1
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Majid A, Raza NZ, Haider S, Alam K, Naeem S. Electronic Transport Properties of Molecular Clusters Sb 4O 6, P 4Se 3, and P 4O 6. J Phys Chem A 2024; 128:4814-4822. [PMID: 38857364 DOI: 10.1021/acs.jpca.4c02757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Inorganic molecular crystal (IMC) is a trending class of materials in which structural units comprise molecular cages or clusters bonded via van der Waal forces. The structure-property relationship in IMCs is less known due to the unusual assembly of molecular clusters in these materials. In this paper, the density functional theory-calculated electronic transport properties of the molecular clusters of antimony oxide (Sb4O6), phosphorus triselenide (P4Se3), and phosphorus trioxide (P4O6) are described in detail. The calculated values of highest occupied molecular orbital-lowest unoccupied molecular orbital gaps appeared as 5.487, 2.296, and 4.425 eV for Sb4O6, P4Se3, and P4O6, respectively. The work was carried out to explore the charge transport mechanism in IMCs in order to disclose their potential in practical applications. The calculations involved charge-transfer integral based on Marcus theory to compute the electronic coupling (V), reorganization energies (λ), and hopping rate (k) in the structures. The hopping rate for Sb4O6, P4Se3, and P4O6 is found as 8.49 × 10-12, 1.28 × 10-14, and 2.51 × 10-20 s-1, respectively. The transport properties of Sb4O6 are found better, which predicts the application of the relevant IMC for device grade applications. The findings of this study are important for future application of the IMCs in electronic and optoelectronic applications.
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Affiliation(s)
- Abdul Majid
- Department of Physics, University of Gujrat, Gujrat 50700, Pakistan
| | - Nimra Zaib Raza
- Department of Physics, University of Gujrat, Gujrat 50700, Pakistan
| | - Sajjad Haider
- Chemical Engineering Department, College of Engineering, King Saud University, P.O.Box 800, Riyadh 11421, Saudi Arabia
| | - Kamran Alam
- Department of Chemical Engineering Materials Environment Sapienza, University of Rome, Roma RM 00185, Italy
| | - Samia Naeem
- Department of Physics, Government College Women University Sialkot, Sialkot 51310, Pakistan
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2
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Fujimoto KJ, Seki T, Minoda T, Yanai T. Spectral Tuning and Excitation-Energy Transfer by Unique Carotenoids in Diatom Light-Harvesting Antenna. J Am Chem Soc 2024; 146:3984-3991. [PMID: 38236721 PMCID: PMC10870758 DOI: 10.1021/jacs.3c12045] [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: 10/28/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 02/15/2024]
Abstract
The light-harvesting antennae of diatoms and spinach are composed of similar chromophores; however, they exhibit different absorption wavelengths. Recent advances in cryoelectron microscopy have revealed that the diatom light-harvesting antenna fucoxanthin chlorophyll a/c-binding protein (FCPII) forms a tetramer and differs from the spinach antenna in terms of the number of protomers; however, the detailed molecular mechanism remains elusive. Herein, we report the physicochemical factors contributing to the characteristic light absorption of the diatom light-harvesting antenna based on spectral calculations using an exciton model. Spectral analysis reveals the significant contribution of unique fucoxanthin molecules (fucoxanthin-S) in FCPII to the diatom-specific spectrum, and further analysis determines their essential role in excitation-energy transfer to chlorophyll. It was revealed that the specificity of these fucoxanthin-S molecules is caused by the proximity between protomers associated with the tetramerization of FCPII. The findings of this study demonstrate that diatoms employ fucoxanthin-S to harvest energy under the ocean in the absence of long-wavelength sunlight and can provide significant information about the survival strategies of photosynthetic organisms to adjust to their living environment.
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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
| | - Takuya Seki
- 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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3
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Einsele R, Hoche J, Mitrić R. Long-range corrected fragment molecular orbital density functional tight-binding method for excited states in large molecular systems. J Chem Phys 2023; 158:044121. [PMID: 36725509 DOI: 10.1063/5.0136844] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the long-range corrected tight-binding density functional fragment molecular orbital method (FMO-LC-DFTB) with an excitonic Hamiltonian, which is constructed in the basis of locally excited and charge-transfer configuration state functions calculated for embedded monomers and dimers and accounts explicitly for the electronic coupling between all types of excitons. We first evaluate both the accuracy and efficiency of our fragmentation approach for molecular dimers and aggregates by comparing it with the full LC-TD-DFTB method. The comparison of the calculated spectra of an anthracene cluster shows a very good agreement between our method and the LC-TD-DFTB reference. The effective computational scaling of our method has been explored for anthracene clusters and for perylene bisimide aggregates. We demonstrate the applicability of our method by the calculation of the excited state properties of pentacene crystal models consisting of up to 319 molecules. Furthermore, the participation ratio of the monomer fragments to the excited states is analyzed by the calculation of natural transition orbital participation numbers, which are verified by the hole and particle density for a chosen pentacene cluster. The use of our FMO-LC-TDDFTB method will allow for future studies of excitonic dynamics and charge transport to be performed on complex molecular systems consisting of thousands of atoms.
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Affiliation(s)
- Richard Einsele
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
| | - Joscha Hoche
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Strasse 42, 97074 Würzburg, Germany
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4
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Chen WK, Fang WH, Cui G. Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems. J Chem Phys 2023; 158:044110. [PMID: 36725521 DOI: 10.1063/5.0129458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently, we developed a low-scaling Multi-Layer Energy-Based Fragment (MLEBF) method for accurate excited-state calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the many-body energy expansion theory, in combination with the inclusion-exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a two-layer MLEBF model, the photochemically active and inert layers are calculated with high-level and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two- or three-body interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground- and excited-state energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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5
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Fujimoto KJ, Miyashita T, Dewa T, Yanai T. Determination of FRET orientation factor between artificial fluorophore and photosynthetic light-harvesting 2 complex (LH2). Sci Rep 2022; 12:15091. [PMID: 36065053 PMCID: PMC9445053 DOI: 10.1038/s41598-022-19375-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
The orientation factor of fluorescence resonance energy transfer (FRET) between photosynthetic light-harvesting 2 complex (LH2) and artificial fluorophore (Alexa Fluor 647: A647) was theoretically investigated. The orientation factor of 2/3, i.e., the isotropic mean, is widely used to predict the donor–acceptor distance from FRET measurements. However, this approximation seems inappropriate because the movement of A647 is possibly restricted by the bifunctional linker binding to LH2. In this study, we performed molecular dynamics (MD) simulations and electronic coupling calculations on the LH2-A647 conjugate to analyze its orientation factor. The MD results showed that A647 keeps a position approximately 26 Å away from the bacteriochlorophyll (BChl) assembly in LH2. The effective orientation factor was extracted from the electronic coupling calculated using the transition charge from electrostatic potential (TrESP) method. With MD snapshots, an averaged orientation factor was predicted to be 1.55, significantly different from the isotropic mean value. The analysis also suggested that the value of the refractive index employed in the previous studies is not suitable for this system. Furthermore, optimal orientations of A647 with larger orientation factors to improve FRET efficiency were searched using Euler angles. The present approach is useful for extending the applicability of FRET analysis.
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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.
| | - Tomoya Miyashita
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Takehisa Dewa
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, 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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6
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Glebov IO, Poddubnyy VV, Khokhlov DV. Perturbative Expansion of Nonorthogonal Product Approach for Charge Transfer States. J Phys Chem A 2022; 126:5800-5813. [PMID: 35998639 DOI: 10.1021/acs.jpca.2c02612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modeling of the excited states of multichromophoric systems is crucial for the understanding of photosynthesis functioning. The excitonic Hamiltonian method is widely used for such calculations. Excited states of the combined system are constructed from the wave functions of individual chromophores while their interactions are described by excitonic couplings. In the current study, we enhance a previously proposed nonorthogonal product approach to incorporate dynamic correlation effects accounted for by the multireference perturbation theory. We discuss the problems of constructing the excitonic Hamiltonian including charge transfer states for the molecular systems where the overlap contribution to the excitonic couplings is non-negligible. The benchmark calculations were performed for a model system. It was shown that the overlap component of the excitonic coupling is of great importance. The enhanced method provides an accurate description of the excited state energies and other properties.
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Affiliation(s)
- Ilya O Glebov
- Chemistry Department, Moscow State University, Leninskie gory 1-3, Moscow 119991, Russia
| | - Vladimir V Poddubnyy
- Chemistry Department, Moscow State University, Leninskie gory 1-3, Moscow 119991, Russia
| | - Daniil V Khokhlov
- Chemistry Department, Moscow State University, Leninskie gory 1-3, Moscow 119991, Russia
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7
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Nishio S, Kurashige Y. Importance of dynamical electron correlation in diabatic couplings of electron-exchange processes. J Chem Phys 2022; 156:114107. [PMID: 35317578 DOI: 10.1063/5.0075978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We demonstrate the importance of the dynamical electron correlation effect in diabatic couplings of electron-exchange processes in molecular aggregates. To perform a multireference perturbation theory with large active space of molecular aggregates, an efficient low-rank approximation is applied to the complete active space self-consistent field reference functions. It is known that kinetic rates of electron-exchange processes, such as singlet fission, triplet-triplet annihilation, and triplet exciton transfer, are not sufficiently explained by the direct term of the diabatic couplings but efficiently mediated by the low-lying charge transfer states if the two molecules are in close proximity. It is presented in this paper, however, that regardless of the distance of the molecules, the direct term is considerably underestimated by up to three orders of magnitude without the dynamical electron correlation, i.e., the diabatic states expressed in the active space are not adequate to quantitatively reproduce the electron-exchange processes.
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Affiliation(s)
- Soichiro Nishio
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuki Kurashige
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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8
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Tölle J, Neugebauer J. The Seamless Connection of Local and Collective Excited States in Subsystem Time-Dependent Density Functional Theory. J Phys Chem Lett 2022; 13:1003-1018. [PMID: 35061387 DOI: 10.1021/acs.jpclett.1c04023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The theoretical understanding of photoinduced processes in multichromophoric systems requires, as an essential ingredient, the possibility of accurately describing their electronically excited states. However, the size of these systems often prohibits the usage of conventional electronic-structure methods, so that often multiscale approaches based on phenomenologically motivated models are employed. In contrast, subsystem time-dependent density functional theory (sTDDFT) allows for a subsystem-based ab initio description of multichromophoric systems and therefore allows for, in principle, an exact description of photoinduced processes. This Perspective aims to outline the theoretical foundations and commonly used practical realizations as well as to illustrate benefits of recent developments and open issues in the field of sTDDFT. Prospective, potential future applications and possible methodological developments are discussed.
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Affiliation(s)
- Johannes Tölle
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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9
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Fujita T, Noguchi Y. Fragment-Based Excited-State Calculations Using the GW Approximation and the Bethe-Salpeter Equation. J Phys Chem A 2021; 125:10580-10592. [PMID: 34871000 DOI: 10.1021/acs.jpca.1c07337] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we present a fragment-based approach for calculating the charged and neutral excited states in molecular systems, based on the many-body Green's function method within the GW approximation and the Bethe-Salpeter equation (BSE). The implementation relies on the many-body expansion of the total irreducible polarizability on the basis of fragment molecular orbitals. The GW quasi-particle energies in complex molecular environments are obtained by the GW calculation for the target fragment plus induced polarization contributions of the surrounding fragments at the static Coulomb-hole plus screened exchange level. In addition, we develop a large-scale GW/BSE method for calculating the delocalized excited states of molecular aggregates, based on the fragment molecular orbital method and the exciton model. The accuracy of fragment-based GW and GW/BSE methods was evaluated on molecular clusters and molecular crystals. We found that the accuracy of the total irreducible polarizability can be improved systematically by including two-body correction terms, and the fragment-based calculations can reasonably reproduce the results of the corresponding unfragmented calculations with a relative error of less than 100 meV. The proposed approach enables efficient excited-state calculations for large molecular systems with reasonable accuracy.
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Affiliation(s)
- Takatoshi Fujita
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Yoshifumi Noguchi
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, Shizuoka 432-8561, Japan
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10
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Abraham V, Mayhall NJ. Revealing the Contest between Triplet-Triplet Exchange and Triplet-Triplet Energy Transfer Coupling in Correlated Triplet Pair States in Singlet Fission. J Phys Chem Lett 2021; 12:10505-10514. [PMID: 34677988 DOI: 10.1021/acs.jpclett.1c03217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding the separation of the correlated triplet pair state 1(TT) intermediate is critical for leveraging singlet fission to improve solar cell efficiency. This separation mechanism is dominated by two key interactions: (i) the exchange interaction (K) between the triplets which leads to the spin splitting of the biexciton state into 1(TT),3(TT) and 5(TT) states, and (ii) the triplet-triplet energy transfer integral (t) which enables the formation of the spatially separated (but still spin entangled) state 1(T···T). We develop a simple ab initio technique to compute both the biexciton exchange (K) and biexciton transfer coupling. Our key findings reveal new conditions for successful correlated triplet pair state dissociation. The biexciton exchange interaction needs to be ferromagnetic or negligible to the triplet energy transfer for favorable dissociation. We also explore the effect of chromophore packing to reveal geometries where these conditions are achieved for tetracene.
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Affiliation(s)
- Vibin Abraham
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States
| | - Nicholas J Mayhall
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States
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11
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Fujimoto KJ. Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins. Front Mol Biosci 2021; 8:752700. [PMID: 34604313 PMCID: PMC8480471 DOI: 10.3389/fmolb.2021.752700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
The photo-functional chromophore retinal exhibits a wide variety of optical absorption properties depending on its intermolecular interactions with surrounding proteins and other chromophores. By utilizing these properties, microbial and animal rhodopsins express biological functions such as ion-transport and signal transduction. In this review, we present the molecular mechanisms underlying light absorption in rhodopsins, as revealed by quantum chemical calculations. Here, symmetry-adapted cluster-configuration interaction (SAC-CI), combined quantum mechanical and molecular mechanical (QM/MM), and transition-density-fragment interaction (TDFI) methods are used to describe the electronic structure of the retinal, the surrounding protein environment, and the electronic coupling between chromophores, respectively. These computational approaches provide successful reproductions of experimentally observed absorption and circular dichroism (CD) spectra, as well as insights into the mechanisms of unique optical properties in terms of chromophore-protein electrostatic interactions and chromophore-chromophore electronic couplings. On the basis of the molecular mechanisms revealed in these studies, we also discuss strategies for artificial design of the optical absorption properties of rhodopsins.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
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12
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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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13
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Błasiak B, Bartkowiak W, Góra RW. An effective potential for Frenkel excitons. Phys Chem Chem Phys 2021; 23:1923-1935. [PMID: 33459313 DOI: 10.1039/d0cp04636a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Excitation energy transfer (EET) is a ubiquitous process in life and materials sciences. Here, a new and computationally efficient method of evaluating the electronic EET couplings between interacting chromophores is introduced that is valid in a wide range of intermolecular distances. The proposed approach is based on the effective elimination of electron repulsion integrals from the excitonic Hamiltonian matrix elements via the density-fitting approach and distributed multipole approximation. The excitonic Hamiltonian represented in a basis including charge transfer (CT) states is re-cast in terms of the effective one-electron potential functions (EOPs) and adapted into the effective fragment parameter (EFP) framework. Calculations for model systems indicate that the speedup of at least three orders of magnitude, as compared to the state-of-the-art methods, can be achieved while maintaining the accuracy of the EET couplings even at short intermolecular distances.
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Affiliation(s)
- Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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14
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Fujimoto KJ, Inoue K. Excitonic coupling effect on the circular dichroism spectrum of sodium-pumping rhodopsin KR2. J Chem Phys 2020; 153:045101. [DOI: 10.1063/5.0013642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Kazuhiro J. Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8581, Japan
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15
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Kusano S, Ichikura Y, Fujimoto KJ, Konishi S, Yamada Y, Hayashida O. Exciton-coupled Circular Dichroism-based Glucose and Galactose Selective Sensing in Aqueous Media with an Anthracene-appended Benzoxaborole Dimer. CHEM LETT 2020. [DOI: 10.1246/cl.200244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Shuhei Kusano
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Yuma Ichikura
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Kazuhiro J. Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Sae Konishi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Yuji Yamada
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Osamu Hayashida
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
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16
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Nishio S, Kurashige Y. Rank-one basis made from matrix-product states for a low-rank approximation of molecular aggregates. J Chem Phys 2019; 151:084110. [DOI: 10.1063/1.5093346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Soichiro Nishio
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502, Japan
| | - Yuki Kurashige
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502, Japan
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17
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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18
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Glebov IO, Kozlov MI, Poddubnyy VV. Comparison of the Coulomb and non-orthogonal approaches to the construction of the exciton Hamiltonian. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Fujita T, Alam MK, Hoshi T. Thousand-atom ab initio calculations of excited states at organic/organic interfaces: toward first-principles investigations of charge photogeneration. Phys Chem Chem Phys 2018; 20:26443-26452. [PMID: 30306163 DOI: 10.1039/c8cp05574b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Predicting electronically excited states across electron-donor/electron acceptor interfaces is essential for understanding the charge photogeneration process in organic solar cells. However, organic solar cells are large and disordered systems, and their excited states cannot be easily accessed by conventional quantum chemistry approaches. Moreover, a large number of excited states must be obtained to fully understand the charge separation mechanism. Recently, we have developed a novel fragment-based excited state method which can efficiently calculate a large number of states in molecular aggregates. In this article, we demonstrate the large-scale excited-state calculations by investigating interfacial charge transfer (ICT) states across the electron-donor/electron acceptor interfaces. As the model systems, we considered the face-on and edge-on configurations of pentacene/C60 bilayer heterojunction structures. These model structures contain approximately 1.8 × 105 atoms, and their local interface regions containing 2000 atoms were treated quantum mechanically, embedded in the electrostatic potentials from the remaining parts. Therefore, the charge delocalization effect, structural disorder, and the resulting heterogeneous electrostatic and polarizable environments were taken into account in the excited-state calculations. The computed energies of the low-lying ICT states are in reasonable agreement with experimental estimates. By comparing the edge-on and face-on configurations of the pentacene/C60 interfaces, we discuss the influence of interfacial morphologies on the energetics and charge delocalization of ICT states. In addition, we present the detailed characterization of excited states and highlight the importance of hybridization effects between pentacene excited states and ICT states. The large-scale ab initio calculations for the interface systems enabled the exploration of the ICT states, leading to first-principles investigation of the charge separation mechanism in organic solar cells.
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Affiliation(s)
- Takatoshi Fujita
- Institute for Molecular Science, Okazaki, Aichi 444-0865, Japan.
| | - Md Khorshed Alam
- Department of Physics, University of Barisal, Barisal-8200, Bangladesh
| | - Takeo Hoshi
- Department of Applied Mathmatics and Physics, Tottori University, Tottori 680-8550, Japan
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20
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Liu W, Canola S, Köhn A, Engels B, Negri F, Fink RF. A model hamiltonian tuned toward high level ab initio
calculations to describe the character of excitonic states in perylenebisimide aggregates. J Comput Chem 2018; 39:1979-1989. [DOI: 10.1002/jcc.25374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Wenlan Liu
- Chongqing Key Laboratory of Green Synthesis and Applications & College of Chemistry; Chongqing Normal University; Chongqing 401331 China
- Institute of Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55, 70569 Stuttgart Germany
- Institute of Physical and Theoretical Chemistry, Auf der Morgenstelle 18; University of Tübingen; 72076 Tübingen Germany
| | - Sofia Canola
- Institute of Physical and Theoretical Chemistry, Auf der Morgenstelle 18; University of Tübingen; 72076 Tübingen Germany
- Universitá di Bologna Dipartimento di Chimica 'G. Ciamician'; Via F. Selmi 2, Bologna 40126 Italy
| | - Andreas Köhn
- Institute of Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55, 70569 Stuttgart Germany
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Emil-Fischer-Str. 42; University of Würzburg; 97074 Würzburg Germany
| | - Fabrizia Negri
- Universitá di Bologna Dipartimento di Chimica 'G. Ciamician'; Via F. Selmi 2, Bologna 40126 Italy
| | - Reinhold F. Fink
- Institute of Physical and Theoretical Chemistry, Auf der Morgenstelle 18; University of Tübingen; 72076 Tübingen Germany
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21
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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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22
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Fujimoto KJ, Balashov SP. Vibronic coupling effect on circular dichroism spectrum: Carotenoid–retinal interaction in xanthorhodopsin. J Chem Phys 2017. [DOI: 10.1063/1.4977045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Kazuhiro J. Fujimoto
- Faculty of Pharmaceutical Sciences, Hokuriku University, Ho-3 Kanagawa-machi, Kanazawa 920-1181, Japan
| | - Sergei P. Balashov
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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23
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Spiegel JD, Lyskov I, Kleinschmidt M, Marian CM. Charge-transfer contributions to the excitonic coupling matrix element in BODIPY-based energy transfer cassettes. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Sisto A, Stross C, van der Kamp MW, O’Connor M, McIntosh-Smith S, Johnson GT, Hohenstein EG, Manby FR, Glowacki DR, Martinez TJ. Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. Phys Chem Chem Phys 2017; 19:14924-14936. [DOI: 10.1039/c7cp00492c] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present GPU-accelerated ab initio molecular dynamics simulations of nonadiabatic dynamics in the LH2 complex in full atomistic detail.
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Affiliation(s)
- Aaron Sisto
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
| | - Clem Stross
- School of Chemistry
- University of Bristol
- Bristol
- UK
| | | | - Michael O’Connor
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | | | - Graham T. Johnson
- California Institute for Quantitative Biosciences (QB3)
- University of California
- San Francisco
- USA
- Department of Bioengineering and Therapeutic Sciences
| | | | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | - Todd J. Martinez
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
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25
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Tamura H. Diabatization for Time-Dependent Density Functional Theory: Exciton Transfers and Related Conical Intersections. J Phys Chem A 2016; 120:9341-9347. [PMID: 27801581 DOI: 10.1021/acs.jpca.6b09854] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intermolecular exciton transfers and related conical intersections are analyzed by diabatization for time-dependent density functional theory. The diabatic states are expressed as a linear combination of the adiabatic states so as to emulate the well-defined reference states. The singlet exciton coupling calculated by the diabatization scheme includes contributions from the Coulomb (Förster) and electron exchange (Dexter) couplings. For triplet exciton transfers, the Dexter coupling, charge transfer integral, and diabatic potentials of stacked molecules are calculated for analyzing direct and superexchange pathways. We discuss some topologies of molecular aggregates that induce conical intersections on the vanishing points of the exciton coupling, namely boundary of H- and J-aggregates and T-shape aggregates, as well as canceled exciton coupling to the bright state of H-aggregate, i.e., selective exciton transfer to the dark state. The diabatization scheme automatically accounts for the Berry phase by fixing the signs of reference states while scanning the coordinates.
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Affiliation(s)
- Hiroyuki Tamura
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo , 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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26
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Spiegel JD, Fulle S, Kleinschmidt M, Gohlke H, Marian CM. Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ2 Values. J Phys Chem B 2016; 120:8845-62. [DOI: 10.1021/acs.jpcb.6b05754] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Simone Fulle
- BioMed X Innovation Center, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
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27
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Fujita T, Atahan-Evrenk S, Sawaya NPD, Aspuru-Guzik A. Coherent Dynamics of Mixed Frenkel and Charge-Transfer Excitons in Dinaphtho[2,3-b:2'3'-f]thieno[3,2-b]-thiophene Thin Films: The Importance of Hole Delocalization. J Phys Chem Lett 2016; 7:1374-1380. [PMID: 27011327 DOI: 10.1021/acs.jpclett.6b00364] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Charge-transfer states in organic semiconductors play crucial roles in processes such as singlet fission and exciton dissociation at donor/acceptor interfaces. Recently, a time-resolved spectroscopy study of dinaphtho[2,3-b:2'3'-f]thieno[3,2-b]-thiophene (DNTT) thin films provided evidence for the formation of mixed Frenkel and charge-transfer excitons after the photoexcitation. Here, we investigate optical properties and excitation dynamics of the DNTT thin films by combining ab initio calculations and a stochastic Schrödinger equation. Our theory predicts that the low-energy Frenkel exciton band consists of 8-47% CT character. The quantum dynamics simulations show coherent dynamics of Frenkel and CT states in 50 fs after the optical excitation. We demonstrate the role of charge delocalization and localization in the mixing of CT states with Frenkel excitons as well as the role of their decoherence.
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Affiliation(s)
- Takatoshi Fujita
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Sule Atahan-Evrenk
- TOBB University of Economics and Technology , Sogutozu, Ankara 06560, Turkey
| | - Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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28
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KAWADA S, SAKAGUCHI M, YONEKURA I, OKUWAKI K, MOCHIZUKI Y, FUKUZAWA K. Fragment Molecular Orbital (FMO) Calculations of Peptoids. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shutaro KAWADA
- Rikkyo University, Depertment of Chemistry, Faculty of Science, Nishiikebukuro Toshima Tokyo 3-34-1
| | - Masataka SAKAGUCHI
- Rikkyo University, Depertment of Chemistry, Faculty of Science, Nishiikebukuro Toshima Tokyo 3-34-1
| | - Ibuki YONEKURA
- Rikkyo University, Depertment of Chemistry, Faculty of Science, Nishiikebukuro Toshima Tokyo 3-34-1
| | - Kouji OKUWAKI
- Rikkyo University, Depertment of Chemistry, Faculty of Science, Nishiikebukuro Toshima Tokyo 3-34-1
| | - Yuji MOCHIZUKI
- Rikkyo University, Depertment of Chemistry, Faculty of Science, Nishiikebukuro Toshima Tokyo 3-34-1
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29
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Kenny EP, Kassal I. Benchmarking Calculations of Excitonic Couplings between Bacteriochlorophylls. J Phys Chem B 2015; 120:25-32. [DOI: 10.1021/acs.jpcb.5b08817] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elise P. Kenny
- Centre
for Engineered Quantum
Systems, Centre for Quantum Computation and Communication Technology,
and School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072, Australia
| | - Ivan Kassal
- Centre
for Engineered Quantum
Systems, Centre for Quantum Computation and Communication Technology,
and School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072, Australia
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30
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Spiegel JD, Kleinschmidt M, Larbig A, Tatchen J, Marian CM. Quantum-Chemical Studies on Excitation Energy Transfer Processes in BODIPY-Based Donor-Acceptor Systems. J Chem Theory Comput 2015; 11:4316-27. [PMID: 26575926 DOI: 10.1021/acs.jctc.5b00501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BODIPY-based excitation energy transfer (EET) cassettes are experimentally extensively studied and serve as excellent model systems for the investigation of photophysical processes, since they occur in any photosynthetic system and in organic photovoltaics. In the present work, the EET rates in five BODIPY-based EET cassettes in which anthracene serves as the donor have been determined, employing the monomer transition density approach (MTD) and the ideal dipole approximation (IDA). To this end, a new computer program has been devised that calculates the direct and exchange contributions to the excitonic coupling (EC) matrix element from transition density matrices generated by a combined density functional and multireference configuration interaction (DFT/MRCI) calculation for the monomers. EET rates have been calculated according to Fermi's Golden Rule from the EC and the spectral overlap, which was obtained from the calculated vibrationally resolved emission and absorption spectra of donor and acceptor, respectively. We find that the direct contribution to the EC matrix element is dominant in the studied EET cassettes. Furthermore, we show that the contribution of the molecular linker to the EET rate cannot be neglected. In our best fragment model, the molecular linker is attached to the donor moiety. For cassettes in which the transition dipole moments of donor and acceptor are oriented in parallel manner, our results confirm the experimental findings reported by Kim et al. [J. Phys. Chem. A 2006, 110, 20-27]. In cassettes with a perpendicular orientation of the donor and acceptor transition dipole moments, dynamic effects turn out to be important.
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Affiliation(s)
- J Dominik Spiegel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Martin Kleinschmidt
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Alexander Larbig
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Jörg Tatchen
- Departamento de Química, Universidad de los Andes , Car. 1 No. 18A-12, Bogotá, Colombia
| | - Christel M Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstr. 1, D-40225 Düsseldorf, Germany
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31
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Błasiak B, Maj M, Cho M, Góra RW. Distributed Multipolar Expansion Approach to Calculation of Excitation Energy Transfer Couplings. J Chem Theory Comput 2015; 11:3259-66. [DOI: 10.1021/acs.jctc.5b00216] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bartosz Błasiak
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 136-701, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Michał Maj
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 136-701, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Minhaeng Cho
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 136-701, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 136-701, Republic of Korea
| | - Robert W. Góra
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego
27, Wrocław 50-370, Poland
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32
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Fujimoto KJ. Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting. J Chem Phys 2014; 141:214105. [DOI: 10.1063/1.4902758] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Kazuhiro J. Fujimoto
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1, Rokkodai, Nada, Kobe 657-8501, Japan
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33
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Renger T, Madjet MEA, Schmidt am Busch M, Adolphs J, Müh F. Structure-based modeling of energy transfer in photosynthesis. PHOTOSYNTHESIS RESEARCH 2013; 116:367-388. [PMID: 23921525 DOI: 10.1007/s11120-013-9893-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment-protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton-vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria,
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34
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Fujimoto KJ, Kitamura C. A theoretical study of crystallochromy: Spectral tuning of solid-state tetracenes. J Chem Phys 2013; 139:084511. [DOI: 10.1063/1.4819133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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35
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König C, Neugebauer J. Exciton Coupling Mechanisms Analyzed with Subsystem TDDFT: Direct vs Pseudo Exchange Effects. J Phys Chem B 2013; 117:3480-7. [DOI: 10.1021/jp3105419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Carolin König
- Theoretische Organische
Chemie, Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster,
Germany
| | - Johannes Neugebauer
- Theoretische Organische
Chemie, Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster,
Germany
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36
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Renger T, Müh F. Understanding photosynthetic light-harvesting: a bottom up theoretical approach. Phys Chem Chem Phys 2013; 15:3348-71. [PMID: 23361062 DOI: 10.1039/c3cp43439g] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discuss a bottom up approach for modeling photosynthetic light-harvesting. Methods are reviewed for a full structure-based parameterization of the Hamiltonian of pigment-protein complexes (PPCs). These parameters comprise (i) the local transition energies of the pigments in their binding sites in the protein, the site energies; (ii) the couplings between optical transitions of the pigments, the excitonic couplings; and (iii) the spectral density characterizing the dynamic modulation of pigment transition energies and excitonic couplings by protein vibrations. Starting with quantum mechanics perturbation theory, we provide a microscopic foundation for the standard PPC Hamiltonian and relate the expressions obtained for its matrix elements to quantities that can be calculated with classical molecular mechanics/electrostatics approaches including the whole PPC in atomic detail and using charge and transition densities obtained with quantum chemical calculations on the isolated building blocks of the PPC. In the second part of this perspective, the Hamiltonian is utilized to describe the quantum dynamics of excitons. Situations are discussed that differ in the relative strength of excitonic and exciton-vibrational coupling. The predictive power of the approaches is demonstrated in application to different PPCs, and challenges for future work are outlined.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Linz, Austria.
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