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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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2
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Mai M, Zazubovich V, Mansbach RA. Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1371-1384. [PMID: 38299975 PMCID: PMC10876061 DOI: 10.1021/acs.jpcb.3c06889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.
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Affiliation(s)
- Martina Mai
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Rachael A. Mansbach
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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3
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Götze JP, Lokstein H. Excitation Energy Transfer between Higher Excited States of Photosynthetic Pigments: 2. Chlorophyll b is a B Band Excitation Trap. ACS OMEGA 2023; 8:40015-40023. [PMID: 37929150 PMCID: PMC10620878 DOI: 10.1021/acsomega.3c05896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/21/2023] [Indexed: 11/07/2023]
Abstract
Chlorophylls (Chls) are known for fast, subpicosecond internal conversion (IC) from ultraviolet/blue absorbing ("B" or "Soret" states) to the energetically lower, red light-absorbing Q states. Consequently, excitation energy transfer (EET) in photosynthetic pigment-protein complexes involving the B states has so far not been considered. We present, for the first time, a theoretical framework for the existence of B-B EET in tightly coupled Chl aggregates such as photosynthetic pigment-protein complexes. We show that according to a Förster resonance energy transport (FRET) scheme, unmodulated B-B EET has an unexpectedly high range. Unsuppressed, it could pose an existential threat-the damage potential of blue light for photochemical reaction centers (RCs) is well-known. This insight reveals so-far undescribed roles for carotenoids (Crts, cf. previous article in this series) and Chl b (this article) of possibly vital importance. Our model system is the photosynthetic antenna pigment-protein complex (CP29). The focus of the study is on the role of Chl b for EET in the Q and B bands. Further, the initial excited pigment distribution in the B band is computed for relevant solar irradiation and wavelength-centered laser pulses. It is found that both accessory pigment classes compete efficiently with Chl a absorption in the B band, leaving only 40% of B band excitations for Chl a. B state population is preferentially relocated to Chl b after excitation of any Chls, due to a near-perfect match of Chl b B band absorption with Chl a B state emission spectra. This results in an efficient depletion of the Chl a population (0.66 per IC/EET step, as compared to 0.21 in a Chl a-only system). Since Chl b only occurs in the peripheral antenna complexes of plants and algae, and RCs contain only Chl a, this would automatically trap potentially dangerous B state population in the antennae, preventing forwarding to the RCs.
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Affiliation(s)
- Jan P. Götze
- Institut
für Chemie und Biochemie, Fachbereich Biologie Chemie Pharmazie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Heiko Lokstein
- Department
of Chemical Physics and Optics, Charles
University, Ke Karlovu
3, 121 16 Prague
2, Czech Republic
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4
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Kaiser A, Daoud RE, Aquilante F, Kühn O, De Vico L, Bokarev SI. A Multiconfigurational Wave Function Implementation of the Frenkel Exciton Model for Molecular Aggregates. J Chem Theory Comput 2023; 19:2918-2928. [PMID: 37115036 DOI: 10.1021/acs.jctc.3c00185] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
We present an implementation of the Frenkel exciton model into the OpenMolcas program package enabling calculations of collective electronic excited states of molecular aggregates based on a multiconfigurational wave function description of the individual monomers. The computational protocol avoids using diabatization schemes and, thus, supermolecule calculations. Additionally, the use of the Cholesky decomposition of the two-electron integrals entering pair interactions enhances the efficiency of the computational scheme. The application of the method is exemplified for two test systems, that is, a formaldehyde oxime and a bacteriochlorophyll-like dimer. For the sake of comparison with the dipole approximation, we restrict our considerations to situations where intermonomer exchange can be neglected. The protocol is expected to be beneficial for aggregates composed of molecules with extended π systems, unpaired electrons such as radicals or transition metal centers, where it should outperform widely used methods based on time-dependent density functional theory.
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Affiliation(s)
- Andy Kaiser
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock. Germany
| | - Razan E Daoud
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Francesco Aquilante
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock. Germany
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Sergey I Bokarev
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock. Germany
- Chemistry Department, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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5
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Brütting M, Foerster JM, Kümmel S. Understanding Primary Charge Separation in the Heliobacterial Reaction Center. J Phys Chem Lett 2023; 14:3092-3102. [PMID: 36951395 DOI: 10.1021/acs.jpclett.3c00377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The homodimeric reaction center of heliobacteria retains features of the ancestral reaction center and can thus provide insights into the evolution of photosynthesis. Primary charge separation is expected to proceed in a two-step mechanism along either of the two reaction center branches. We reveal the first charge-separation step from first-principles calculations based on time-dependent density functional theory with an optimally tuned range-separated hybrid and ab initio Born-Oppenheimer molecular dynamics: the electron is most likely localized on the electron transfer cofactor 3 (EC3, OH-chlorophyll a), and the hole on the adjacent EC2. Including substantial parts of the surrounding protein environment into the calculations shows that a distinct structural mechanism is decisive for the relative energetic positioning of the electronic excitations: specific charged amino acids in the vicinity of EC3 lower the energy of charge-transfer excitations and thus facilitate efficient charge separation. These results are discussed considering recent experimental insights.
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Cupellini L, Qian P, Nguyen-Phan TC, Gardiner AT, Cogdell RJ. Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex. PHOTOSYNTHESIS RESEARCH 2023; 156:75-87. [PMID: 35672557 PMCID: PMC10070313 DOI: 10.1007/s11120-022-00925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique near-infrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
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Affiliation(s)
- Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Nordic 5, 5651 GTC, Eindhoven, The Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 01, Třeboň, Czech Republic
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
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7
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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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8
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Hu YY, Liu XL, Yao HD, Jiang YL, Li K, Chen MQ, Wang P, Zhang JP. PEG effects on excitonic properties of LH2 from Rhodobacter sphaeroides 2.4.1 in different environments. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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9
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Liu XL, Hu YY, Li K, Chen MQ, Wang P. Reconstituted LH2 in multilayer membranes induced by poly-L-lysine: structure of supramolecular and electronic states. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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10
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Elvers I, Nguyen-Phan TC, Gardiner AT, Hunter CN, Cogdell RJ, Köhler J. Phasor Analysis Reveals Multicomponent Fluorescence Kinetics in the LH2 Complex from Marichromatium purpuratum. J Phys Chem B 2022; 126:10335-10346. [PMID: 36449272 DOI: 10.1021/acs.jpcb.2c04983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We investigated the fluorescence kinetics of LH2 complexes from Marichromatium purpuratum, the cryo-EM structure of which has been recently elucidated with 2.4 Å resolution. The experiments have been carried out as a function of the excitation density by varying both the excitation fluence and the repetition rate of the laser excitation. Instead of the usual multiexponential fitting procedure, we applied the less common phasor formalism for evaluating the transients because this allows for a model-free analysis of the data without a priori knowledge about the number of processes that contribute to a particular decay. For the various excitation conditions, this analysis reproduces consistently three lifetime components with decay times below 100 ps, 500 ps, and 730 ps, which were associated with the quenched state, singlet-triplet annihilation, and fluorescence decay, respectively. Moreover, it reveals that the number of decay components that contribute to the transients depends on whether the excitation wavelength is in resonance with the B800 BChl a molecules or with the carotenoids. Based on the mutual arrangement of the chromophores in their binding pockets, this leads us to conclude that the energy transfer pathways within the LH2 complex of this species differ significantly from each other for exciting either the B800 BChl molecules or the carotenoids. Finally, we speculate whether the illumination with strong laser light converts the LH2 complexes studied here into a quenched conformation that might be related to the development of the non-photochemical quenching mechanism that occurs in higher plants.
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Affiliation(s)
- Inga Elvers
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany
| | - Tu C Nguyen-Phan
- School of Infection and Immunity, Glasgow University, Glasgow G12 8TA, U.K
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
| | - Richard J Cogdell
- School of Molecular Biosciences, Glasgow University, Glasgow G12 8QQ, U.K
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany.,Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany.,Bavarian Polymer Institute, University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany
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11
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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12
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Mao R, Wang X, Gao J. Bridging Carotenoid-to-Bacteriochlorophyll Energy Transfer of Purple Bacteria LH2 With Temperature Variations: Insights From Conformational Changes. Front Chem 2021; 9:764107. [PMID: 34671594 PMCID: PMC8521103 DOI: 10.3389/fchem.2021.764107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Photosynthesis is a key process for converting light energy into chemical energy and providing food for lives on Earth. Understanding the mechanism for the energy transfers could provide insights into regulating energy transfers in photosynthesis and designing artificial photosynthesis systems. Many efforts have been devoted to exploring the mechanism of temperature variations affecting the excitonic properties of LH2. In this study, we performed all-atom molecular dynamics (MD) simulations and quantum mechanics calculations for LH2 complex from purple bacteria along with its membrane environment under three typical temperatures: 270, 300, and 330 K. The structural analysis from validated MD simulations showed that the higher temperature impaired interactions at N-terminus of both α and β polypeptide helices and led to the dissociation of this hetero polypeptide dimer. Rhodopin-β-D-glucosides (RG1) moved centripetally with α polypeptide helices when temperature increased and enlarged their distances with bacteriochlorophylls molecules that have the absorption peak at 850 nm (B850), which resulted in reducing the coupling strengths between RG1 and B850 molecules. The present study reported a cascading mechanism for temperature regulating the energy transfers in LH2 of purple bacteria.
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Affiliation(s)
- Ruichao Mao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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13
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Fujimoto KJ, Minoda T, Yanai T. Spectral Tuning Mechanism of Photosynthetic Light-Harvesting Complex II Revealed by Ab Initio Dimer Exciton Model. J Phys Chem B 2021; 125:10459-10470. [PMID: 34521196 DOI: 10.1021/acs.jpcb.1c04457] [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
Excited states of two kinds of bacteriochlorophyll (BChl) aggregates, B850 and B800, in photosynthetic light-harvesting complex II (LH2) are theoretically investigated by developing and using an extended exciton model considering efficiently evaluated excitonic coupling. Our exciton model based on dimer fragmentation is shown to reproduce the experimental absorption spectrum of LH2 with good accuracy, entailing their different redshifts originating from aggregations of B850 and B800. The systematic analysis has been performed on the spectra by quantitatively decomposing their spectral shift energies into the contributions of various effects: structural distortion, electrostatic, excitonic coupling, and charge-transfer (CT) effects. Our results show that the spectral redshift of B800 is mainly attributed to its electrostatic interaction with the protein environment, while that of B850 arises from the marked effect of the excitonic coupling between BChl units. The interchromophore CT excitation also plays a key role in the spectral redshift of B850. This CT effect can be effectively described using our dimer model. This suited characterization reveals that the pronounced CT effect originates from the characteristics of B850 that has closely spaced BChls as dimers. We highlight the importance of the refinement of the crystal structure with the use of quantum chemical methods for prediction of the spectrum.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Takumi Minoda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
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14
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15
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Lokstein H, Renger G, Götze JP. Photosynthetic Light-Harvesting (Antenna) Complexes-Structures and Functions. Molecules 2021; 26:molecules26113378. [PMID: 34204994 PMCID: PMC8199901 DOI: 10.3390/molecules26113378] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Chlorophylls and bacteriochlorophylls, together with carotenoids, serve, noncovalently bound to specific apoproteins, as principal light-harvesting and energy-transforming pigments in photosynthetic organisms. In recent years, enormous progress has been achieved in the elucidation of structures and functions of light-harvesting (antenna) complexes, photosynthetic reaction centers and even entire photosystems. It is becoming increasingly clear that light-harvesting complexes not only serve to enlarge the absorption cross sections of the respective reaction centers but are vitally important in short- and long-term adaptation of the photosynthetic apparatus and regulation of the energy-transforming processes in response to external and internal conditions. Thus, the wide variety of structural diversity in photosynthetic antenna “designs” becomes conceivable. It is, however, common for LHCs to form trimeric (or multiples thereof) structures. We propose a simple, tentative explanation of the trimer issue, based on the 2D world created by photosynthetic membrane systems.
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Affiliation(s)
- Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 12116 Prague, Czech Republic
- Correspondence:
| | - Gernot Renger
- Max-Volmer-Laboratorium, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Jan P. Götze
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany;
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16
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Coccia E, Fregoni J, Guido CA, Marsili M, Pipolo S, Corni S. Hybrid theoretical models for molecular nanoplasmonics. J Chem Phys 2020; 153:200901. [PMID: 33261492 DOI: 10.1063/5.0027935] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The multidisciplinary nature of the research in molecular nanoplasmonics, i.e., the use of plasmonic nanostructures to enhance, control, or suppress properties of molecules interacting with light, led to contributions from different theory communities over the years, with the aim of understanding, interpreting, and predicting the physical and chemical phenomena occurring at molecular- and nano-scale in the presence of light. Multiscale hybrid techniques, using a different level of description for the molecule and the plasmonic nanosystems, permit a reliable representation of the atomistic details and of collective features, such as plasmons, in such complex systems. Here, we focus on a selected set of topics of current interest in molecular plasmonics (control of electronic excitations in light-harvesting systems, polaritonic chemistry, hot-carrier generation, and plasmon-enhanced catalysis). We discuss how their description may benefit from a hybrid modeling approach and what are the main challenges for the application of such models. In doing so, we also provide an introduction to such models and to the selected topics, as well as general discussions on their theoretical descriptions.
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Affiliation(s)
- E Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universit di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - J Fregoni
- Dipartimento di Scienze Fisiche, Informatiche e Matematiche, Universit di Modena e Reggio Emilia, via Campi 213/A, 41125 Modena, Italy
| | - C A Guido
- Dipartimento di Scienze Chimiche, Universit di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - M Marsili
- Dipartimento di Scienze Chimiche, Universit di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - S Pipolo
- Université de Lille, CNRS, Centrale Lille, ENSCL, Université d'Artois UMR 8181-UCCS Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - S Corni
- Istituto Nanoscienze-CNR, via Campi 213/A, 41125 Modena, Italy
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17
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Kehrer J, Richter R, Foerster JM, Schelter I, Kümmel S. Self-interaction correction, electrostatic, and structural influences on time-dependent density functional theory excitations of bacteriochlorophylls from the light-harvesting complex 2. J Chem Phys 2020; 153:144114. [PMID: 33086803 DOI: 10.1063/5.0014938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
First-principles calculations offer the chance to obtain a microscopic understanding of light-harvesting processes. Time-dependent density functional theory can have the computational efficiency to allow for such calculations. However, the (semi-)local exchange-correlation approximations that are computationally most efficient fail to describe charge-transfer excitations reliably. We here investigate whether the inexpensive average density self-interaction correction (ADSIC) remedies the problem. For the systems that we study, ADSIC is even more prone to the charge-transfer problem than the local density approximation. We further explore the recently reported finding that the electrostatic potential associated with the chromophores' protein environment in the light-harvesting complex 2 beneficially shifts spurious excitations. We find a great sensitivity on the chromophores' atomistic structure in this problem. Geometries obtained from classical molecular dynamics are more strongly affected by the spurious charge-transfer problem than the ones obtained from crystallography or density functional theory. For crystal structure geometries and density-functional theory optimized ones, our calculations confirm that the electrostatic potential shifts the spurious excitations out of the energetic range that is most relevant for electronic coupling.
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Affiliation(s)
- Juliana Kehrer
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Rian Richter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | | | - Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
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18
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Cupellini L, Lipparini F, Cao J. Absorption and Circular Dichroism Spectra of Molecular Aggregates With the Full Cumulant Expansion. J Phys Chem B 2020; 124:8610-8617. [PMID: 32901476 PMCID: PMC7901647 DOI: 10.1021/acs.jpcb.0c05180] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic
techniques such as linear absorption and circular dichroism. To compare calculated
Hamiltonians to experiments, a lineshape theory is needed, which takes into account the
coupling of the excitons with inter- and intramolecular vibrations. This coupling is
normally introduced in a perturbative way through the cumulant expansion formalism and
further approximated by assuming a Markovian exciton dynamics, for example with the
modified Redfield theory. Here, we present the implementation of the full cumulant
expansion (FCE) formalism (J. Chem.
Phys.142, 2015, 09410625747060) to
efficiently compute absorption and circular dichroism spectra of molecular aggregates
beyond the Markov approximation, without restrictions on the form of
exciton–phonon coupling. By employing the LH2 system of purple bacteria as a
challenging test case, we compare the FCE lineshapes with the Markovian lineshapes
obtained with the modified Redfield theory, showing that the latter presents a less
satisfying agreement with experiments. The FCE approach instead accurately describes the
lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the
FCE approach will become a valuable tool for accurately comparing model exciton
Hamiltonians with optical spectroscopy experiments.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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19
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Bondarenko AS, Patmanidis I, Alessandri R, Souza PCT, Jansen TLC, de Vries AH, Marrink SJ, Knoester J. Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chem Sci 2020; 11:11514-11524. [PMID: 34094396 PMCID: PMC8162738 DOI: 10.1039/d0sc03110k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Supramolecular aggregates of synthetic dye molecules offer great perspectives to prepare biomimetic functional materials for light-harvesting and energy transport. The design is complicated by the fact that structure–property relationships are hard to establish, because the molecular packing results from a delicate balance of interactions and the excitonic properties that dictate the optics and excited state dynamics, in turn sensitively depend on this packing. Here we show how an iterative multiscale approach combining molecular dynamics and quantum mechanical exciton modeling can be used to obtain accurate insight into the packing of thousands of cyanine dye molecules in a complex double-walled tubular aggregate in close interaction with its solvent environment. Our approach allows us to answer open questions not only on the structure of these prototypical aggregates, but also about their molecular-scale structural and energetic heterogeneity, as well as on the microscopic origin of their photophysical properties. This opens the route to accurate predictions of energy transport and other functional properties. Multiscale modeling resolves the molecular structure of a synthetic light-harvesting complex, unraveling the microscopic origin of its photophysical properties.![]()
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Affiliation(s)
- Anna S Bondarenko
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands
| | - Ilias Patmanidis
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Riccardo Alessandri
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Paulo C T Souza
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands
| | - Alex H de Vries
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Siewert J Marrink
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Jasper Knoester
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands
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20
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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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21
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Gardiner AT, Nguyen-Phan TC, Cogdell RJ. A comparative look at structural variation among RC-LH1 'Core' complexes present in anoxygenic phototrophic bacteria. PHOTOSYNTHESIS RESEARCH 2020; 145:83-96. [PMID: 32430765 PMCID: PMC7423801 DOI: 10.1007/s11120-020-00758-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/10/2020] [Indexed: 05/30/2023]
Abstract
All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.
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Affiliation(s)
- Alastair T Gardiner
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradska 237, 379 01, Třeboň, Czech Republic.
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Richard J Cogdell
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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22
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Li X, Buda F, de Groot HJM, Sevink GJA. Dynamic Disorder Drives Exciton Transfer in Tubular Chlorosomal Assemblies. J Phys Chem B 2020; 124:4026-4035. [PMID: 32343578 PMCID: PMC7246976 DOI: 10.1021/acs.jpcb.0c00441] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chlorosomes stand out for their highly efficient excitation energy transfer (EET) in extreme low light conditions. Yet, little is known about the EET when a chlorosome is excited to a pure state that is an eigenstate of the exciton Hamiltonian. In this work, we consider the dynamic disorder in the intermolecular electronic coupling explicitly by calculating the electronic coupling terms in the Hamiltonian using nuclear coordinates that are taken from molecular dynamics simulation trajectories. We show that this dynamic disorder is capable of driving the evolution of the exciton, being a stationary state of the initial Hamiltonian. In particular, long-distance excitation energy transfer between domains of high exciton population and oscillatory behavior of the population in the site basis are observed, in line with two-dimensional electronic spectroscopy studies. We also found that in the high exciton population domains, their population variation is correlated with their overall coupling strength. Analysis in a reference state basis shows that such dynamic disorder, originating from thermal energy, creates a fluctuating landscape for the exciton and promotes the EET process. We propose such dynamic disorder as an important microscopic origin for the high efficient EET widely observed in different types of chlorosomes, bioinspired tubular aggregates, or other light-harvesting complexes.
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Affiliation(s)
- Xinmeng Li
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Francesco Buda
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Huub J M de Groot
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - G J Agur Sevink
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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23
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Liguori N, Croce R, Marrink SJ, Thallmair S. Molecular dynamics simulations in photosynthesis. PHOTOSYNTHESIS RESEARCH 2020; 144:273-295. [PMID: 32297102 PMCID: PMC7203591 DOI: 10.1007/s11120-020-00741-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
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Affiliation(s)
- Nicoletta Liguori
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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24
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Bold BM, Sokolov M, Maity S, Wanko M, Dohmen PM, Kranz JJ, Kleinekathöfer U, Höfener S, Elstner M. Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes. Phys Chem Chem Phys 2020; 22:10500-10518. [PMID: 31950960 DOI: 10.1039/c9cp05753f] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.
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Affiliation(s)
- Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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25
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Cardoso Ramos F, Nottoli M, Cupellini L, Mennucci B. The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling. Chem Sci 2019; 10:9650-9662. [PMID: 32055335 PMCID: PMC6988754 DOI: 10.1039/c9sc02886b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022] Open
Abstract
The light-harvesting in photosynthetic purple bacteria can be tuned in response to the light conditions during cell growth. One of the used strategies is to change the energy of the excitons in the major fight-harvesting complex, commonly known as LH2. In the present study we report the first systematic investigation of the microscopic origin of the exciton tuning using three complexes, namely the common (high-light) and the low-light forms of LH2 from Rps. acidophila plus a third complex analogous to the PucD complex from Rps. palustris. The study is based on the combination of classical molecular dynamics of each complex in a lipid membrane and excitonic calculations based on a multiscale quantum mechanics/molecular mechanics approach including a polarizable embedding. From the comparative analysis, it comes out that the mechanisms that govern the adaptation of the complex to different light conditions use the different H-bonding environment around the bacteriochlorophyll pigments to dynamically control both internal and inter-pigment degrees of freedom. While the former have a large effect on the site energies, the latter significantly change the electronic couplings, but only the combination of the two effects can fully reproduce the tuning of the final excitons and explain the observed spectroscopic differences.
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Affiliation(s)
- Felipe Cardoso Ramos
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
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26
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Schelter I, Foerster JM, Gardiner AT, Roszak AW, Cogdell RJ, Ullmann GM, de Queiroz TB, Kümmel S. Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2. J Chem Phys 2019; 151:134114. [DOI: 10.1063/1.5116779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, Bayreuth, Germany
| | - Johannes M. Foerster
- Theoretical Physics IV and Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
| | | | - Aleksander W. Roszak
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, Bayreuth, Germany
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27
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Cupellini L, Bondanza M, Nottoli M, Mennucci B. Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148049. [PMID: 31386831 DOI: 10.1016/j.bbabio.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
Abstract
Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy.
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29
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Sáez-Blázquez R, Feist J, Romero E, Fernández-Domínguez AI, García-Vidal FJ. Cavity-Modified Exciton Dynamics in Photosynthetic Units. J Phys Chem Lett 2019; 10:4252-4258. [PMID: 31291109 PMCID: PMC6907886 DOI: 10.1021/acs.jpclett.9b01495] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 06/09/2023]
Abstract
Recently, exciton-photon strong coupling has been proposed as a means to control and enhance energy transfer in ensembles of organic molecules. Here, we demonstrate that the exciton dynamics in an archetypal purple bacterial photosynthetic unit, composed of six LH2 antennas surrounding a single LH1 complex, is greatly modified by its interaction with an optical cavity. We develop a Bloch-Redfield master equation approach that accounts for the interplay between the B800 and B850 bacteriochlorophyll molecules within each LH2 antenna, as well as their interactions with the central LH1 complex. Using a realistic parametrization of both the photosynthetic unit and optical cavity, we investigate the formation of polaritons in the system, revealing that these can be tuned to accelerate its exciton dynamics by 3 orders of magnitude. This yields a significant occupation of the LH1 complex, the stage immediately prior to the reaction center, with only a few-femtosecond delay after the initial excitation of the LH2 B800 pigments. Our theoretical findings unveil polaritonic phenomena as a promising route for the characterization, tailoring, and optimization of light-harvesting mechanisms in natural and artificial photosynthetic processes.
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Affiliation(s)
- Rocío Sáez-Blázquez
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Johannes Feist
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Elisabet Romero
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science
and Technology (BIST), E-43007 Tarragona, Spain
| | - Antonio I. Fernández-Domínguez
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Francisco J. García-Vidal
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
- Donostia
International Physics Center (DIPC), E-20018 Donostia−San Sebastián, Spain
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30
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Anda A, Hansen T, De Vico L. Qy and Qx Absorption Bands for Bacteriochlorophyll a Molecules from LH2 and LH3. J Phys Chem A 2019; 123:5283-5292. [DOI: 10.1021/acs.jpca.9b02877] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- André Anda
- Chemical and Quantum Physics, School of Science, RMIT University, Melbourne, VIC 3001, Australia
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Thorsten Hansen
- Department of Chemistry, Copenhagen University, Universitetsparken 5, DK-2100, Copenhagen Ø, Denmark
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100, Siena, Italy
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32
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Campetella M, Perfetto A, Ciofini I. Quantifying partial hole-particle distance at the excited state: A revised version of the DCT index. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.10.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Cupellini L, Caprasecca S, Guido CA, Müh F, Renger T, Mennucci B. Coupling to Charge Transfer States is the Key to Modulate the Optical Bands for Efficient Light Harvesting in Purple Bacteria. J Phys Chem Lett 2018; 9:6892-6899. [PMID: 30449098 DOI: 10.1021/acs.jpclett.8b03233] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The photosynthetic apparatus of purple bacteria uses exciton delocalization and static disorder to modulate the position and broadening of its absorption bands, leading to efficient light harvesting. Its main antenna complex, LH2, contains two rings of identical bacteriochlorophyll pigments, B800 and B850, absorbing at 800 and 850 nm, respectively. It has been an unsolved problem why static disorder of the strongly coupled B850 ring is several times larger than that of the B800 ring. Here we show that mixing between excitons and charge transfer states in the B850 ring is responsible for the effect. The linear absorption spectrum of the LH2 system is simulated by using a multiscale approach with an exciton Hamiltonian generalized to include the charge transfer states that involve adjacent pigment pairs, with static disorder modeled microscopically by molecular dynamics simulations. Our results show that sufficient inhomogeneous broadening of the B850 band, needed for efficient light harvesting, is only obtained by utilizing static disorder in the coupling between local excited and interpigment charge transfer states.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale , University of Pisa , via G. Moruzzi 13 , 56124 Pisa , Italy
| | - Stefano Caprasecca
- Dipartimento di Chimica e Chimica Industriale , University of Pisa , via G. Moruzzi 13 , 56124 Pisa , Italy
| | - Ciro A Guido
- Dipartimento di Chimica e Chimica Industriale , University of Pisa , via G. Moruzzi 13 , 56124 Pisa , Italy
| | - Frank Müh
- Institute of Theoretical Physics, Department of Theoretical Biophysics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
| | - Thomas Renger
- Institute of Theoretical Physics, Department of Theoretical Biophysics , Johannes Kepler University Linz , Altenberger Strasse 69 , 4040 Linz , Austria
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , University of Pisa , via G. Moruzzi 13 , 56124 Pisa , Italy
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Mallus MI, Shakya Y, Prajapati JD, Kleinekathöfer U. Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Cupellini L, Corbella M, Mennucci B, Curutchet C. Electronic energy transfer in biomacromolecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1392] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale University of Pisa Pisa Italy
| | - Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC‐UB), Facultat de Farmàcia i Ciències de l'Alimentació Universitat de Barcelona Barcelona Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale University of Pisa Pisa Italy
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC‐UB), Facultat de Farmàcia i Ciències de l'Alimentació Universitat de Barcelona Barcelona Spain
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Bouvier R, Durand R, Favereau L, Srebro‐Hooper M, Dorcet V, Roisnel T, Vanthuyne N, Vesga Y, Donnelly J, Hernandez F, Autschbach J, Trolez Y, Crassous J. Helicenes Grafted with 1,1,4,4‐Tetracyanobutadiene Moieties: π‐Helical Push–Pull Systems with Strong Electronic Circular Dichroism and Two‐Photon Absorption. Chemistry 2018; 24:14484-14494. [DOI: 10.1002/chem.201802763] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Romain Bouvier
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
| | - Raphaël Durand
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
| | - Ludovic Favereau
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
| | - Monika Srebro‐Hooper
- Faculty of Chemistry Jagiellonian University Gronostajowa 2 30-387 Krakow Poland
| | - Vincent Dorcet
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
| | - Thierry Roisnel
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
| | - Nicolas Vanthuyne
- Aix Marseille Université CNRS Centrale Marseille, iSm2 13007 Marseille France
| | - Yuly Vesga
- Department of Chemistry, The College of Optics and Photonics, CREOL University of Central Florida Orlando FL 32816-2366 USA
| | - Julie Donnelly
- Department of Chemistry, The College of Optics and Photonics, CREOL University of Central Florida Orlando FL 32816-2366 USA
| | - Florencio Hernandez
- Department of Chemistry, The College of Optics and Photonics, CREOL University of Central Florida Orlando FL 32816-2366 USA
| | - Jochen Autschbach
- Department of Chemistry University at Buffalo State University of New York Buffalo NY 14260 USA
| | - Yann Trolez
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
| | - Jeanne Crassous
- Université Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS, ISCR–UMR6226 35000 Rennes France
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37
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Caprasecca S, Corni S, Mennucci B. Shaping excitons in light-harvesting proteins through nanoplasmonics. Chem Sci 2018; 9:6219-6227. [PMID: 30090309 PMCID: PMC6062888 DOI: 10.1039/c8sc01162a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/18/2018] [Indexed: 01/01/2023] Open
Abstract
Nanoplasmonics has been used to enhance molecular spectroscopic signals, with exquisite spatial resolution down to the sub-molecular scale. By means of a rigorous, state-of-the-art multiscale model based on a quantum chemical description, here we show that optimally tuned tip-shaped metal nanoparticles can selectively excite localized regions of typically coherent systems, eventually narrowing down to probing one single pigment. The well-known major light-harvesting complex LH2 of purple bacteria has been investigated because of its unique properties, as it presents both high and weak delocalization among subclusters of pigments. This finding opens the way to the direct spectroscopic investigation of quantum-based processes, such as the quantum diffusion of the excitation among the chromophores, and their external manipulation.
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Affiliation(s)
- Stefano Caprasecca
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , I-56124 Pisa , Italy . ;
| | - Stefano Corni
- Dipartimento di Scienze Chimiche , Università di Padova , I-35131 Padova , Italy .
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , I-56124 Pisa , Italy . ;
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Nottoli M, Jurinovich S, Cupellini L, Gardiner AT, Cogdell R, Mennucci B. The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria. PHOTOSYNTHESIS RESEARCH 2018; 137:215-226. [PMID: 29502240 DOI: 10.1007/s11120-018-0492-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/23/2018] [Indexed: 05/21/2023]
Abstract
The LH2 antenna complexes of purple bacteria occur, depending on light conditions, in various different spectroscopic forms, with a similar structure but different absorption spectra. The differences are related to point changes in the primary amino acid sequence, but the molecular-level relationship between these changes and the resulting spectrum is still not well understood. We undertook a systematic quantum chemical analysis of all the main factors that contribute to the exciton structure, looking at how the environment modulates site energies and couplings in the B800-850 and B800-820 spectroscopic forms of LH2. A multiscale approach combining quantum chemistry and an atomistic classical embedding has been used where mutual polarization effects between the two parts are taken into account. We find that the loss of hydrogen bonds following amino acid changes can only explain a part of the observed blue-shift in the B850 band. The coupling of excitonic states to charge-transfer states, which is different in the two forms, contributes with a similar amount to the overall blue-shift.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Alastair T Gardiner
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow, G12 8TA, Scotland, UK
| | - Richard Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow, G12 8TA, Scotland, UK
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy.
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39
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Wang Y, Ke Y, Zhao Y. The hierarchical and perturbative forms of stochastic Schrödinger equations and their applications to carrier dynamics in organic materials. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yu‐Chen Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
| | - Yaling Ke
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
| | - Yi Zhao
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University Xiamen China
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40
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Campetella M, Mariani A, Sadun C, Wu B, Castner EW, Gontrani L. Structure and dynamics of propylammonium nitrate-acetonitrile mixtures: An intricate multi-scale system probed with experimental and theoretical techniques. J Chem Phys 2018; 148:134507. [PMID: 29626911 DOI: 10.1063/1.5021868] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this article, we report the study of structural and dynamical properties for a series of acetonitrile/propylammonium nitrate mixtures as a function of their composition. These systems display an unusual increase in intensity in their X-ray diffraction patterns in the low-q regime, and their 1H-NMR diffusion-ordered NMR spectroscopy (DOSY) spectra display unusual diffusivities. However, the magnitude of both phenomena for mixtures of propylammonium nitrate is smaller than those observed for ethylammonium nitrate mixtures with the same cosolvent, suggesting that the cation alkyl tail plays an important role in these observations. The experimental X-ray scattering data are compared with the results of molecular dynamics simulations, including both ab initio studies used to interpret short-range interactions and classical simulations to describe longer range interactions. The higher level calculations highlight the presence of a strong hydrogen bond network within the ionic liquid, only slightly perturbed even at high acetonitrile concentration. These strong interactions lead to the symmetry breaking of the NO3- vibrations, with a splitting of about 88 cm-1 in the ν3 antisymmetric stretch. The classical force field simulations use a greater number of ion pairs, but are not capable of fully describing the longest range interactions, although they do successfully account for the observed concentration trend, and the analysis of the models confirms the nano-inhomogeneity of these kinds of samples.
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Affiliation(s)
- Marco Campetella
- Institut de Recherche de Chimie Paris, CNRS, PSL Research University, Chimie ParisTech, F-75005 Paris, France
| | - Alessandro Mariani
- Beamline ID02, ESRF-European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Claudia Sadun
- Università degli Studi di Roma "La Sapienza," P. le Aldo Moro 5, I-00185 Roma, Italy
| | - Boning Wu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
| | - Edward W Castner
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
| | - Lorenzo Gontrani
- Università degli Studi di Roma "La Sapienza," P. le Aldo Moro 5, I-00185 Roma, Italy
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41
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Caprasecca S, Cupellini L, Jurinovich S, Loco D, Lipparini F, Mennucci B. A polarizable QM/MM description of environment effects on NMR shieldings: from solvated molecules to pigment–protein complexes. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2264-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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42
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Montemayor D, Rivera E, Jang SJ. Computational Modeling of Exciton-Bath Hamiltonians for Light Harvesting 2 and Light Harvesting 3 Complexes of Purple Photosynthetic Bacteria at Room Temperature. J Phys Chem B 2018. [PMID: 29533664 DOI: 10.1021/acs.jpcb.8b00358] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light harvesting 2 (LH2) complex is the primary component of the photosynthetic unit of purple bacteria that is responsible for harvesting and relaying excitons. The electronic absorption line shape of LH2 contains two major bands at 800 and 850 nm wavelength regions. Under low light conditions, some species of purple bacteria replace LH2 with light harvesting 3 (LH3), a variant form with almost the same structure as the former but with distinctively different spectral features. The major difference between the absorption line shapes of LH2 and LH3 is the shift of the 850 nm band of the former to a new 820 nm region. The microscopic origin of this difference has been the subject of some theoretical/computational investigations. However, the genuine molecular level source of such a difference is not clearly understood yet. This work reports a comprehensive computational study of LH2 and LH3 complexes so as to clarify different molecular level features of LH2 and LH3 complexes and to construct simple exciton-bath models with a common form. All-atomistic molecular dynamics simulations of both LH2 and LH3 complexes provide detailed molecular level structural differences of bacteriochlorophylls (BChls) in the two complexes, in particular, in their patterns of hydrogen bonding (HB) and torsional angles of the acetyl group. Time-dependent density functional theory calculation of the excitation energies of BChls for structures sampled from the MD simulations suggests that the observed differences in the HB and torsional angles cannot fully account for the experimentally observed spectral shift of LH3. Potential sources that can explain the actual spectral shift of LH3 are discussed, and their magnitudes are assessed through fitting of experimental line shapes. These results demonstrate the feasibility of developing simple exciton-bath models for both LH2 and LH3, which can be employed for large-scale exciton quantum dynamics in their aggregates.
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Affiliation(s)
- Daniel Montemayor
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Eva Rivera
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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43
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Fujita T, Mochizuki Y. Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems. J Phys Chem A 2018; 122:3886-3898. [DOI: 10.1021/acs.jpca.8b00446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute for Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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44
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Ianeselli A, Orioli S, Spagnolli G, Faccioli P, Cupellini L, Jurinovich S, Mennucci B. Atomic Detail of Protein Folding Revealed by an Ab Initio Reappraisal of Circular Dichroism. J Am Chem Soc 2018; 140:3674-3682. [DOI: 10.1021/jacs.7b12399] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alan Ianeselli
- Centre for Integrative Biology, Trento University, Via Sommarive 9, 38128 Povo, Trento, Italy
| | - Simone Orioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Giovanni Spagnolli
- Centre for Integrative Biology, Trento University, Via Sommarive 9, 38128 Povo, Trento, Italy
| | - Pietro Faccioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
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45
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Kim CW, Choi B, Rhee YM. Excited state energy fluctuations in the Fenna-Matthews-Olson complex from molecular dynamics simulations with interpolated chromophore potentials. Phys Chem Chem Phys 2018; 20:3310-3319. [PMID: 29186231 DOI: 10.1039/c7cp06303b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We analyze the environment-induced fluctuation of pigment excitation energies in the Fenna-Matthews-Olson (FMO) complex from various perspectives, by employing an interpolation-based all-atom potential energy model for describing realistic pigment vibrations. We conduct molecular dynamics simulations on a 100 ns timescale, which is an extent that can enclose the effect of static disorder, and demonstrate its timescale separation from fast dynamic disorder. We extract the spectral densities of the complex by considering both the site and the exciton bases. We show that exciton delocalization reduces the effective environmental fluctuation and rationalize this aspect based on a model of fluctuating molecular aggregates. We also obtained the spectral density of the lowest exciton state under low temperature conditions and show that it reasonably well reproduces the experimental result. Finally, by additionally performing non-equilibrium excited state trajectory simulations, we show that the system lies well within the linear response regime after photo-absorption and that the pigments do not visit anharmonic regions of the potential surface to a significant extent. This indicates that methodologies based on harmonic bath models are indeed reasonable approaches for describing the excited state dynamics of the FMO complex.
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Affiliation(s)
- Chang Woo Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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46
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Rätsep M, Muru R, Freiberg A. High temperature limit of photosynthetic excitons. Nat Commun 2018; 9:99. [PMID: 29311621 PMCID: PMC5758513 DOI: 10.1038/s41467-017-02544-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/06/2017] [Indexed: 11/24/2022] Open
Abstract
Excitons in light-harvesting complexes are known to significantly improve solar-energy harnessing. Here we demonstrate photosynthetic excitons at super-physiological temperatures reaching 60–80 °C in different species of mesophilic photosynthetic bacteria. It is shown that the survival of light-harvesting excitons in the peripheral LH2 antennae is restricted by thermal decomposition of the pigment–protein complex rather than by any intrinsic property of excitons. The regular spatial organization of the bacteriochlorophyll a pigments supporting excitons in this complex is lost upon the temperature-induced breakdown of its tertiary structure. Secondary structures of the complexes survive even higher temperatures. The discovered pivotal role of the protein scaffold in the stabilization of excitons comprises an important aspect of structure–function relationship in biology. These results also intimately entangle the fundamental issues of quantum mechanical concepts in biology and in the folding of proteins. Excitons in light-harvesting complexes are known to significantly improve solar energy harnessing. Here, the authors investigate and explain extreme robustness against temperature of excitons in purple photosynthetic bacteria.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411, Tartu, Estonia
| | - Renata Muru
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, W. Ostwald Str. 1, 50411, Tartu, Estonia. .,Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
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47
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Dachev M, Bína D, Sobotka R, Moravcová L, Gardian Z, Kaftan D, Šlouf V, Fuciman M, Polívka T, Koblížek M. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica. PLoS Biol 2017; 15:e2003943. [PMID: 29253871 PMCID: PMC5749889 DOI: 10.1371/journal.pbio.2003943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/02/2018] [Accepted: 11/22/2017] [Indexed: 11/29/2022] Open
Abstract
The majority of life on Earth depends directly or indirectly on the sun as a source of energy. The initial step of photosynthesis is facilitated by light-harvesting complexes, which capture and transfer light energy into the reaction centers (RCs). Here, we analyzed the organization of photosynthetic (PS) complexes in the bacterium G. phototrophica, which so far is the only phototrophic representative of the bacterial phylum Gemmatimonadetes. The isolated complex has a molecular weight of about 800 ± 100 kDa, which is approximately 2 times larger than the core complex of Rhodospirillum rubrum. The complex contains 62.4 ± 4.7 bacteriochlorophyll (BChl) a molecules absorbing in 2 distinct infrared absorption bands with maxima at 816 and 868 nm. Using femtosecond transient absorption spectroscopy, we determined the energy transfer time between these spectral bands as 2 ps. Single particle analyses of the purified complexes showed that they were circular structures with an outer diameter of approximately 18 nm and a thickness of 7 nm. Based on the obtained, we propose that the light-harvesting complexes in G. phototrophica form 2 concentric rings surrounding the type 2 RC. The inner ring (corresponding to the B868 absorption band) is composed of 15 subunits and is analogous to the inner light-harvesting complex 1 (LH1) in purple bacteria. The outer ring is composed of 15 more distant BChl dimers with no or slow energy transfer between them, resulting in the B816 absorption band. This completely unique and elegant organization offers good structural stability, as well as high efficiency of light harvesting. Our results reveal that while the PS apparatus of Gemmatimonadetes was acquired via horizontal gene transfer from purple bacteria, it later evolved along its own pathway, devising a new arrangement of its light harvesting complexes. The majority of life on Earth depends directly or indirectly on the sun as a source of energy. Phototrophic organisms use energy from light to power various cellular and metabolic processes. The initial step of photosynthesis is facilitated by light-harvesting complexes, which capture and transfer light energy into the reaction centers where it is used to power proton gradients or to form new chemical bonds. Here, we analyzed photosynthetic complexes in Gemmatimonas phototrophica, the only known phototrophic representative of the bacterial phylum Gemmatimonadetes. Using a combination of biochemical and spectroscopic techniques, we show that the light-harvesting complexes of G. phototrophica are organized in 2 concentric rings around the reaction center. This organization is unique among anoxygenic phototrophs. It offers both structural stability and high efficiency of light harvesting. The structural unit of both antenna rings is a dimer of photosynthetic pigments called bacteriochlorophyll. The inner ring is populated by more densely packed dimers, while the outer ring contains more distant dimers with a minimal excitation exchange. Such an arrangement modifies the spectral properties of bacteriochlorophylls in the complex and ensures efficient capture of light in the near-infrared part of the solar spectrum.
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Affiliation(s)
- Marko Dachev
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Roman Sobotka
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Lenka Moravcová
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - David Kaftan
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Václav Šlouf
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Marcel Fuciman
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Polívka
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
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48
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Jurinovich S, Cupellini L, Guido CA, Mennucci B. EXAT: EXcitonic analysis tool. J Comput Chem 2017; 39:279-286. [PMID: 29151259 DOI: 10.1002/jcc.25118] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 01/09/2023]
Abstract
We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Ciro A Guido
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Benedetta Mennucci
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
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Alberto ME, Adamo C. Synergistic Effects in Pt II -Porphyrinoid Dyes as Candidates for a Dual-Action Anticancer Therapy: A Theoretical Exploration. Chemistry 2017; 23:15124-15132. [PMID: 28846823 DOI: 10.1002/chem.201702876] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Indexed: 01/08/2023]
Abstract
The combination of a photosensitizer (PS) with a cisplatin-like unit represents a challenging strategy to increase the effectiveness of photodynamic therapy and to afford a dual-action anticancer treatment. Recently, new tetra-PtII -porphyrin conjugates have been proposed as promising multitarget agents. To reveal the effect of the PtII center on the chemical and physical properties of the PS and to explore the effect of the PS on the activation mechanism of PtII ligand before reaching its biological target, we carried out a first-principle investigation on these tetra-PtII -porphyrin conjugates. To propose a further advance in this novel field and to gain useful insights for the design of new, more efficient PtII -PS conjugates, we introduced structural modifications into the porphyrin dye, which involved the synthesis of the tetra-PtII -chlorin and tetra-PtII -bacteriochlorin derivatives. Results showed that the designed dyes better met the criteria to be successful in a dual-action therapy, as they displayed improved optical properties and reduced the hydrolysis rate of the PtII moiety, the latter being a desirable feature to avoid many side reactions of the conjugate during their transport to the biological target.
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Affiliation(s)
- Marta Erminia Alberto
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), 75005, Paris, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), 75005, Paris, France
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50
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Campetella M, Maschietto F, Frisch MJ, Scalmani G, Ciofini I, Adamo C. Charge transfer excitations in TDDFT: A ghost-hunter index. J Comput Chem 2017; 38:2151-2156. [DOI: 10.1002/jcc.24862] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Marco Campetella
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris; F-75005 Paris France
| | - Federica Maschietto
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris; F-75005 Paris France
| | - Mike J. Frisch
- Gaussian, Inc.; 340 Quinnipiac St., Bldg. 40, Wallingford Connecticut 06492
| | - Giovanni Scalmani
- Gaussian, Inc.; 340 Quinnipiac St., Bldg. 40, Wallingford Connecticut 06492
| | - Ilaria Ciofini
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris; F-75005 Paris France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris; F-75005 Paris France
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