Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities, and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system along with the computed site-dependent spectral densities was used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained, which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areas of molecular dynamics simulations, quantum chemistry, and open quantum systems, it is possible to obtain first-principle results for photosynthetic complexes, which are in accord with experimental findings.
REFERENCES
1.
Y.-C.
Cheng
and G. R.
Fleming
, “Dynamics of light harvesting in photosynthesis
,” Annu. Rev. Phys. Chem.
60
, 241
(2009
).2.
G. D.
Scholes
, G. R.
Fleming
, A.
Olaya-Castro
, and R.
van Grondelle
, “Lessons from nature about solar light harvesting
,” Nat. Chem.
3
, 763
(2011
).3.
T.
Mirkovic
, E. E.
Ostroumov
, J. M.
Anna
, R.
van Grondelle
, Govindjee
, and G. D.
Scholes
, “Light absorption and energy transfer in the antenna complexes of photosynthetic organisms
,” Chem. Rev.
117
, 249
(2017
).4.
V.
Krewald
, M.
Retegan
, N.
Cox
, J.
Messinger
, W.
Lubitz
, S.
DeBeer
, F.
Neese
, and D. A.
Pantazis
, “Metal oxidation states in biological water splitting
,” Chem. Sci.
6
, 1676
(2015
).5.
H.
van Amerongen
and R.
Croce
, “Light harvesting in photosystem II
,” Photosynth. Res.
116
, 251
(2013
).6.
7.
N.
Kamiya
and J.-R.
Shen
, “Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-Å resolution
,” Proc. Natl. Acad. Sci. U. S. A.
100
, 98
(2003
).8.
Y.
Umena
, K.
Kawakami
, J.-R.
Shen
, and N.
Kamiya
, “Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å
,” Nature
473
, 55
(2011
).9.
M. L.
Groot
, J. P.
Dekker
, R.
Van Grondelle
, F. T. H.
Den Hartog
, and S.
Völker
, “Energy transfer and trapping in isolated photosystem II reaction centers of green plants at low temperature. A study by spectral hole burning
,” J. Phys. Chem.
100
, 11488
(1996
).10.
T.
Renger
and E.
Schlodder
, “Optical properties, excitation energy and primary charge transfer in photosystem II: Theory meets experiment
,” J. Photochem. Photobiol., B
104
, 126
(2011
).11.
D. I. G.
Bennett
, K.
Amarnath
, and G. R.
Fleming
, “A structure-based model of energy transfer reveals the principles of light harvesting in photosystem II supercomplexes
,” J. Am. Chem. Soc.
135
, 9164
(2013
).12.
S.-T.
Hsieh
, L.
Zhang
, D.-W.
Ye
, X.
Huang
, and Y.-C.
Cheng
, “A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: Regulation and robustness of energy transfer pathways
,” Faraday Discuss.
216
, 94
(2019
).13.
F.
Müh
and A.
Zouni
, “Structural basis of light-harvesting in the photosystem II core complex
,” Protein Sci.
29
, 1090
(2020
).14.
R.
Croce
and H.
van Amerongen
, “Light harvesting in oxygenic photosynthesis: Structural biology meets spectroscopy
,” Science
369
, eaay2058
(2020
).15.
E.
Cignoni
, V.
Slama
, L.
Cupellini
, and B.
Mennucci
, “The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol
,” J. Chem. Phys.
156
, 120901
(2022
).16.
G.
Raszewski
and T.
Renger
, “Light harvesting in photosystem II core complexes is limited by the transfer to the trap: Can the core complex turn into a photoprotective mode?
,” J. Am. Chem. Soc.
130
, 4431
(2008
).17.
L.
Cupellini
, S.
Jurinovich
, I. G.
Prandi
, S.
Caprasecca
, and B.
Mennucci
, “Photoprotection and triplet energy transfer in higher plants: The role of electronic and nuclear fluctuations
,” Phys. Chem. Chem. Phys.
18
, 11288
(2016
).18.
V.
Mascoli
, V.
Novoderezhkin
, N.
Liguori
, P.
Xu
, and R.
Croce
, “Design principles of solar light harvesting in plants: Functional architecture of the monomeric antenna CP29
,” Biochim. Biophys. Acta, Bioenerg.
1861
, 148156
(2020
).19.
E.
Cignoni
, M.
Lapillo
, L.
Cupellini
, S.
Acosta-Gutiérrez
, F. L.
Gervasio
, and B.
Mennucci
, “A different perspective for nonphotochemical quenching in plant antenna complexes
,” Nat. Commun.
12
, 7152
(2021
).20.
S.
Maity
, V.
Daskalakis
, M.
Elstner
, and U.
Kleinekathöfer
, “Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II
,” Phys. Chem. Chem. Phys.
23
, 7407
(2021
).21.
M. K.
Sener
, D.
Lu
, T.
Ritz
, S.
Park
, P.
Fromme
, and K.
Schulten
, “Robustness and optimality of light harvesting in cyanobacterial photosystem I
,” J. Phys. Chem. B
106
, 7948
(2002
).22.
M.-L.
Groot
, R. N.
Frese
, F. L.
de Weerd
, K.
Bromek
, Å.
Pettersson
, E. J. G.
Peterman
, I. H. M.
van Stokkum
, R.
van Grondelle
, and J. P.
Dekker
, “Spectroscopic properties of the CP43 core antenna protein of photosystem II
,” Biophys. J.
77
, 3328
(1999
).23.
F. L.
De Weerd
, I. H. M.
van Stokkum
, H.
van Amerongen
, J. P.
Dekker
, and R.
van Grondelle
, “Pathways for energy transfer in the core light-harvesting complexes CP43 and CP47 of photosystem II
,” Biophys. J.
82
, 1586
(2002
).24.
M.
Di Donato
, R.
van Grondelle
, I. H. M.
van Stokkum
, and M. L.
Groot
, “Excitation energy transfer in the photosystem II core antenna complex CP43 studied by femtosecond visible/visible and visible/mid-infrared pump probe spectroscopy
,” J. Phys. Chem. B
111
, 7345
(2007
).25.
A. P.
Casazza
, M.
Szczepaniak
, M. G.
Müller
, G.
Zucchelli
, and A. R.
Holzwarth
, “Energy transfer processes in the isolated core antenna complexes CP43 and CP47 of photosystem II
,” Biochim. Biophys. Acta, Bioenerg.
1797
, 1606
(2010
).26.
R.
Jankowiak
, V.
Zazubovich
, M.
Rätsep
, S.
Matsuzaki
, M.
Alfonso
, R.
Picorel
, M.
Seibert
, and G. J.
Small
, “The CP43 core antenna complex of photosystem II possesses two quasi-degenerate and weakly coupled Qy-trap states
,” J. Phys. Chem. B
104
, 11805
(2000
).27.
G.
Raszewski
, W.
Saenger
, and T.
Renger
, “Theory of optical spectra of photosystem II reaction centers: Location of the triplet state and the identity of the primary electron donor
,” Biophys. J.
88
, 986
(2005
).28.
V.
Zazubovich
and R.
Jankowiak
, “On the energy transfer between quasi-degenerate states with uncorrelated site distribution functions: An application to the CP43 complex of photosystem II
,” J. Lumin.
127
, 245
(2007
).29.
M.
Reppert
, V.
Zazubovich
, N. C.
Dang
, M.
Seibert
, and R.
Jankowiak
, “Low-energy chlorophyll states in the CP43 antenna protein complex: Simulation of various optical spectra. II
,” J. Phys. Chem. B
112
, 9934
(2008
).30.
N. C.
Dang
, V.
Zazubovich
, M.
Reppert
, B.
Neupane
, R.
Picorel
, M.
Seibert
, and R.
Jankowiak
, “The CP43 proximal antenna complex of higher plant photosystem II revisited: Modeling and hole burning study. I
,” J. Phys. Chem. B
112
, 9921
(2008
).31.
F.
Müh
, M. E.-A.
Madjet
, and T.
Renger
, “Structure-based simulation of linear optical spectra of the CP43 core antenna of photosystem II
,” Photosynth. Res.
111
, 87
(2012
).32.
F.
Müh
, M.
Plöckinger
, H.
Ortmayer
, M.
Schmidt am Busch
, D.
Lindorfer
, J.
Adolphs
, and T.
Renger
, “The quest for energy traps in the CP43 Antenna of photosystem II
,” J. Photochem. Photobiol., B
152
, 286
(2015
).33.
S.
Vasil’ev
and D.
Bruce
, “A protein dynamics study of photosystem II: The effects of protein conformation on reaction center function
,” Biophys. J.
90
, 3062
(2006
).34.
S.
Maity
, A.
Gelessus
, V.
Daskalakis
, and U.
Kleinekathöfer
, “On a chlorophyll-caroteinoid coupling in LHCII
,” Chem. Phys.
526
, 110439
(2019
).35.
V.
May
and O.
Kühn
, Charge and Energy Transfer in Molecular Systems
, 3rd ed. (Wiley-VCH
, 2011
).36.
A.
Damjanović
, I.
Kosztin
, U.
Kleinekathöfer
, and K.
Schulten
, “Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry and polaron model study
,” Phys. Rev. E
65
, 031919
(2002
).37.
C.
Olbrich
and U.
Kleinekathöfer
, “Time-dependent atomistic view on the electronic relaxation in light-harvesting system II
,” J. Phys. Chem. B
114
, 12427
(2010
).38.
C.
Olbrich
, J.
Strümpfer
, K.
Schulten
, and U.
Kleinekathöfer
, “Theory and simulation of the environmental effects on FMO electronic transitions
,” J. Phys. Chem. Lett.
2
, 1771
(2011
).39.
M.
Aghtar
, J.
Strümpfer
, C.
Olbrich
, K.
Schulten
, and U.
Kleinekathöfer
, “Different types of vibrations interacting with electronic excitations in phycoerythrin 545 and Fenna-Matthews-Olson antenna systems
,” J. Phys. Chem. Lett.
5
, 3131
(2014
).40.
J.
Gao
, W.-J.
Shi
, J.
Ye
, X.
Wang
, H.
Hirao
, and Y.
Zhao
, “QM/MM modeling of environmental effects on electronic transitions of the FMO complex
,” J. Phys. Chem. B
117
, 3488
(2013
).41.
S.
Shim
, P.
Rebentrost
, S.
Valleau
, and A.
Aspuru-Guzik
, “Atomistic study of the long-lived quantum coherences in the Fenna-Matthew-Olson complex
,” Biophys. J.
102
, 649
(2012
).42.
S.
Chandrasekaran
, M.
Aghtar
, S.
Valleau
, A.
Aspuru-Guzik
, and U.
Kleinekathöfer
, “Influence of force fields and quantum chemistry approach on spectral densities of BChl a in solution and in FMO proteins
,” J. Phys. Chem. B
119
, 9995
(2015
).43.
S.
Jurinovich
, L.
Viani
, C.
Curutchet
, and B.
Mennucci
, “Limits and potentials of quantum chemical methods in modelling photosynthetic antennae
,” Phys. Chem. Chem. Phys.
17
, 30783
(2015
).44.
M. K.
Lee
and D. F.
Coker
, “Modeling electronic-nuclear interactions for excitation energy transfer processes in light-harvesting complexes
,” J. Phys. Chem. Lett.
7
, 3171
(2016
).45.
D.
Padula
, M. H.
Lee
, K.
Claridge
, and A.
Troisi
, “Chromophore-dependent intramolecular exciton-vibrational coupling in the FMO complex: Quantification and importance for exciton dynamics
,” J. Phys. Chem. B
121
, 10026
(2017
).46.
C.
Curutchet
and B.
Mennucci
, “Quantum chemical studies of light harvesting
,” Chem. Rev.
117
, 294
(2017
).47.
C. W.
Kim
, B.
Choi
, and Y. M.
Rhee
, “Excited state energy fluctuations in the Fenna-Matthews-Olson complex from molecular dynamics simulations with interpolated chromophore potentials
,” Phys. Chem. Chem. Phys.
20
, 3310
(2018
).48.
B.
Mennucci
and S.
Corni
, “Multiscale modelling of photoinduced processes in composite systems
,” Nat. Rev. Chem.
3
, 315
(2019
).49.
F.
Segatta
, L.
Cupellini
, M.
Garavelli
, and B.
Mennucci
, “Quantum chemical modeling of the photoinduced activity of multichromophoric biosystems
,” Chem. Rev.
119
, 9361
(2019
).50.
S.
Maity
, B. M.
Bold
, J. D.
Prajapati
, M.
Sokolov
, T.
Kubař
, M.
Elstner
, and U.
Kleinekathöfer
, “DFTB/MM molecular dynamics simulations of the FMO light-harvesting complex
,” J. Phys. Chem. Lett.
11
, 8660
(2020
).51.
S.
Maity
, P.
Sarngadharan
, V.
Daskalakis
, and U.
Kleinekathöfer
, “Time-dependent atomistic simulations of the CP29 light-harvesting complex
,” J. Chem. Phys.
155
, 055103
(2021
).52.
M.
Elstner
, D.
Porezag
, G.
Jungnickel
, J.
Elsner
, M.
Haugk
, T.
Frauenheim
, S.
Suhai
, and G.
Seifert
, “Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
,” Phys. Rev. B
58
, 7260
(1998
).53.
B. M.
Bold
, M.
Sokolov
, S.
Maity
, M.
Wanko
, P. M.
Dohmen
, J. J.
Kranz
, U.
Kleinekathöfer
, S.
Höfener
, and M.
Elstner
, “Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes
,” Phys. Chem. Chem. Phys.
22
, 10500
(2020
).54.
L.
Chen
, R.
Zheng
, Q.
Shi
, and Y.
Yan
, “Optical line shapes of molecular aggregates: Hierarchical equations of motion method
,” J. Chem. Phys.
131
, 094502
(2009
).55.
A.
Ishizaki
and G. R.
Fleming
, “Unified treatment of quantum coherent and incoherent hopping dynamics in electronic energy transfer: Reduced hierarchy equation approach
,” J. Chem. Phys.
130
, 234111
(2009
).56.
T. J.
Zuehlsdorff
, A.
Montoya-castillo
, J. A.
Napoli
, T. E.
Markland
, and C. M.
Isborn
, “Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches
,” J. Chem. Phys.
151
, 074111
(2019
).57.
A.
Ishizaki
and G. R.
Fleming
, “On the adequacy of the Redfield equation and related approaches to the study of quantum dynamics in electronic energy transfer
,” J. Chem. Phys.
130
, 234110
(2009
).58.
V. I.
Novoderezhkin
and R.
van Grondelle
, “Physical origins and models of energy transfer in photosynthetic light-harvesting
,” Phys. Chem. Chem. Phys.
12
, 7352
(2010
).59.
T.
Renger
and F.
Müh
, “Understanding photosynthetic light-harvesting: A bottom up theoretical approach
,” Phys. Chem. Chem. Phys.
15
, 3348
(2013
).60.
M.
Schröder
, M.
Schreiber
, and U.
Kleinekathöfer
, “A time-dependent modified Redfield theory for absorption spectra applied to light-harvesting systems
,” J. Lumin.
125
, 126
(2007
).61.
A.
Gelzinis
, D.
Abramavicius
, and L.
Valkunas
, “Absorption lineshapes of molecular aggregates revisited
,” J. Chem. Phys.
142
, 154107
(2015
).62.
T.-C.
Dinh
and T.
Renger
, “Lineshape theory of pigment-protein complexes: How the finite relaxation time of nuclei influences the exciton relaxation-induced lifetime broadening
,” J. Chem. Phys.
145
, 034105
(2016
).63.
J.
Ma
and J.
Cao
, “Förster resonance energy transfer, absorption and emission spectra in multichromophoric systems. I. Full cumulant expansions and system-bath entanglement
,” J. Chem. Phys.
142
, 094106
(2015
).64.
L.
Cupellini
, F.
Lipparini
, and J.
Cao
, “Absorption and circular dichroism spectra of molecular aggregates with the full cumulant expansion
,” J. Phys. Chem. B
124
, 8610
(2020
).65.
B.
Webb
and A.
Sali
, “Comparative protein structure modeling using MODELLER
,” Curr. Protoc. Bioinf.
54
, 5
(2016
).66.
S.
Jo
, T.
Kim
, V. G.
Iyer
, and W.
Im
, “CHARMM-GUI: A web-based graphical user interface for CHARMM
,” J. Comput. Chem.
29
, 1859
(2008
).67.
L.
Zhang
, D.-A.
Silva
, Y.
Yan
, and X.
Huang
, “Force field development for cofactors in the photosystem II
,” J. Comput. Chem.
33
, 1969
(2012
).68.
A. W.
Sousa da Silva
and W. F.
Vranken
, “ACPYPE-Antechamber Python parser interface
,” BMC Res. Notes
5
, 367
(2012
).69.
C.
Olbrich
, J.
Strümpfer
, K.
Schulten
, and U.
Kleinekathöfer
, “Quest for spatially correlated fluctuations in the FMO light-harvesting complex
,” J. Phys. Chem. B
115
, 758
(2011
).70.
M.
Gaus
, A.
Goez
, and M.
Elstner
, “Parametrization and benchmark of DFTB3 for organic molecules
,” J. Chem. Theory Comput.
9
, 338
(2013
).71.
T.
Kubař
, K.
Welke
, and G.
Groenhof
, “New QM/MM implementation of the DFTB3 method in the gromacs package
,” J. Comput. Chem.
36
, 1978
(2015
).72.
B.
Hourahine
, B.
Aradi
, V.
Blum
, F.
Bonafé
, A.
Buccheri
, C.
Camacho
, C.
Cevallos
, M. Y.
Deshaye
, T.
Dumitrică
, A.
Dominguez
, S.
Ehlert
, M.
Elstner
, T.
Van Der Heide
, J.
Hermann
, S.
Irle
, J. J.
Kranz
, C.
Köhler
, T.
Kowalczyk
, T.
Kubař
, I. S.
Lee
, V.
Lutsker
, R. J.
Maurer
, S. K.
Min
, I.
Mitchell
, C.
Negre
, T. A.
Niehaus
, A. M. N.
Niklasson
, A. J.
Page
, A.
Pecchia
, G.
Penazzi
, M. P.
Persson
, J.
Řezáč
, C. G.
Sánchez
, M.
Sternberg
, M.
Stöhr
, F.
Stuckenberg
, A.
Tkatchenko
, V. W.-Z.
Yu
, and T.
Frauenheim
, “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations
,” J. Chem. Phys.
152
, 124101
(2020
).73.
J. J.
Kranz
, M.
Elstner
, B.
Aradi
, T.
Frauenheim
, V.
Lutsker
, A. D.
Garcia
, and T. A.
Niehaus
, “Time-dependent extension of the long-range corrected density functional based tight-binding method
,” J. Chem. Theory Comput.
13
, 1737
(2017
).74.
G. S.
Engel
, T. R.
Calhoun
, E. L.
Read
, T.-K.
Ahn
, T.
Mančal
, Y.-C.
Cheng
, R. E.
Blankenship
, and G. R.
Fleming
, “Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems
,” Nature
446
, 782
(2007
).75.
C.
Olbrich
, T. L. C.
Jansen
, J.
Liebers
, M.
Aghtar
, J.
Strümpfer
, K.
Schulten
, J.
Knoester
, and U.
Kleinekathöfer
, “From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex
,” J. Phys. Chem. B
115
, 8609
(2011
).76.
L.
Zhang
, D.-A.
Silva
, H.
Zhang
, A.
Yue
, Y.
Yan
, and X.
Huang
, “Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre
,” Nat. Commun.
5
, 4170
(2014
).77.
N.
Liguori
, X.
Periole
, S. J.
Marrink
, and R.
Croce
, “From light-harvesting to photoprotection: Structural basis of the dynamic switch of the major antenna complex of plants (LHCII)
,” Sci. Rep.
5
, 15661
(2015
).78.
M.
Aghtar
, U.
Kleinekathöfer
, C.
Curutchet
, and B.
Mennucci
, “Impact of electronic fluctuations and their description on the exciton dynamics in the light-harvesting complex PE545
,” J. Phys. Chem. B
121
, 1330
(2017
).79.
J.
Adolphs
, F.
Müh
, M. E.-A.
Madjet
, and T.
Renger
, “Calculation of pigment transition energies in the fmo protein: From simplicity to complexity and back
,” Photosynth. Res.
95
, 197
(2008
).80.
J.
Adolphs
, F.
Müh
, M. E.-A.
Madjet
, M.
Schmidt am Busch
, and T.
Renger
, “Structure-based calculations of optical spectra of photosystem I suggest an asymmetric light-harvesting process
,” J. Am. Chem. Soc.
132
, 3331
(2010
).81.
C.
Curutchet
, G. D.
Scholes
, B.
Mennucci
, and R.
Cammi
, “How solvent controls electronic energy transfer and light harvesting: Toward a quantum-mechanical description of reaction field and screening effects
,” J. Phys. Chem. B
111
, 13253
(2007
).82.
G. D.
Scholes
, C.
Curutchet
, B.
Mennucci
, R.
Cammi
, and J.
Tomasi
, “How solvent controls electronic energy transfer and light harvesting
,” J. Phys. Chem. B
111
, 6978
(2007
).83.
T.
Renger
and F.
Müh
, “Theory of excitonic couplings in dielectric media: Foundation of Poisson-TrEsp method and application to photosystem I trimers
,” Photosynth. Res.
111
, 47
(2012
).84.
M.
Schröder
, U.
Kleinekathöfer
, and M.
Schreiber
, “Calculation of absorption spectra for light-harvesting systems using non-Markovian approaches as well as modified Redfield theory
,” J. Chem. Phys.
124
, 084903
(2006
).85.
J.
Cao
, R. J.
Cogdell
, D. F.
Coker
, H.-G.
Duan
, J.
Hauer
, U.
Kleinekathöfer
, T. L. C.
Jansen
, T.
Mančal
, R. J. D.
Miller
, J. P.
Ogilvie
, V. I.
Prokhorenko
, T.
Renger
, H.-S.
Tan
, R.
Tempelaar
, M.
Thorwart
, E.
Thyrhaug
, S.
Westenhoff
, and D.
Zigmantas
, “Quantum biology revisited
,” Sci. Adv.
6
, eaaz4888
(2020
).86.
L.
Cupellini
and F.
Lipparini
(2020
). “FCE program to compute optical spectra with the full cumulant expansion
,” OpenAIRE. 10.5281/ZENODO.390019987.
V. I.
Novoderezhkin
, M. A.
Palacios
, H.
van Amerongen
, and R.
van Grondelle
, “Energy-transfer dynamics in the LHCII complex of higher plants: Modified Redfield approach
,” J. Phys. Chem. B
108
, 10363
(2004
).88.
V. I.
Novoderezhkin
, M. A.
Palacios
, H.
van Amerongen
, and R.
van Grondelle
, “Excitation dynamics in the LHCII complex of higher plants: Modeling based on the 2.72 Å crystal structure
,” J. Phys. Chem. B
109
, 10493
(2005
).89.
F.
Müh
, M. E.-A.
Madjet
, and T.
Renger
, “Structure-based identification of energy sinks in plant light-harvesting complex II
,” J. Phys. Chem. B
114
, 13517
(2010
).90.
D.
Loco
, S.
Jurinovich
, L.
Cupellini
, M. F. S. J.
Menger
, and B.
Mennucci
, “The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach
,” Photochem. Photobiol. Sci.
17
, 552
(2018
).91.
V.
Sláma
, L.
Cupellini
, and B.
Mennucci
, “Exciton properties and optical spectra of light harvesting complex II from a fully atomistic description
,” Phys. Chem. Chem. Phys.
22
, 16783
(2020
).92.
O.
Rancova
and D.
Abramavicius
, “Static and dynamic disorder in bacterial light-harvesting complex LH2: A 2DES simulation study
,” J. Phys. Chem. B
118
, 7533
(2014
).93.
D.
Loco
and L.
Cupellini
, “Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review
,” Int. J. Quantum Chem.
119
, e25726
(2018
).94.
A.
Singharoy
, C.
Maffeo
, K. H.
Delgado-Magnero
, D. J. K.
Swainsbury
, M.
Sener
, U.
Kleinekathöfer
, J. W.
Vant
, J.
Nguyen
, A.
Hitchcock
, B.
Isralewitz
, I.
Teo
, D. E.
Chandler
, J. E.
Stone
, J. C.
Phillips
, T. V.
Pogorelov
, M. I.
Mallus
, C.
Chipot
, Z.
Luthey-Schulten
, D. P.
Tieleman
, C. N.
Hunter
, E.
Tajkhorshid
, A.
Aksimentiev
, and K.
Schulten
, “Atoms to phenotypes: Molecular design principles of cellular energy metabolism
,” Cell
179
, 1098
(2019
).© 2022 Author(s). Published under an exclusive license by AIP Publishing.
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