge. Because the irreversibility of the system dynamics is a result of quantum thermal activation and dissipation caused by the surrounding environment, it is necessary to include infinite environmental degrees of freedom in the simulation. Because the capabilities of full quantum dynamics simulations that include the surrounding molecular degrees of freedom are limited, employing a system-bath model is a practical approach. In such a model, the dynamics of excitons or electrons are described by a system Hamiltonian, while the other degrees of freedom that arise from the environmental molecules are described by a harmonic oscillator bath (HOB) and system-bath interaction parameters. By extending on a previous study of molecular liquids [ J. Chem. Theory Comput. 2020, 16, 2099], here, we construct a system-bath model for exciton- and electron-transfer problems by means of a machine learning approach. We determine both the system and system-bath interaction parameters, including the spectral distribution of the bath, using the electronic excitation energies obtained from a quantum mechanics/molecular mechanics (QM/MM) simulation that is conducted as a function of time. Using the analytical expressions of optical response functions, we calculate linear and two-dimensional electronic spectra (2DES) for indocarbocyanine dimers in methanol. From these results, we demonstrate the capability of our approach to elucidate the nonequilibrium exciton dynamics of a quantum system in a nonintuitive manner.
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27
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Brian D, Liu Z, Dunietz BD, Geva E, Sun X. Three-state harmonic models for photoinduced charge transfer. J Chem Phys 2021; 154:174105. [PMID: 34241055 DOI: 10.1063/5.0050289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A widely used strategy for simulating the charge transfer between donor and acceptor electronic states in an all-atom anharmonic condensed-phase system is based on invoking linear response theory to describe the system in terms of an effective spin-boson model Hamiltonian. Extending this strategy to photoinduced charge transfer processes requires also taking into consideration the ground electronic state in addition to the excited donor and acceptor electronic states. In this paper, we revisit the problem of describing such nonequilibrium processes in terms of an effective three-state harmonic model. We do so within the framework of nonequilibrium Fermi's golden rule (NE-FGR) in the context of photoinduced charge transfer in the carotenoid-porphyrin-C60 (CPC60) molecular triad dissolved in explicit tetrahydrofuran (THF). To this end, we consider different ways for obtaining a three-state harmonic model from the equilibrium autocorrelation functions of the donor-acceptor, donor-ground, and acceptor-ground energy gaps, as obtained from all-atom molecular dynamics simulations of the CPC60/THF system. The quantum-mechanically exact time-dependent NE-FGR rate coefficients for two different charge transfer processes in two different triad conformations are then calculated using the effective three-state model Hamiltonians as well as a hierarchy of more approximate expressions that lead to the instantaneous Marcus theory limit. Our results show that the photoinduced charge transfer in CPC60/THF can be described accurately by the effective harmonic three-state models and that nuclear quantum effects are small in this system.
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Affiliation(s)
- Dominikus Brian
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
| | - Zengkui Liu
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
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28
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Shchepanovska D, Shannon RJ, Curchod BFE, Glowacki DR. Nonadiabatic Kinetics in the Intermediate Coupling Regime: Comparing Molecular Dynamics to an Energy-Grained Master Equation. J Phys Chem A 2021; 125:3473-3488. [PMID: 33880919 DOI: 10.1021/acs.jpca.1c01260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose and test an extension of the energy-grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different electronic states of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat NA passages beyond the simple Landau-Zener approximation, along with the corresponding treatments of zero-point energy and tunneling probability. To evaluate the performance of this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C6-hydroperoxy aldehyde (C6-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multichromophore molecule, we show that the EGME is able to capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photoexcited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.
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Affiliation(s)
| | - Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | | | - David R Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.,Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, U.K.,Department of Computer Science, University of Bristol, Bristol BS8 1UB, U.K
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29
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Zuehlsdorff TJ, Shedge SV, Lu SY, Hong H, Aguirre VP, Shi L, Isborn CM. Vibronic and Environmental Effects in Simulations of Optical Spectroscopy. Annu Rev Phys Chem 2021; 72:165-188. [DOI: 10.1146/annurev-physchem-090419-051350] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.
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Affiliation(s)
- Tim J. Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Sapana V. Shedge
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Shao-Yu Lu
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hanbo Hong
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Vincent P. Aguirre
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Liang Shi
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Christine M. Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
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30
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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31
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Maity S, Daskalakis V, Elstner M, Kleinekathöfer U. Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II. Phys Chem Chem Phys 2021; 23:7407-7417. [PMID: 33876100 DOI: 10.1039/d1cp01011e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light-Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. To the best of our knowledge, this is the first theoretical attempt on this large complex system is ever made to accurately simulate the spectral density. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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32
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Chaillet M, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. J Phys Chem Lett 2020; 11:10306-10314. [PMID: 33227205 PMCID: PMC7751012 DOI: 10.1021/acs.jpclett.0c03123] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.
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Affiliation(s)
- Marten
L. Chaillet
- Bijvoet
Centre for Biomolecular Research, University
of Utrecht, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Florian Lengauer
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Julian Adolphs
- Leibniz
Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Frank Müh
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Alexander S. Fokas
- TCM
Group, Cavendish Laboratory, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Alex W. Chin
- Centre
National de la Recherce Scientifique, Institute des Nanosciences de
Paris, Sorbonne Université, Paris, France
| | - Thomas Renger
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
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33
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Klinger A, Lindorfer D, Müh F, Renger T. Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer. J Chem Phys 2020; 153:215103. [PMID: 33291900 DOI: 10.1063/5.0027994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intermolecular contribution to the spectral density of the exciton-vibrational coupling of the homotrimeric Fenna-Matthews-Olson (FMO) light-harvesting protein of green sulfur bacteria P. aestuarii is analyzed by combining a normal mode analysis of the protein with the charge density coupling method for the calculation of local transition energies of the pigments. Correlations in site energy fluctuations across the whole FMO trimer are found at low vibrational frequencies. Including, additionally, the high-frequency intrapigment part of the spectral density, extracted from line-narrowing spectra, we study intra- and intermonomer exciton transfer. Whereas the intrapigment part of the spectral density is important for fast intramonomer exciton relaxation, the intermolecular contributions (due to pigment-environment coupling) determine the intermonomer exciton transfer. Neither the variations of the local Huang-Rhys factors nor the correlations in site energy fluctuations have a critical influence on energy transfer. At room temperature, the intermonomer transfer in the FMO protein occurs on a 10 ps time scale, whereas intramonomer exciton equilibration is roughly two orders of magnitude faster. At cryogenic temperatures, intermonomer transfer limits the lifetimes of the lowest exciton band. The lifetimes are found to increase between 20 ps in the center of this band up to 100 ps toward lower energies, which is in very good agreement with the estimates from hole burning data. Interestingly, exciton delocalization in the FMO monomers is found to slow down intermonomer energy transfer, at both physiological and cryogenic temperatures.
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Affiliation(s)
- Alexander Klinger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
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34
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Sato Y, Navarro Hernández A, Gillespie LD, Valete D. Effects of intramolecular vibrations on excitation energy transfer dynamics of the Fenna-Matthews-Olson complex. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Maity S, Bold BM, Prajapati JD, Sokolov M, Kubař T, Elstner M, Kleinekathöfer U. DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex. J Phys Chem Lett 2020; 11:8660-8667. [PMID: 32991176 DOI: 10.1021/acs.jpclett.0c02526] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum-classical description. To this end, Born-Oppenheimer molecular dynamics simulations have been employed in a quantum mechanics/molecular mechanics (QM/MM) fashion for the ground state followed by excitation energy calculations again in a QM/MM scheme for the Fenna-Matthews-Olson (FMO) complex. The self-consistent-charge density functional tight-binding (DFTB) method electrostatically coupled to a classical description of the environment was applied to perform the ground-state dynamics. Subsequently, long-range-corrected time-dependent DFTB calculations were performed to determine the excitation energy fluctuations of the individual bacteriochlorophyll a molecules. The spectral densities obtained using this approach show an excellent agreement with experimental findings. In addition, the fluctuating site energies and couplings were used to estimate the exciton transfer dynamics.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | | | - Monja Sokolov
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
- Institute of Biological Interfaces, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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36
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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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37
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Chen MS, Zuehlsdorff TJ, Morawietz T, Isborn CM, Markland TE. Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. J Phys Chem Lett 2020; 11:7559-7568. [PMID: 32808797 DOI: 10.1021/acs.jpclett.0c02168] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. Here, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore-environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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38
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Häse F, Roch LM, Friederich P, Aspuru-Guzik A. Designing and understanding light-harvesting devices with machine learning. Nat Commun 2020; 11:4587. [PMID: 32917886 PMCID: PMC7486390 DOI: 10.1038/s41467-020-17995-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/16/2020] [Indexed: 01/27/2023] Open
Abstract
Understanding the fundamental processes of light-harvesting is crucial to the development of clean energy materials and devices. Biological organisms have evolved complex metabolic mechanisms to efficiently convert sunlight into chemical energy. Unraveling the secrets of this conversion has inspired the design of clean energy technologies, including solar cells and photocatalytic water splitting. Describing the emergence of macroscopic properties from microscopic processes poses the challenge to bridge length and time scales of several orders of magnitude. Machine learning experiences increased popularity as a tool to bridge the gap between multi-level theoretical models and Edisonian trial-and-error approaches. Machine learning offers opportunities to gain detailed scientific insights into the underlying principles governing light-harvesting phenomena and can accelerate the fabrication of light-harvesting devices.
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Affiliation(s)
- Florian Häse
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, 02138, MA, USA
- CIFAR AI Chair, Vector Institute for Artificial Intelligence, 661 University Avenue, Toronto, ON, M5S 1M1, Canada
- Department of Computer Science, University of Toronto, 214 College Street, Toronto, ON, M5S 3H6, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Loïc M Roch
- CIFAR AI Chair, Vector Institute for Artificial Intelligence, 661 University Avenue, Toronto, ON, M5S 1M1, Canada
- Department of Computer Science, University of Toronto, 214 College Street, Toronto, ON, M5S 3H6, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- ChemOS Sàrl, Lausanne, VD, 1006, Switzerland
| | - Pascal Friederich
- Department of Computer Science, University of Toronto, 214 College Street, Toronto, ON, M5S 3H6, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- Institute of Nanotechnology, Karlsruhe Insititute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Alán Aspuru-Guzik
- CIFAR AI Chair, Vector Institute for Artificial Intelligence, 661 University Avenue, Toronto, ON, M5S 1M1, Canada.
- Department of Computer Science, University of Toronto, 214 College Street, Toronto, ON, M5S 3H6, Canada.
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
- Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR), 661 University Avenue, Toronto, ON, M5S 1M1, Canada.
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39
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Gao X, Lai Y, Geva E. Simulating Absorption Spectra of Multiexcitonic Systems via Quasiclassical Mapping Hamiltonian Methods. J Chem Theory Comput 2020; 16:6465-6480. [DOI: 10.1021/acs.jctc.0c00709] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xing Gao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yifan Lai
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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40
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Gao X, Geva E. A Nonperturbative Methodology for Simulating Multidimensional Spectra of Multiexcitonic Molecular Systems via Quasiclassical Mapping Hamiltonian Methods. J Chem Theory Comput 2020; 16:6491-6502. [DOI: 10.1021/acs.jctc.0c00843] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xing Gao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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41
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Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Nonlinear spectroscopy in the condensed phase: The role of Duschinsky rotations and third order cumulant contributions. J Chem Phys 2020; 153:044127. [PMID: 32752702 DOI: 10.1063/5.0013739] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. Here, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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42
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Tong Z, Gao X, Cheung MS, Dunietz BD, Geva E, Sun X. Charge transfer rate constants for the carotenoid-porphyrin-C60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation. J Chem Phys 2020; 153:044105. [DOI: 10.1063/5.0016160] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Zhengqing Tong
- 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
| | - Xing Gao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Barry D. Dunietz
- Department of Chemistry, Kent State University, 1787 Summit Street, Kent, Ohio 44242, USA
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - 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
- Department of Chemistry, New York University, New York, New York 10003, USA
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43
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Kim CW, Rhee YM. Toward monitoring the dissipative vibrational energy flows in open quantum systems by mixed quantum-classical simulations. J Chem Phys 2020; 152:244109. [PMID: 32610983 DOI: 10.1063/5.0009867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In open quantum system dynamics, rich information about the major energy relaxation channels and corresponding relaxation rates can be elucidated by monitoring the vibrational energy flow among individual bath modes. However, such calculations often become tremendously difficult as the complexity of the subsystem-bath coupling increases. In this paper, we attempt to make this task feasible by using a mixed quantum-classical method, the Poisson-bracket mapping equation with non-Hamiltonian modification (PBME-nH) [H. W. Kim and Y. M. Rhee, J. Chem. Phys. 140, 184106 (2014)]. For a quantum subsystem bilinearly coupled to harmonic bath modes, we derive an expression for the mode energy in terms of the classical positions and momenta of the nuclei, while keeping consistency with the energy of the quantum subsystem. The accuracy of the resulting expression is then benchmarked against a numerically exact method by using relatively simple models. Although our expression predicts a qualitatively correct dissipation rate for a range of situations, cases involving a strong vibronic resonance are quite challenging. This is attributed to the inherent lack of quantum back reaction in PBME-nH, which becomes significant when the subsystem strongly interacts with a small number of bath modes. A rigorous treatment of such an effect will be crucial for developing quantitative simulation methods that can handle generic subsystem-bath coupling.
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Affiliation(s)
- Chang Woo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
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44
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Zhang J, Borrelli R, Tanimura Y. Proton tunneling in a two-dimensional potential energy surface with a non-linear system–bath interaction: Thermal suppression of reaction rate. J Chem Phys 2020; 152:214114. [DOI: 10.1063/5.0010580] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Jiaji Zhang
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Raffaele Borrelli
- DISAFA, University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, Italy
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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45
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Tong Z, Huai Z, Mei Y, Mo Y. Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian. J Chem Phys 2020; 152:135101. [DOI: 10.1063/1.5135999] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Zhengqing Tong
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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46
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Cui X, Yan Y, Wei J. Theoretical Study on the Effect of Environment on Excitation Energy Transfer in Photosynthetic Light-Harvesting Systems. J Phys Chem B 2020; 124:2354-2362. [PMID: 32130013 DOI: 10.1021/acs.jpcb.0c00266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, two-dimensional (2D) electronic spectroscopy experiments prove that the excitation energy transfer (EET) in photosynthetic light-harvesting systems presents long-lived electronic quantum beating signals. After being discovered in the light-harvesting system, the quantum coherence effect has aroused widespread discussion. To illustrate the EET process in the Fenna-Matthews-Olson (FMO) and phycocyanin 645 (PC645) complex, the local protein environment is often thought to be the same; however, this is ambivalent to the practical structural analysis of the light-harvesting complex. By adopting the dissipaton equation of motion theory, we present the effect of a heterogeneous protein environment on the energy transfer process with accurate numerical results. We demonstrate that the energy transfer process relies on the local heterogeneous environment for the FMO complex. A similar good agreement is found for the PC645 complex. Furthermore, we discuss the optimal value of different chromophores in the excitation energy transfer process by controlling the environmental characteristics.
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Affiliation(s)
- XueYan Cui
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
| | - YiJing Yan
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - JianHua Wei
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
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47
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Ueno S, Tanimura Y. Modeling Intermolecular and Intramolecular Modes of Liquid Water Using Multiple Heat Baths: Machine Learning Approach. J Chem Theory Comput 2020; 16:2099-2108. [DOI: 10.1021/acs.jctc.9b01288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seiji Ueno
- HPC Systems Inc., Nakagyoku, Kyoto 604, Japan
- Department of Chemistry, Kyoto University, Kyoto 606-8502, Japan
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48
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Cerezo J, Aranda D, Avila Ferrer FJ, Prampolini G, Santoro F. Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the Condensed Phase. J Chem Theory Comput 2020; 16:1215-1231. [PMID: 31855424 DOI: 10.1021/acs.jctc.9b01009] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a general mixed quantum classical method that couples classical molecular dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible molecules in the condensed phase without, in principle, any phenomenological broadening. It is based on a partition of the nuclear motions of the solute + solvent system in "soft" and "stiff" vibrational modes and an adiabatic hypothesis that assumes that stiff modes are much faster than soft ones. In this framework, the spectrum is rigorously expressed as a conformational integral of quantum vibronic spectra along the stiff coordinates only. Soft modes enter at the classical level through the conformational distribution that is sampled with classical MD runs. In each configuration, reduced-dimensionality quadratic Hamiltonians are built in the space of the stiff coordinates only, thanks to a generalization of the Vertical Hessian harmonic model and an iterative application of projectors in internal coordinates to remove soft modes. Quantum vibronic spectra, specific for each sampled configuration of the soft coordinates, are then computed at the desired temperature with efficient time-dependent techniques, and the global spectrum simply arises from their average. For consistency of the whole procedure, classical MD runs are performed with quantum-mechanically derived force fields, parameterized at the same level of theory selected for generating the quadratic Hamiltonians along the stiff coordinates. Application to N-methyl-6-oxyquinolinium betaine in water, dithiophene in ethanol, and cyanidine in water is presented to show the performance of the method.
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Affiliation(s)
| | - Daniel Aranda
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy.,Departamento de Química Física, Facultad de Ciencias, Andalucía Tech , Universidad de Málaga , E-29071 Málaga , Spain
| | - Francisco José Avila Ferrer
- Departamento de Química Física, Facultad de Ciencias, Andalucía Tech , Universidad de Málaga , E-29071 Málaga , Spain
| | - Giacomo Prampolini
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
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49
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Segarra-Martí J, Segatta F, Mackenzie TA, Nenov A, Rivalta I, Bearpark MJ, Garavelli M. Modeling multidimensional spectral lineshapes from first principles: application to water-solvated adenine. Faraday Discuss 2020; 221:219-244. [DOI: 10.1039/c9fd00072k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We theoretically describe spectral lineshape from first principles, providing insight into solvent–solute interactions in terms of static and dynamic disorder and how these shape experimental signals in linear and non-linear optical spectroscopies.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Tristan A. Mackenzie
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
- Univ Lyon
| | - Michael J. Bearpark
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
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50
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Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Influence of Electronic Polarization on the Spectral Density. J Phys Chem B 2019; 124:531-543. [DOI: 10.1021/acs.jpcb.9b10250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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