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Kimura A, Kitoh-Nishioka H, Kondo T, Oh-Oka H, Itoh S, Azai C. Experimental and Theoretical Mutation of Exciton States on the Smallest Type-I Photosynthetic Reaction Center Complex of a Green Sulfur Bacterium Chlorobaclum tepidum. J Phys Chem B 2024; 128:731-743. [PMID: 38198639 DOI: 10.1021/acs.jpcb.3c07424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The exciton states on the smallest type-I photosynthetic reaction center complex of a green sulfur bacterium Chlorobaculum tepidum (GsbRC) consisting of 26 bacteriochlorophylls a (BChl a) and four chlorophylls a (Chl a) located on the homodimer of two PscA reaction center polypeptides were investigated. This analysis involved the study of exciton states through a combination of theoretical modeling and the genetic removal of BChl a pigments at eight sites. (1) A theoretical model of the pigment assembly exciton state on GsbRC was constructed using Poisson TrESP (P-TrESP) and charge density coupling (CDC) methods based on structural information. The model reproduced the experimentally obtained absorption spectrum, circular dichroism spectrum, and excitation transfer dynamics, as well as explained the effects of mutation. (2) Eight BChl a molecules at different locations on the GsbRC were selectively removed by genetic exchange of the His residue, which ligates the central Mg atom of BChl a, with the Leu residue on either one or two PscAs in the RC. His locations are conserved among all type-I RC plant polypeptide, cyanobacteria, and bacteria amino acid sequences. (3) Purified mutant-GsbRCs demonstrated distinct absorption and fluorescence spectra at 77 K, which were different from each other, suggesting successful pigment removal. (4) The same mutations were applied to the constructed theoretical model to analyze the outcomes of these mutations. (5) The combination of theoretical predictions and experimental mutations based on structural information is a new tool for studying the function and evolution of photosynthetic reaction centers.
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Affiliation(s)
- Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hirotaka Kitoh-Nishioka
- Department of Energy and Materials, Faculty of Science and Engineering, Kindai University, Osaka 577-8502, Japan
| | - Toru Kondo
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Hirozo Oh-Oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Chihiro Azai
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
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2
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Noji T, Tamura H, Ishikita H, Saito K. Difference in the Charge-Separation Energetics between Distinct Conformers in the PixD Photoreceptor. J Phys Chem B 2023; 127:10351-10359. [PMID: 38014591 DOI: 10.1021/acs.jpcb.3c06483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Blue light using flavin (BLUF) domain proteins are photoreceptors in various organisms. The PixD BLUF domain can adopt two conformations, W91out and W91in, with Trp91 either proximal or distal to flavin (FMN). Using a quantum mechanical/molecular mechanical/polarizable continuum model approach, the energetics of charge-separated and biradical states in the two conformations were investigated. In the W91out conformation, the charge-separated state (FMN•-) is more stable than the photoexcited state (FMN*), whereas it is less stable due to an electrostatic repulsive interaction with the Ser28 side chain in the W91in conformation. This leads to a lower activation energy for the charge separation in the W91out conformation, resulting in a faster charge separation compared to that in the W91in conformation. In the W91out conformation, the radical state (FMNH•) is more stable than FMN•- and forms from FMN•-, leading to reorientation of the Gln50 side chain adjacent to FMN and formation of a hydrogen bond between Gln50 and FMN. Subsequently, a signaling state forms through charge recombination. In contrast, in the W91in conformation, FMN•- cannot proceed further, returning to the dark-adapted state, as FMNH• is less stable. Thus, formation of the signaling state exclusively occurs in the W91out conformation.
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Affiliation(s)
- Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroyuki Tamura
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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3
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Saito K, Mitsuhashi K, Tamura H, Ishikita H. Quantum mechanical analysis of excitation energy transfer couplings in photosystem II. Biophys J 2023; 122:470-483. [PMID: 36609140 PMCID: PMC9941724 DOI: 10.1016/j.bpj.2023.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/21/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
We evaluated excitation energy transfer (EET) coupling (J) between all pairs of chlorophylls (Chls) and pheophytins (Pheos) in the protein environment of photosystem II based on the time-dependent density functional theory with a quantum mechanical/molecular mechanics approach. In the reaction center, the EET coupling between Chls PD1 and PD2 is weaker (|J(PD1/PD2)| = 79 cm-1), irrespective of a short edge-to-edge distance of 3.6 Å (Mg-to-Mg distance of 8.1 Å), than the couplings between PD1 and the accessory ChlD1 (|J(PD1/ChlD2)| = 104 cm-1) and between PD2 and ChlD2 (|J(PD2/ChlD1)| = 101 cm-1), suggesting that PD1 and PD2 are two monomeric Chls rather than a "special pair". There exist strongly coupled Chl pairs (|J| > ∼100 cm-1) in the CP47 and CP43 core antennas, which may be candidates for the red-shifted Chls observed in spectroscopic studies. In CP47 and CP43, Chls ligated to CP47-His26 and CP43-His56, which are located in the middle layer of the thylakoid membrane, play a role in the "hub" that mediates the EET from the lumenal to stromal layers. In the stromal layer, Chls ligated to CP47-His466, CP43-His441, and CP43-His444 mediate the EET from CP47 to ChlD2/PheoD2 and from CP43 to ChlD1/PheoD1 in the reaction center. Thus, the excitation energy from both CP47 and CP43 can always be utilized for the charge-separation reaction in the reaction center.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Koji Mitsuhashi
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Tamura
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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4
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Tsujimura M, Sugano M, Ishikita H, Saito K. Mechanism of Absorption Wavelength Shift Depending on the Protonation State of the Acrylate Group in Chlorophyll c. J Phys Chem B 2023; 127:505-513. [PMID: 36607907 PMCID: PMC9869891 DOI: 10.1021/acs.jpcb.2c07232] [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: 10/14/2022] [Revised: 12/15/2022] [Indexed: 01/07/2023]
Abstract
Diatoms can use light in the blue-green region because they have chlorophyll c (Chlc) in light-harvesting antenna proteins, fucoxanthin and chlorophyll a/c-binding protein (FCP). Chlc has a protonatable acrylate group (-CH═CH-COOH/COO-) conjugated to the porphyrin ring. As the absorption wavelength of Chlc changes upon the protonation of the acrylate group, Chlc is a candidate component that is responsible for photoprotection in diatoms, which switches the FCP function between light-harvesting and energy-dissipation modes depending on the light intensity. Here, we investigate the mechanism by which the absorption wavelength of Chlc changes owing to the change in the protonation state of the acrylate group, using a quantum mechanical/molecular mechanical approach. The calculated absorption wavelength of the Soret band of protonated Chlc is ∼25 nm longer than that of deprotonated Chlc, which is due to the delocalization of the lowest (LUMO) and second lowest (LUMO+1) unoccupied molecular orbitals toward the acrylate group. These results suggest that in FCP, the decrease in pH on the lumenal side under high-light conditions leads to protonation of Chlc and thereby a red shift in the absorption wavelength.
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Affiliation(s)
- Masaki Tsujimura
- Department
of Advanced Interdisciplinary Studies, The
University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Minaka Sugano
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Keisuke Saito
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
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5
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Förster A, Visscher L. Quasiparticle Self-Consistent GW-Bethe-Salpeter Equation Calculations for Large Chromophoric Systems. J Chem Theory Comput 2022; 18:6779-6793. [PMID: 36201788 PMCID: PMC9648197 DOI: 10.1021/acs.jctc.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The GW-Bethe–Salpeter equation
(BSE) method
is promising for calculating the low-lying excitonic states of molecular
systems. However, so far it has only been applied to rather small
molecules and in the commonly implemented diagonal approximations
to the electronic self-energy, it depends on a mean-field starting
point. We describe here an implementation of the self-consistent and
starting-point-independent quasiparticle self-consistent (qsGW)-BSE approach, which is suitable for calculations on
large molecules. We herein show that eigenvalue-only self-consistency
can lead to an unfaithful description of some excitonic states for
chlorophyll dimers while the qsGW-BSE vertical excitation
energies (VEEs) are in excellent agreement with spectroscopic experiments
for chlorophyll monomers and dimers measured in the gas phase. Furthermore,
VEEs from time-dependent density functional theory calculations tend
to disagree with experimental values and using different range-separated
hybrid (RSH) kernels does change the VEEs by up to 0.5 eV. We use
the new qsGW-BSE implementation to calculate the
lowest excitation energies of the six chromophores of the photosystem
II (PSII) reaction center (RC) with nearly 2000 correlated electrons.
Using more than 11,000 (6000) basis functions, the calculation could
be completed in less than 5 (2) days on a single modern compute node.
In agreement with previous TD-DFT calculations using RSH kernels on
models that also do not include environmental effects, our qsGW-BSE calculations only yield states with local characters
in the low-energy spectrum of the hexameric complex. Earlier works
with RSH kernels have demonstrated that the protein environment facilitates
the experimentally observed interchromophoric charge transfer. Therefore,
future research will need to combine correlation effects beyond TD-DFT
with an explicit treatment of environmental electrostatics.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
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The Ability of Chlorophyll to Trap Carcinogen Aflatoxin B1: A Theoretical Approach. Int J Mol Sci 2022; 23:ijms23116068. [PMID: 35682746 PMCID: PMC9181093 DOI: 10.3390/ijms23116068] [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: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
The coordination of one and two aflatoxin B1 (AFB1, a potent carcinogen) molecules with chlorophyll a (chl a) was studied at a theoretical level. Calculations were performed using the M06-2X method in conjunction with the 6-311G(d,p) basis set, in both gas and water phases. The molecular electrostatic potential map shows the chemical activity of various sites of the AFB1 and chl a molecules. The energy difference between molecular orbitals of AFB1 and chl a allowed for the establishment of an intermolecular interaction. A charge transfer from AFB1 to the central cation of chl a was shown. The energies of the optimized structures for chl a show two configurations, unfolded and folded, with a difference of 15.41 kcal/mol. Chl a appeared axially coordinated to the plane (α-down or β-up) of the porphyrin moiety, either with the oxygen atom of the ketonic group, or with the oxygen atom of the lactone moiety of AFB1. The complexes of maximum stability were chl a 1-α-E-AFB1 and chl a 2-β-E-AFB1, at −36.4 and −39.2 kcal/mol, respectively. Additionally, with two AFB1 molecules were chl a 1-D-2AFB1 and chl a 2-E-2AFB1, at −60.0 and −64.8 kcal/mol, respectively. Finally, biosorbents containing chlorophyll could improve AFB1 adsorption.
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7
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Kimura A, Kitoh-Nishioka H, Aota T, Hamaguchi T, Yonekura K, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Ifuku K, Yamashita E, Kashino Y, Itoh S. Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange. J Phys Chem B 2022; 126:4009-4021. [PMID: 35617171 DOI: 10.1021/acs.jpcb.2c00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A theoretical model of the far-red-light-adapted photosystem I (PSI) reaction center (RC) complex of a cyanobacterium, Acaryochloris marina (AmPSI), was constructed based on the exciton theory and the recently identified molecular structure of AmPSI by Hamaguchi et al. (Nat. Commun., 2021, 12, 2333). A. marina performs photosynthesis under the visible to far-red light (400-750 nm), which is absorbed by chlorophyll d (Chl-d). It is in contrast to the situation of all the other oxygenic photosynthetic processes of cyanobacteria and plants, which contains chlorophyll a (Chl-a) that absorbs only 400-700 nm visible light. AmPSI contains 70 Chl-d, 1 Chl-d', 2 pheophytin a (Pheo-a), and 12 carotenoids in the currently available structure. A special pair of Chl-d/Chl-d' acts as the electron donor (P740) and two Pheo-a act as the primary electron acceptor A0 as the counterparts of P700 and Chl-a, respectively, of Chl-a-type PSIs. The exciton Hamiltonian of AmPSI was constructed considering the excitonic coupling strength and site energy shift of individual pigments using the Poisson-TrESP (P-TrESP) and charge density coupling (CDC) methods. The model was constructed to fit the experimentally measured spectra of absorption and circular dichroism (CD) spectra during downhill/uphill excitation energy transfer processes. The constructed theoretical model of AmPSI was further compared with the Chl-a-type PSI of Thermosynechococcus elongatus (TePSI), which contains only Chl-a and Chl-a'. The functional properties of AmPSI and TePSI were further examined by the in silico exchange of Chl-d by Chl-a in the models.
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Affiliation(s)
- Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | | | - Toshimichi Aota
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 776 Sayo, Hyogo 679-5148, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 776 Sayo, Hyogo 679-5148, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 776 Sayo, Hyogo 679-5148, Japan
| | - Kyoko Shinzawa-Itoh
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | | | - Kentaro Ifuku
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Eiki Yamashita
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuhiro Kashino
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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ZHU ZHE, Higashi M, Saito S. Excited states of chlorophyll a and b in solution by time-dependent density functional theory. J Chem Phys 2022; 156:124111. [DOI: 10.1063/5.0083395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in functionals. Here, we optimize the range-separated parameter, µ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of µ for Chl a and Chl b are smaller than the default value of µ and that for bacteriochlorophyll a, indicating the change in electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.
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Affiliation(s)
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
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9
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Zahn C, Stensitzki T, Heyne K. Femtosecond anisotropy excitation spectroscopy to disentangle the Q x and Q y absorption in chlorophyll a. Chem Sci 2022; 13:12426-12432. [DOI: 10.1039/d2sc03538c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
Femtosecond anisotropy excitation spectroscopy is a powerful tool for unraveling contributions of electronic transitions. Here, we applied it to chlorophyll a, identifying the contribution of Qx and Qy transitions within its absorption spectrum.
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Affiliation(s)
- Clark Zahn
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Till Stensitzki
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Karsten Heyne
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
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Srivastava R. Physicochemical, antioxidant properties of carotenoids and its optoelectronic and interaction studies with chlorophyll pigments. Sci Rep 2021; 11:18365. [PMID: 34526535 PMCID: PMC8443628 DOI: 10.1038/s41598-021-97747-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
The physicochemical and antioxidant properties of seven carotenoids: antheraxanthin, β-carotene, neoxanthin, peridinin, violaxanthin, xanthrophyll and zeaxanthin were studied by theoretical means. Then the Optoelectronic properties and interaction of chlorophyll-carotenoid complexes are analysed by TDDFT and IGMPLOT. Global reactivity descriptors for carotenoids and chlorophyll (Chla, Chlb) are calculated via conceptual density functional theory (CDFT). The higher HOMO-LUMO (HL) gap indicated structural stability of carotenoid, chlorophyll and chlorophyll-carotenoid complexes. The chemical hardness for carotenoids and Chlorophyll is found to be lower in the solvent medium than in the gas phase. Results showed that carotenoids can be used as good reactive nucleophile due to lower µ and ω. As proton affinities (PAs) are much lower than the bond dissociation enthalpies (BDEs), it is anticipated that direct antioxidant activity in these carotenoids is mainly due to the sequential proton loss electron transfer (SPLET) mechanism with dominant solvent effects. Also lower PAs of carotenoid suggest that antioxidant activity by the SPLET mechanism should be a result of a balance between proclivities to transfer protons. Reaction rate constant with Transition-State Theory (TST) were estimated for carotenoid-Chlorophyll complexes in gas phase. Time dependent Density Functional Theory (TDDFT) showed that all the chlorophyll (Chla, Chlb)-carotenoid complexes show absorption wavelength in the visible region. The lower S1-T1 adiabatic energy gap indicated ISC transition from S1 to T1 state.
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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11
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12
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Mitsuhashi K, Tamura H, Saito K, Ishikita H. Nature of Asymmetric Electron Transfer in the Symmetric Pathways of Photosystem I. J Phys Chem B 2021; 125:2879-2885. [DOI: 10.1021/acs.jpcb.0c10885] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Koji Mitsuhashi
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroyuki Tamura
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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13
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Sirohiwal A, Neese F, Pantazis DA. How Can We Predict Accurate Electrochromic Shifts for Biochromophores? A Case Study on the Photosynthetic Reaction Center. J Chem Theory Comput 2021; 17:1858-1873. [PMID: 33566610 PMCID: PMC8023663 DOI: 10.1021/acs.jctc.0c01152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 01/28/2023]
Abstract
Protein-embedded chromophores are responsible for light harvesting, excitation energy transfer, and charge separation in photosynthesis. A critical part of the photosynthetic apparatus are reaction centers (RCs), which comprise groups of (bacterio)chlorophyll and (bacterio)pheophytin molecules that transform the excitation energy derived from light absorption into charge separation. The lowest excitation energies of individual pigments (site energies) are key for understanding photosynthetic systems, and form a prime target for quantum chemistry. A major theoretical challenge is to accurately describe the electrochromic (Stark) shifts in site energies produced by the inhomogeneous electric field of the protein matrix. Here, we present large-scale quantum mechanics/molecular mechanics calculations of electrochromic shifts for the RC chromophores of photosystem II (PSII) using various quantum chemical methods evaluated against the domain-based local pair natural orbital (DLPNO) implementation of the similarity-transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD). We show that certain range-separated density functionals (ωΒ97, ωΒ97X-V, ωΒ2PLYP, and LC-BLYP) correctly reproduce RC site energy shifts with time-dependent density functional theory (TD-DFT). The popular CAM-B3LYP functional underestimates the shifts and is not recommended. Global hybrid functionals are too insensitive to the environment and should be avoided, while nonhybrid functionals are strictly nonapplicable. Among the applicable approximate coupled cluster methods, the canonical versions of CC2 and ADC(2) were found to deviate significantly from the reference results both for the description of the lowest excited state and for the electrochromic shifts. By contrast, their spin-component-scaled (SCS) and particularly the scale-opposite-spin (SOS) variants compare well with the reference DLPNO-STEOM-CCSD and the best range-separated DFT methods. The emergence of RC excitation asymmetry is discussed in terms of intrinsic and protein electrostatic potentials. In addition, we evaluate a minimal structural scaffold of PSII, the D1-D2-CytB559 RC complex often employed in experimental studies, and show that it would have the same site energy distribution of RC chromophores as the full PSII supercomplex, but only under the unlikely conditions that the core protein organization and cofactor arrangement remain identical to those of the intact enzyme.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fakultät
für Chemie und Biochemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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14
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Do TN, Sim JHN, Nguyen HL, Lu Y, Tan HS. Observing the Fluctuation Dynamics of Dative Bonds Using Two-Dimensional Electronic Spectroscopy. J Phys Chem Lett 2021; 12:165-170. [PMID: 33320689 DOI: 10.1021/acs.jpclett.0c03243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We perform two-dimensional electronic spectroscopy on chlorophyll (Chl) a and b molecules in aprotic solvents of different Lewis basicity. By analyzing the ultrafast spectral diffusion dynamics of the Qy transition, we show that a certain timescale of the spectral diffusion dynamics is affected by the solvents' Lewis basicity. Control experiments with Chlorin-e6-a Chl molecule analog-and ab initio time-dependent density functional theory calculations confirm that we are directly probing the fluctuation dynamics of the dative bond between the solvent's lone pair and the Mg2+ center in Chls that is responsible for the Lewis basicity. The observation is indicative of dative bond length and angular fluctuations with timescales ranging between ∼30 and 150 ps and the dative bond-strength-dependent perturbation on the Qy transition frequency of Chls.
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Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Jamie Hung Ni Sim
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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15
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Tsujimura M, Noji T, Saito K, Kojima K, Sudo Y, Ishikita H. Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148349. [PMID: 33248117 DOI: 10.1016/j.bbabio.2020.148349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/05/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
Abstract
Using a quantum mechanical/molecular mechanical approach, we show the mechanisms of how the protein environment of Guillardia theta anion channelrhodopsin-1 (GtACR1) can shift the absorption wavelength. The calculated absorption wavelengths for GtACR1 mutants, M105A, C133A, and C237A are in agreement with experimentally measured wavelengths. Among 192 mutant structures investigated, mutations at Thr101, Cys133, Pro208, and Cys237 are likely to increase the absorption wavelength. In particular, T101A GtACR1 was expressed in HEK293T cells. The measured absorption wavelength is 10 nm higher than that of wild type, consistent with the calculated wavelength. (i) Removal of a polar residue from the Schiff base moiety, (ii) addition of a polar or acidic residue to the β-ionone ring moiety, and (iii) addition of a bulky residue to increase the planarity of the β-ionone and Schiff base moieties are the basis of increasing the absorption wavelength.
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Affiliation(s)
- Masaki Tsujimura
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Tomoyasu Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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16
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Tsujimura M, Ishikita H. Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins. J Phys Chem B 2020; 124:11819-11826. [PMID: 33236904 DOI: 10.1021/acs.jpcb.0c08910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using a quantum mechanical/molecular mechanical approach, the absorption wavelength of the retinal Schiff base was calculated based on 13 microbial rhodopsin crystal structures. The results showed that the protein electrostatic environment decreases the absorption wavelength significantly in the cation-conducting rhodopsin but only slightly in the sensory rhodopsin. Among the microbial rhodopsins with different functions, the differences in the absorption wavelengths are caused by differences in the arrangement of the charged residues at the retinal Schiff base binding moiety, namely, one or two counterions at the three common positions. Among the microbial rhodopsins with similar functions, the differences in the polar residues at the retinal Schiff base binding site are responsible for the differences in the absorption wavelengths. Counterions contribute to an absorption wavelength shift of 50-120 nm, whereas polar groups contribute to a shift of up to ∼10 nm. It seems likely that protein function is directly associated with the absorption wavelength in microbial rhodopsins.
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Affiliation(s)
- Masaki Tsujimura
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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17
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Dependence of the chlorophyll wavelength on the orientation of a charged group: Why does the accessory chlorophyll have a low site energy in photosystem II? J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112799] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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18
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Sirohiwal A, Berraud-Pache R, Neese F, Izsák R, Pantazis DA. Accurate Computation of the Absorption Spectrum of Chlorophyll a with Pair Natural Orbital Coupled Cluster Methods. J Phys Chem B 2020; 124:8761-8771. [PMID: 32930590 PMCID: PMC7584356 DOI: 10.1021/acs.jpcb.0c05761] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The
ability to accurately compute low-energy excited states of
chlorophylls is critically important for understanding the vital roles
they play in light harvesting, energy transfer, and photosynthetic
charge separation. The challenge for quantum chemical methods arises
both from the intrinsic complexity of the electronic structure problem
and, in the case of biological models, from the need to account for
protein–pigment interactions. In this work, we report electronic
structure calculations of unprecedented accuracy for the low-energy
excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local
pair natural orbital (DLPNO) implementation of the similarity transformed
equation of motion coupled cluster theory with single and double excitations
(STEOM-CCSD) in combination with sufficiently large and flexible basis
sets. The results of our DLPNO–STEOM-CCSD calculations are
compared with more approximate approaches. The results demonstrate
that, in contrast to time-dependent density functional theory, the
DLPNO–STEOM-CCSD method provides a balanced performance for
both absorption bands. In addition to vertical excitation energies,
we have calculated the vibronic spectrum for the Q and B bands through
a combination of DLPNO–STEOM-CCSD and ground-state density
functional theory frequency calculations. These results serve as a
basis for comparison with gas-phase experiments.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.,Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Romain Berraud-Pache
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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19
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Chan B, Hirao K. Rapid Prediction of Ultraviolet-Visible Spectra from Conventional (Non-Time-Dependent) Density Functional Theory Calculations. J Phys Chem Lett 2020; 11:7882-7885. [PMID: 32893637 DOI: 10.1021/acs.jpclett.0c02146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We present an approximate approach for the simulation of UV/vis spectra using conventional [non-time-dependent (non-TD)] DFT computations. It uses Kohn-Sham orbitals and orbital energies to estimate both the excitation energies and the associated oscillator strengths. For a wide range of systems from small molecules to large molecular dyes used in electrochromic and solar-cell applications, reasonable UV/vis spectra are generated, each with just two conventional DFT computations. The accuracy is generally comparable to what one would expect from TD-DFT calculations. In comparison to TD-DFT, the protocol of the present study provides an intuitive and notably more rapid means for simulating electronic absorption properties. It enables efficient screening of materials for a wide range of relevant applications.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Kimihiko Hirao
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
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20
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Kavanagh MA, Karlsson JKG, Colburn JD, Barter LMC, Gould IR. A TDDFT investigation of the Photosystem II reaction center: Insights into the precursors to charge separation. Proc Natl Acad Sci U S A 2020; 117:19705-19712. [PMID: 32747579 PMCID: PMC7443915 DOI: 10.1073/pnas.1922158117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Photosystem II (PS II) captures solar energy and directs charge separation (CS) across the thylakoid membrane during photosynthesis. The highly oxidizing, charge-separated state generated within its reaction center (RC) drives water oxidation. Spectroscopic studies on PS II RCs are difficult to interpret due to large spectral congestion, necessitating modeling to elucidate key spectral features. Herein, we present results from time-dependent density functional theory (TDDFT) calculations on the largest PS II RC model reported to date. This model explicitly includes six RC chromophores and both the chlorin phytol chains and the amino acid residues <6 Å from the pigments' porphyrin ring centers. Comparing our wild-type model results with calculations on mutant D1-His-198-Ala and D2-His-197-Ala RCs, our simulated absorption-difference spectra reproduce experimentally observed shifts in known chlorophyll absorption bands, demonstrating the predictive capabilities of this model. We find that inclusion of both nearby residues and phytol chains is necessary to reproduce this behavior. Our calculations provide a unique opportunity to observe the molecular orbitals that contribute to the excited states that are precursors to CS. Strikingly, we observe two high oscillator strength, low-lying states, in which molecular orbitals are delocalized over ChlD1 and PheD1 as well as one weaker oscillator strength state with molecular orbitals delocalized over the P chlorophylls. Both these configurations are a match for previously identified exciton-charge transfer states (ChlD1+PheD1-)* and (PD2+PD1-)*. Our results demonstrate the power of TDDFT as a tool, for studies of natural photosynthesis, or indeed future studies of artificial photosynthetic complexes.
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Affiliation(s)
- Maeve A Kavanagh
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
| | - Joshua K G Karlsson
- Molecular Photonics Laboratory, School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Jonathan D Colburn
- School of Chemistry, University of St. Andrews, St. Andrews KY16 9ST, Scotland
| | - Laura M C Barter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom;
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
| | - Ian R Gould
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom;
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
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21
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Acquirement of water-splitting ability and alteration of the charge-separation mechanism in photosynthetic reaction centers. Proc Natl Acad Sci U S A 2020; 117:16373-16382. [PMID: 32601233 PMCID: PMC7368266 DOI: 10.1073/pnas.2000895117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In photosynthetic reaction centers from purple bacteria (PbRC) and the water-oxidizing enzyme, photosystem II (PSII), charge separation occurs along one of the two symmetrical electron-transfer branches. Here we report the microscopic origin of the unidirectional charge separation, fully considering electron-hole interaction, electronic coupling of the pigments, and electrostatic interaction with the polarizable entire protein environments. The electronic coupling between the pair of bacteriochlorophylls is large in PbRC, forming a delocalized excited state with the lowest excitation energy (i.e., the special pair). The charge-separated state in the active branch is stabilized by uncharged polar residues in the transmembrane region and charged residues on the cytochrome c 2 binding surface. In contrast, the accessory chlorophyll in the D1 protein (ChlD1) has the lowest excitation energy in PSII. The charge-separated state involves ChlD1 •+ and is stabilized predominantly by charged residues near the Mn4CaO5 cluster and the proceeding proton-transfer pathway. It seems likely that the acquirement of water-splitting ability makes ChlD1 the initial electron donor in PSII.
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22
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Agostini A, Meneghin E, Gewehr L, Pedron D, Palm DM, Carbonera D, Paulsen H, Jaenicke E, Collini E. How water-mediated hydrogen bonds affect chlorophyll a/b selectivity in Water-Soluble Chlorophyll Protein. Sci Rep 2019; 9:18255. [PMID: 31796824 PMCID: PMC6890793 DOI: 10.1038/s41598-019-54520-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/14/2019] [Indexed: 01/15/2023] Open
Abstract
The Water-Soluble Chlorophyll Protein (WSCP) of Brassicaceae is a remarkably stable tetrapyrrole-binding protein that, by virtue of its simple design, is an exceptional model to investigate the interactions taking place between pigments and their protein scaffold and how they affect the photophysical properties and the functionality of the complexes. We investigated variants of WSCP from Lepidium virginicum (Lv) and Brassica oleracea (Bo), reconstituted with Chlorophyll (Chl) b, to determine the mechanisms by which the different Chl binding sites control their Chl a/b specificities. A combined Raman and crystallographic investigation has been employed, aimed to characterize in detail the hydrogen-bond network involving the formyl group of Chl b. The study revealed a variable degree of conformational freedom of the hydrogen bond networks among the WSCP variants, and an unexpected mixed presence of hydrogen-bonded and not hydrogen-bonded Chls b in the case of the L91P mutant of Lv WSCP. These findings helped to refine the description of the mechanisms underlying the different Chl a/b specificities of WSCP versions, highlighting the importance of the structural rigidity of the Chl binding site in the vicinity of the Chl b formyl group in granting a strong selectivity to binding sites.
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Affiliation(s)
- Alessandro Agostini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy. .,Institute of Molecular Physiology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128, Mainz, Germany.
| | - Elena Meneghin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Lucas Gewehr
- Institute of Molecular Physiology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128, Mainz, Germany
| | - Danilo Pedron
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Daniel M Palm
- Institute of Molecular Physiology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128, Mainz, Germany
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128, Mainz, Germany
| | - Elmar Jaenicke
- Institute of Molecular Physiology, Johannes Gutenberg-University, Jakob-Welder-Weg 26, 55128, Mainz, Germany
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
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23
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Song Y, Schubert A, Maret E, Burdick RK, Dunietz BD, Geva E, Ogilvie JP. Vibronic structure of photosynthetic pigments probed by polarized two-dimensional electronic spectroscopy and ab initio calculations. Chem Sci 2019; 10:8143-8153. [PMID: 31857881 PMCID: PMC6836992 DOI: 10.1039/c9sc02329a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/02/2019] [Indexed: 12/29/2022] Open
Abstract
Bacteriochlorophyll a (Bchl a) and chlorophyll a (Chl a) play important roles as light absorbers in photosynthetic antennae and participate in the initial charge-separation steps in photosynthetic reaction centers. Despite decades of study, questions remain about the interplay of electronic and vibrational states within the Q-band and its effect on the photoexcited dynamics. Here we report results of polarized two-dimensional electronic spectroscopic measurements, performed on penta-coordinated Bchl a and Chl a and their interpretation based on state-of-the-art time-dependent density functional theory calculations and vibrational mode analysis for spectral shapes. We find that the Q-band of Bchl a is comprised of two independent bands, that are assigned following the Gouterman model to Q x and Q y states with orthogonal transition dipole moments. However, we measure the angle to be ∼75°, a finding that is confirmed by ab initio calculations. The internal conversion rate constant from Q x to Q y is found to be 11 ps-1. Unlike Bchl a, the Q-band of Chl a contains three distinct peaks with different polarizations. Ab initio calculations trace these features back to a spectral overlap between two electronic transitions and their vibrational replicas. The smaller energy gap and the mixing of vibronic states result in faster internal conversion rate constants of 38-50 ps-1. We analyze the spectra of penta-coordinated Bchl a and Chl a to highlight the interplay between low-lying vibronic states and their relationship to photoinduced relaxation. Our findings shed new light on the photoexcited dynamics in photosynthetic systems where these chromophores are primary pigments.
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Affiliation(s)
- Yin Song
- Department of Physics , University of Michigan , 450 Church St , Ann Arbor , MI 48109 , USA .
| | - Alexander Schubert
- Department of Chemistry , University of Michigan , 930 N University Ave , Ann Arbor , MI 48109 , USA
- Department of Chemistry and Biochemistry , Kent State University , 1175 Risman Drive , Kent , OH 44242 , USA
| | - Elizabeth Maret
- Applied Physics Program , University of Michigan , 450 Church St , Ann Arbor , MI 48109 , USA
| | - Ryan K Burdick
- Department of Chemistry , University of Michigan , 930 N University Ave , Ann Arbor , MI 48109 , USA
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry , Kent State University , 1175 Risman Drive , Kent , OH 44242 , USA
| | - Eitan Geva
- Department of Chemistry , University of Michigan , 930 N University Ave , Ann Arbor , MI 48109 , USA
| | - Jennifer P Ogilvie
- Department of Physics , University of Michigan , 450 Church St , Ann Arbor , MI 48109 , USA .
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24
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Chojecki M, Rutkowska-Zbik D, Korona T. Dimerization Behavior of Methyl Chlorophyllide a as the Model of Chlorophyll a in the Presence of Water Molecules-Theoretical Study. J Chem Inf Model 2019; 59:2123-2140. [PMID: 30998013 DOI: 10.1021/acs.jcim.8b00984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A dimerization of methyl chlorophyllide a molecules and a role of water in stabilization and properties of methyl chlorophyllide a dimers were studied by means of symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), density-functional theory (DFT), and time-dependent DFT approaches. The quantification of various types of interactions, such as π-π stacking, coordinative, and hydrogen bonding by applying the F-SAPT energy decomposition scheme shows the major role of the magnesium atom and the pheophytin macrocycle in the stability of the complex. The examination of interaction energy components with respect to a mutual orientation of monomers and in the presence or absence of water molecules reveals that the dispersion energy is the main binding factor of the interaction, while water molecules tend to weaken the attraction between methyl chlorophyllide a species. The dimerization can be seen in computed UV-vis spectra, and results in a doubling of the lowest peaks, as compared to the monomer spectrum, and in an intensity rise of the lowest 1.8 and 2.4 eV peaks at a cost of the 3.5 eV peaks for the majority of dimer configurations. The complexation of water has little effect on the peaks' position; however, it affects the overall shape of simulated spectra through changes in peak intensities, which is strongly dependent on the structure of the complex. The VCD spectra for the dimers show several characteristic features attributed to the interaction of substituting groups and/or water ligand attached to macrocycle groups belonging to different monomers. VCD is sensitive to the type of the formed dimer, but not to the number of water molecules it contains. This and several other features, as well as the differential UV-vis spectra, may serve as the indicator of the presence of a given dimer structure in the experiment.
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Affiliation(s)
- Michał Chojecki
- Faculty of Chemistry , University of Warsaw , ul. Pasteura 1 , 02-093 Warsaw , Poland
| | - Dorota Rutkowska-Zbik
- Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , ul. Niezapominajek 8 , 30-239 Cracow , Poland
| | - Tatiana Korona
- Faculty of Chemistry , University of Warsaw , ul. Pasteura 1 , 02-093 Warsaw , Poland
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25
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Fujihashi Y, Higashi M, Ishizaki A. Intramolecular Vibrations Complement the Robustness of Primary Charge Separation in a Dimer Model of the Photosystem II Reaction Center. J Phys Chem Lett 2018; 9:4921-4929. [PMID: 30095266 DOI: 10.1021/acs.jpclett.8b02119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The energy conversion of oxygenic photosynthesis is triggered by primary charge separation in proteins at the photosystem II reaction center. Here, we investigate the impacts of the protein environment and intramolecular vibrations on primary charge separation at the photosystem II reaction center. This is accomplished by combining the quantum dynamic theories of condensed phase electron transfer with quantum chemical calculations to evaluate the vibrational Huang-Rhys factors of chlorophyll and pheophytin molecules. We report that individual vibrational modes play a minor role in promoting charge separation, contrary to the discussion in recent publications. Nevertheless, these small contributions accumulate to considerably influence the charge separation rate, resulting in subpicosecond charge separation almost independent of the driving force and temperature. We suggest that the intramolecular vibrations complement the robustness of the charge separation in the photosystem II reaction center against the inherently large static disorder of the involved electronic energies.
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Affiliation(s)
- Yuta Fujihashi
- Institute for Molecular Science , National Institutes of Natural Sciences , Okazaki 444-8585 , Japan
| | - Masahiro Higashi
- Department of Chemistry, Biology, and Marine Science , University of the Ryukyus , 1 Senbaru , Nishihara , Okinawa 903-0213 , Japan
| | - Akihito Ishizaki
- Institute for Molecular Science , National Institutes of Natural Sciences , Okazaki 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki 444-8585 , Japan
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