Challenges facing an understanding of the nature of low-energy excited states in photosynthesis
Tài liệu tham khảo
Blankenship, 2014
Scholes, 2011, Lessons from nature about solar light harvesting, Nat. Chem., 3, 763, 10.1038/nchem.1145
Scholes, 2011, Quantum biology: coherence in photosynthesis, Nat. Phys., 7, 448, 10.1038/nphys2013
Pullerits, 2013, Beatings in electronic 2D spectroscopy suggest another role of vibrations in photosynthetic light harvesting, Proc. Natl. Acad. Sci. U. S. A., 110, 1148, 10.1073/pnas.1221058110
Miller, 2012, Perspective: quantum or classical coherence?, J. Chem. Phys., 136, 210901, 10.1063/1.4727849
Strümpfer, 2012, How quantum coherence assists photosynthetic light-harvesting, J. Phys. Chem. Lett., 3, 536, 10.1021/jz201459c
Kreisbeck, 2012, Long-lived electronic coherence in dissipative exciton dynamics of light-harvesting complexes, J. Phys. Chem. Lett., 3, 2828, 10.1021/jz3012029
Milder, 2010, Revisiting the optical properties of the FMO protein, Photosynth. Res., 104, 257, 10.1007/s11120-010-9540-1
Raszewski, 2005, 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, 10.1529/biophysj.104.050294
Novoderezhkin, 2007, Mixing of exciton and charge-transfer states in photosystem II reaction centers: modeling of stark spectra with modified redfield theory, Biophys. J., 93, 1293, 10.1529/biophysj.106.096867
Renger, 2011, Optical properties, excitation energy and primary charge transfer in photosystem II: theory meets experiment, J. Photochem. Photobiol. B, 104, 126, 10.1016/j.jphotobiol.2011.03.016
Yano, 2014, Mn4Ca cluster in photosynthesis: where and how water is oxidized to dioxygen, Chem. Rev., 114, 4175, 10.1021/cr4004874
Morton, 2015, Optical identification of the long-wavelength (700–1700nm) electronic excitations of the native reaction centre, Mn4CaO5 cluster and cytochromes of photosystem II in plants and cyanobacteria, Biochim. Biophys. Acta Bioenerg., 1847, 153, 10.1016/j.bbabio.2014.11.003
Demmig-Adams, 2014
Jennings, 1991, Light-induced fluorescence quenching in the light-harvesting chlorophyll a/B protein complex, Photosynth. Res., 27, 57, 10.1007/BF00029976
Barzda, 1996, Structural flexibility of chiral macroaggregates of light-harvesting chlorophyll a/b pigment-protein complexes. Light-induced reversible structural changes associated with energy dissipation, Biochemistry, 35, 8981, 10.1021/bi960114g
Barzda, 1999, Kinetic analysis of the light-induced fluorescence quenching in light-harvesting chlorophyll a/b pigment-protein complex of photosystem II, Photochem. Photobiol., 70, 751, 10.1562/0031-8655(1999)070<0751:KAOTLI>2.3.CO;2
Zer, 1999, Regulation of thylakoid protein phosphorylation at the substrate level: reversible light-induced conformational changes expose the phosphorylation site of the light-harvesting complex II, Proc. Natl. Acad. Sci. U. S. A., 96, 8277, 10.1073/pnas.96.14.8277
Hind, 2014, Membrane crystals of plant light-harvesting complex II disassemble reversibly in light, Plant Cell Physiol., 55, 1296, 10.1093/pcp/pcu064
Iwai, 2014, Visualizing structural dynamics of thylakoid membranes, Sci. Rep., 4, 10.1038/srep03768
Ruban, 2015, Visualizing the dynamic structure of the plant photosynthetic membrane, Nat. Plants, 1, 10.1038/nplants.2015.161
Janik, 2013, Molecular architecture of plant thylakoids under physiological and light stress conditions: a study of lipid–light-harvesting complex II model membranes, Plant Cell, 25, 2155, 10.1105/tpc.113.113076
Adams, 2014, Lessons From Nature: A Personal Perspective, 45
Croce, 1998, A thermal broadening study of the antenna chlorophylls in PSI-200, LHCI, and PSI core, Biochemistry, 37, 17355, 10.1021/bi9813227
Novoderezhkin, 2016, Mixing of exciton and charge-transfer states in light-harvesting complex Lhca4, Phys. Chem. Chem. Phys., 10.1039/C6CP02225A
Hush, 1967, Intervalence-transfer absorption. II. Theoretical considerations and spectroscopic data, Prog. Inorg. Chem., 8, 391
Reimers, 1995, The nature of the near-infrared electronic absorption at 1250nm in the spectra of the radical cations of the special pairs in the photosynthetic reaction centres of Rhodobacter sphaeroides and Rhodopseudomonas viridis, J. Am. Chem. Soc., 117, 1302, 10.1021/ja00109a013
Reimers, 2003, Modelling the bacterial photosynthetic reaction centre: 5. Assignment of the electronic transition observed at 2200cm−1 in the special-pair radical-cation as a SHOMO to HOMO transition, J. Chem. Phys., 119, 3240, 10.1063/1.1569909
Reimers, 2004, Understanding the observed Stark spectra, midpoint potential versus degree of charge localization, and intervalence transition energies of the special-pair radical cation of Rhodobacter sphaeroides and its mutant strains, J. Am. Chem. Soc., 126, 4132, 10.1021/ja036883m
Kanchanawong, 2006, Charge delocalization in the special pair radical cation of mutant reaction centers of rhodobacter sphaeroides from stark spectra and non-adiabatic spectral simulations, J. Phys. Chem. B, 110, 18688, 10.1021/jp0623894
Reimers, 2013, Assignment of the Q-bands of the chlorophylls: coherence loss via Qx - Qy mixing, Sci. Rep., 3, 2761, 10.1038/srep02761
Kell, 2013, On the shape of the phonon spectral density in photosynthetic complexes, J. Phys. Chem. B, 117, 7317, 10.1021/jp405094p
Renger, 2002, On the relation of protein dynamics and exciton relaxation in pigment-protein complexes: an estimation of the spectral density and a theory for the calculation of optical spectra, J. Chem. Phys., 116, 9997, 10.1063/1.1470200
Zazubovich, 2015, Biophotonics of Photosynthesis, 129
Schlodder, 2007, Steady-state and transient polarized absorption spectroscopy of photosytem I complexes from the cyanobacteria Arthrospira platensis and Thermosynechococcus elongatus, Biochim. Biophys. Acta Bioenerg., 1767, 732, 10.1016/j.bbabio.2007.01.013
Yin, 2007, Assignment of the Qy absorption spectrum of photosystem-I from Thermosynechococcus elongatus based on CAM-B3LYP calculations at the PW91-optimized protein structure, J. Phys. Chem. B, 111, 9923, 10.1021/jp070030p
Gobets, 2003, Excitation wavelength dependence of the fluorescence kinetics in photosystem I particles from synechocystis PCC 6803 and Synechococcus elongatus, Biophys. J., 85, 3883, 10.1016/S0006-3495(03)74803-6
Adolphs, 2010, Structure-based calculations of optical spectra of photosystem I suggest an asymmetric light-harvesting process, J. Am. Chem. Soc., 132, 3331, 10.1021/ja9072222
Zazubovich, 2002, Red antenna states of photosystem I from cyanobacterium Synechococcus elongatus: a spectral hole burning study, Chem. Phys., 275, 47, 10.1016/S0301-0104(01)00535-3
Hayes, 2000, Red Chlorophyll a antenna states of photosystem I of the cyanobacterium Synechocystis sp. PCC 6803, J. Phys. Chem. B, 104, 5625, 10.1021/jp000447u
Rätsep, 2000, The red-absorbing chlorophyll a antenna states of photosystem I: a hole-burning study of Synechocystis sp. PCC 6803 and its mutants, J. Phys. Chem. B, 104, 836, 10.1021/jp9929418
Hsin, 2004, Red antenna states of PS I of cyanobacteria: stark effect and interstate energy transfer†, J. Phys. Chem. B, 108, 10515, 10.1021/jp049572m
Ihalainen, 2003, Red spectral forms of chlorophylls in green plant PSI - a site-selective and high-pressure spectroscopy study, J. Phys. Chem. B, 107, 9086, 10.1021/jp034778t
Rivadossi, 1999, The importance of PS I chlorophyll red forms in light-harvesting by leaves, Photosynth. Res., 60, 209, 10.1023/A:1006236829711
Croce, 1996, Excited State Equilibration in the Photosystem I−Light-Harvesting I Complex: P700 Is Almost Isoenergetic with Its Antenna, Biochemistry, 35, 8572, 10.1021/bi960214m
Koehne, 1999, Spectroscopic and molecular characterization of a long wavelength absorbing antenna of Ostreobium sp, Biochim. Biophys. Acta Bioenerg., 1412, 94, 10.1016/S0005-2728(99)00061-4
Trissl, 1993, Long-wavelength absorbing antenna pigments and heterogeneous absorption bands concentrate excitons and increase absorption cross section, Photosynth. Res., 35, 247, 10.1007/BF00016556
Jordan, 2001, Three-dimensional structure of cyanobacterial photosystem I at 2.5Å resolution, Nature, 411, 909, 10.1038/35082000
Qin, 2015, Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex, Science, 348, 989, 10.1126/science.aab0214
Mazor, 2015, The structure of plant photosystem I super-complex at 2.8Å resolution, eLife, 4, e07433, 10.7554/eLife.07433
Raszewski, 2008, 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, 10.1021/ja7099826
Shibata, 2013, Photosystem II does not possess a simple excitation energy funnel: time-resolved fluorescence spectroscopy meets theory, J. Am. Chem. Soc., 135, 6903, 10.1021/ja312586p
Canfield, 2006, Density-functional geometry optimization of the 150000-atom photosystem-I trimer, J. Chem. Phys., 124, 024301, 10.1063/1.2148956
Madjet, 2009, Deciphering the influence of short-range electronic couplings on optical properties of molecular dimers: application to “Special Pairs” in photosynthesis, J. Phys. Chem. B, 113, 12603, 10.1021/jp906009j
Schlodder, 2014, Long-wavelength limit of photochemical energy conversion in photosystem I, J. Am. Chem. Soc., 136, 3904, 10.1021/ja412375j
Moqvist, 2014, Defining the far-red limit of photosystem I. The primary charge separation is functional to 840nm, J. Biol. Chem., 289, 24630, 10.1074/jbc.M114.555649
Frese, 2002, Electric field effects on red chlorophylls, β-carotenes and P700 in cyanobacterial photosystem I complexes, Biochim. Biophys. Acta Bioenerg., 1554, 180, 10.1016/S0005-2728(02)00242-6
Sundström, 1999, Photosynthetic light-harvesting: reconciling dynamics and structure of purple bacterial LH2 reveals function of photosynthetic unit, J. Phys. Chem. B, 103, 2327, 10.1021/jp983722+
Cogdell, 2006, The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes, Q. Rev. Biophys., 39, 227, 10.1017/S0033583506004434
Freiberg, 2012, A comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded LH2 light-harvesting complexes, Biochim. Biophys. Acta Bioenerg., 1817, 1471, 10.1016/j.bbabio.2011.11.019
Linnanto, 1999, Electronic states, absorption spectrum and circular dichroism spectrum of the photosynthetic bacterial LH2 antenna of Rhodopseudomonas acidophila as predicted by exciton theory and semiempirical calculations, J. Phys. Chem. B, 103, 8739, 10.1021/jp9848344
Ihalainen, 2001, Energy transfer in LH2 of Rhodospirillum Molischianum, studied by subpicosecond spectroscopy and configuration interaction exciton calculations, J. Phys. Chem. B, 105, 9849, 10.1021/jp010921b
Hong, 2004, Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering, Biophys. J., 86, 1082, 10.1016/S0006-3495(04)74183-1
Chen, 2005, Protein structural deformation induced lifetime shortening of photosynthetic bacteria light-harvesting complex LH2 excited state, Biophys. J., 88, 4262, 10.1529/biophysj.104.053868
Du, 2012, Photosynthetic bacterial light-harvesting antenna complexes adsorbed on silica nanoparticles revealed by silica shell-isolated Au nanoparticle-enhanced raman spectroscopy, J. Phys. Chem. C, 117, 6993, 10.1021/jp211841a
Wientjes, 2014, Strong antenna-enhanced fluorescence of a single light-harvesting complex shows photon antibunching, Nat. Commun., 5, 4236, 10.1038/ncomms5236
Wientjes, 2014, Nanoantenna enhanced emission of light-harvesting complex 2: the role of resonance, polarization, and radiative and non-radiative rates, Phys. Chem. Chem. Phys., 16, 24739, 10.1039/C4CP03636K
Papiz, 2003, The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 (A)over-circle resolution and 100K: new structural features and functionally relevant motions, J. Mol. Biol., 326, 1523, 10.1016/S0022-2836(03)00024-X
Freiberg, 2003, Self-trapped excitons in LH2 antenna complexes between 5K and ambient temperature, J. Phys. Chem. B, 107, 11510, 10.1021/jp0344848
Rätsep, 2014, Subtle spectral effects accompanying the assembly of bacteriochlorophylls into cyclic light harvesting complexes revealed by high-resolution fluorescence spectroscopy, J. Chem. Phys., 141, 155102, 10.1063/1.4897637
Timpmann, 2001, Short-range exciton couplings in LH2 photosynthetic antenna proteins studied by high hydrostatic pressure absorption spectroscopy, J. Phys. Chem. B, 105, 8436, 10.1021/jp003496f
Kunz, 2012, Exciton self trapping in photosynthetic pigment–protein complexes studied by single-molecule spectroscopy, J. Phys. Chem. B, 116, 11017, 10.1021/jp3040456
Pajusalu, 2015, Unified analysis of ensemble and single-complex optical spectral data from light-harvesting complex-2 chromoproteins for gaining deeper insight into bacterial photosynthesis, Phys. Rev. E, 92, 052709, 10.1103/PhysRevE.92.052709
Beekman, 1997, Characterization of the light-harvesting antennas of photosynthetic purple bacteria by stark spectroscopy. 1. LH1 antenna complex and the B820 subunit from Rhodospirillum rubrum, J. Phys. Chem. B, 101, 7284, 10.1021/jp963445b
Rätsep, 1998, Stark hole-burning studies of three photosynthetic complexes, J. Phys. Chem. B, 102, 4035, 10.1021/jp980421r
Rätsep, 1998, Stark hole-burning spectroscopy of a photosynthetic complex: LH2 of purple bacteria, Spectrochim. Acta A, 54, 1279, 10.1016/S1386-1425(98)00076-6
Ferretti, 2016, Dark states in the light-harvesting complex 2 revealed by two-dimensional electronic spectroscopy, Sci. Rep., 6, 10.1038/srep20834
Alden, 1997, Calculations of spectroscopic properties of the LH2 bacteriochlorophyll-protein antenna complex from Rhodopseudomonas acidophila, J. Phys. Chem. B, 101, 4667, 10.1021/jp970005r
Scholes, 1999, Ab initio molecular orbital calculations of electronic couplings in the LH2 bacterial light-harvesting complex of Rps. Acidophila, J. Phys. Chem. B, 103, 2543, 10.1021/jp9839753
Linnanto, 2011, Quantum chemical simulations of excited-state absorption spectra of photosynthetic bacterial reaction center and antenna complexes, J. Phys. Chem. B, 115, 5536, 10.1021/jp111340w
Liguori, 2015, From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII), Sci. Rep., 5, 15661, 10.1038/srep15661
Croce, 2011, Light-harvesting and structural organization of Photosystem II: From individual complexes to thylakoid membrane, J. Photochem. Photobiol. B, 104, 142, 10.1016/j.jphotobiol.2011.02.015
Ruban, 2012, The photoprotective molecular switch in the photosystem II antenna, Biochim. Biophys. Acta, 1817, 167, 10.1016/j.bbabio.2011.04.007
Akhtar, 2015, Pigment interactions in light-harvesting complex II in different molecular environments, J. Biol. Chem., 290, 4877, 10.1074/jbc.M114.607770
Pieper, 1999, Effects of aggregation on trimeric light-harvesting complex II of green plants: a hole-burning study, J. Phys. Chem. A, 103, 2422, 10.1021/jp983958d
Kell, 2014, Charge-transfer character of the low-energy Chl a Qyabsorption band in aggregated light harvesting complexes II, J. Phys. Chem. B, 118, 6086, 10.1021/jp501735p
Hughes, 1757, Charge separation in photosystem II core complexes induced by 690-730nm excitation at 1.7K, Biochim. Biophys. Acta, 2006, 841
Hughes, 2007, Novel characteristics of persistent spectral hole-burning and hole-filling in Photosystem II core complexes, J. Lumin., 127, 239, 10.1016/j.jlumin.2007.02.030
Wahadoszamen, 2012, Identification of two emitting sites in the dissipative state of the major light harvesting antenna, Phys. Chem. Chem. Phys., 14, 759, 10.1039/C1CP23059J
Holzwarth, 2009, Identification of two quenching sites active in the regulation of photosynthetic light harvesting studied by time-resolved fluorescence, Chem. Phys. Lett., 483, 262, 10.1016/j.cplett.2009.10.085
Miloslavina, 2008, Far-red fluorescence: a direct spectroscopic marker for LHCII oligomer formation in non-photochemical quenching, FEBS Lett., 582, 3625, 10.1016/j.febslet.2008.09.044
Müller, 2010, Singlet energy dissipation in the photosystem II light-harvesting complex does not involve energy transfer to carotenoids, ChemPhysChem, 11, 1289, 10.1002/cphc.200900852
Chmeliov, 2016, The nature of self-regulation in photosynthetic light-harvesting antenna, Nat. Plants, 2, 16045, 10.1038/nplants.2016.45
Liu, 2004, Crystal structure of spinach major light-harvesting complex at 2.72Å resolution, Nature, 428, 287, 10.1038/nature02373
Müh, 2010, Structure-based identification of energy sinks in plant light-harvesting complex II, J. Phys. Chem. B, 114, 13517, 10.1021/jp106323e
Novoderezhkin, 2010, Physical origins and models of energy transfer in photosynthetic light-harvesting, Phys. Chem. Chem. Phys., 12, 7352, 10.1039/c003025b
Müh, 2014, Towards a structure-based exciton Hamiltonian for the CP29 antenna of photosystem II, Phys. Chem. Chem. Phys., 16, 11848, 10.1039/C3CP55166K
Standfuss, 2005, Mechanisms of photoprotection and nonphotochemical quenching in pea light-harvesting complex at 2.5Å resolution, EMBO J., 24, 919, 10.1038/sj.emboj.7600585
Pan, 2011, Structural insights into energy regulation of light-harvesting complex CP29 from spinach, Nat. Struct. Mol. Biol., 18, 309, 10.1038/nsmb.2008
Müh, 2012, Refined structure-based simulation of plant light-harvesting complex II: Linear optical spectra of trimers and aggregates, Biochim. Biophys. Acta, 1817, 1446, 10.1016/j.bbabio.2012.02.016
Novoderezhkin, 2005, Excitation dynamics in the LHCII complex of higher plants: modeling based on the 2.72Å crystal structure, J. Phys. Chem. B, 109, 10493, 10.1021/jp044082f
Mozzo, 2008, Photoprotection in higher plants: the putative quenching site is conserved in all outer light-harvesting complexes of photosystem II, Biochim. Biophys. Acta, 1777, 1263, 10.1016/j.bbabio.2008.04.036
Renger, 2011, How the molecular structure determines the flow of excitation energy in plant light-harvesting complex II, J. Plant Physiol., 168, 1497, 10.1016/j.jplph.2011.01.004
Novoderezhkin, 2011, Intra- and inter-monomeric transfers in the light harvesting LHCII complex: the Redfield-Forster picture, Phys. Chem. Chem. Phys., 13, 17093, 10.1039/c1cp21079c
Marin, 2012, Excitation-induced polarization decay in the plant light-harvesting complex LHCII, J. Photochem. Photobiol. A Chem., 234, 91, 10.1016/j.jphotochem.2011.12.026
Remelli, 1999, Chlorophyll binding to monomeric light-harvesting complex: a mutatiin analysis of chromophore-binding residues, J. Biol. Chem., 274, 33510, 10.1074/jbc.274.47.33510
Rogl, 2002, Assignment of spectral substructures to pigment-binding sites in higher plant light-harvesting complex LHC-II, Biochemistry, 41, 2281, 10.1021/bi015875k
Caffarri, 2007, A specific binding site for neoxanthin in the monomeric antenna proteins CP26 and CP29 of Photosystem II, FEBS Lett., 581, 4704, 10.1016/j.febslet.2007.08.066
Malý, 2016, The role of resonant vibrations in electronic energy transfer, ChemPhysChem, 17, 1356, 10.1002/cphc.201500965
Novoderezhkin, 2015, How exciton-vibrational coherences control charge separation in the photosystem II reaction center, Phys. Chem. Chem. Phys., 17, 30828, 10.1039/C5CP00582E
Renger, 1996, Dissipative exciton motion in a chlorophyll a/b dimer of the light harvesting complex of photosystem II: Simulation of pump - probe spectra, J. Phys. Chem., 100, 15654, 10.1021/jp960486z
Kreisbeck, 2014, Scalable high-performance algorithm for the simulation of exciton-dynamics. Application to the light harvesting complex II in the presence of resonant vibrational modes, J. Chem. Theory Comput., 10, 4045, 10.1021/ct500629s
Fan, 2015, Crystal structures of the PsbS protein essential for photoprotection in plants, Nat. Struct. Mol. Biol., 22, 729, 10.1038/nsmb.3068
Hall, 2016, The lowest-energy chlorophyll of photosystem II is adjacent to the peripheral antenna: emitting states of CP47 assigned via circularly polarized luminescence, Biochim. Biophys. Acta Bioenerg., 10.1016/j.bbabio.2016.06.007
Pettai, 2005, Photosynthetic activity of far-red light in green plants, Biochim. Biophys. Acta, 1708, 311, 10.1016/j.bbabio.2005.05.005
Thapper, 2009, Defining the far-red limit of photosystem II in Spinach, Plant Cell, 21, 2391, 10.1105/tpc.108.064154
Veerman, 2007, Photoprotection in the lichen Parmelia sulcata: the origins of desiccation-induced fluorescence quenching, Plant Physiol., 145, 997, 10.1104/pp.107.106872
Heber, 2006, Thermal energy dissipation in reaction centres and in the antenna of photosystem II protects desiccated poikilohydric mosses against photo-oxidation, J. Exp. Bot., 57, 2993, 10.1093/jxb/erl058
Yamakawa, 2012, Three different mechanisms of energy dissipation of a desiccation-tolerant moss serve one common purpose: to protect reaction centres against photo-oxidation, J. Exp. Bot., 63, 3765, 10.1093/jxb/ers062
Groot, 2005, Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy, Proc. Natl. Acad. Sci. U. S. A., 102, 13087, 10.1073/pnas.0503483102
Holzwarth, 2006, Kinetics and mechanism of electron transfer in intact photosystem II and in the isolated reaction center: Pheophytin is the primary electron acceptor, Proc. Natl. Acad. Sci. U. S. A., 103, 6895, 10.1073/pnas.0505371103
Jankowiak, 2012, Charge separation pathways in Photosystem II, J. Phys. Chem. Lett., 3, 1684, 10.1021/jz300505r
Romero, 2010, Two different charge separation pathways in photosystem II, Biochemistry, 49, 4300, 10.1021/bi1003926
Novoderezhkin, 2011, Multiple charge-separation pathways in photosystem II: modeling of transient absorption kinetics, ChemPhysChem, 12, 681, 10.1002/cphc.201000830
Ishizaki, 2013, Interactions between quantum mixing and the environmental dynamics controlling ultrafast photoinduced electron transfer and its temperature dependence, Chem. Lett., 42, 1406, 10.1246/cl.130608
Schatz, 1987, Picosecond kinetics of fluorescence and absorbance changes in photosystem II particles excited at low photon density, Proc. Natl. Acad. Sci. U. S. A., 84, 8414, 10.1073/pnas.84.23.8414
Vasil'ev, 2001, Excited-state dynamics in photosystem II: insights from the x-ray crystal structure, Proc. Natl. Acad. Sci. U. S. A., 98, 8602, 10.1073/pnas.141239598
Pawlowicz, 2007, Charge separation and energy transfer in the photosystem II core complex studied by femtosecond midinfrared spectroscopy, Biophys. J., 93, 2732, 10.1529/biophysj.107.105452
Miloslavina, 2006, Charge separation kinetics in intact photosystem II core particles is trap-limited. A picosecond fluorescence study, Biochemistry, 45, 2436, 10.1021/bi052248c
van der Weij-de Wit, 2011, Charge separation is virtually irreversible in photosystem II core complexes with oxidized primary quinone acceptor, J. Phys. Chem. A, 115, 3947, 10.1021/jp1083746
Hughes, 2004, Highly efficient spectral hole-burning in oxygen-evolving photosystem II preparations, J. Phys. Chem. B, 108, 10428, 10.1021/jp0492523
Prince, 2004, Persistent spectral hole burning in oxygen-evolving photosystem II from cyanobacteria and higher plants, J. Lumin., 108, 101, 10.1016/j.jlumin.2004.01.024
Kaucikas, 2016
Sun, 2015, Direct energy transfer from the major antenna to the photosystem II core complexes in the absence of minor antennae in liposomesOriginal, Biochim. Biophys. Acta, 1847, 248, 10.1016/j.bbabio.2014.11.005
Moqvist, 2014, The photochemistry in photosystem II at 5K is different in visible and far-red light, Biochemistry, 53, 4228, 10.1021/bi5006392
Müh, 2012, Structure-based simulation of linear optical spectra of the CP43 core antenna of photosystem II, Photosynth. Res., 111, 87, 10.1007/s11120-011-9675-8
Müh, 2015, The quest for energy traps in the CP43 antenna of photosystem II, J. Photochem. Photobiol. B, 152, 286, 10.1016/j.jphotobiol.2015.05.023
Renger, 2013, Understanding photosynthetic light-harvesting: a bottom up theoretical approach, Phys. Chem. Chem. Phys., 15, 3348, 10.1039/C3CP43439G
Koua, 2013, Structure of Sr-substituted photosystem II at 2.1Å resolution and its implications in the mechanism of water oxidation, Proc. Natl. Acad. Sci. U. S. A., 110, 3889, 10.1073/pnas.1219922110
Umena, 2011, Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9Å, Nature, 473, 55, 10.1038/nature09913
Guskov, 2009, Cyanobacterial photosystem II at 2.9Å resolution and the role of quinones, lipids, channels and chloride, Nat. Struct. Mol. Biol., 16, 334, 10.1038/nsmb.1559
Frankcombe, 2015, Explicit calculation of the excited electronic states of the photosystem II reaction centre, Phys. Chem. Chem. Phys., 17, 3295, 10.1039/C4CP04468A
Hellmich, 2014, Native-like photosystem II superstructure at 2.44Å resolution through detergent extraction from the protein crystal, Structure, 22, 1607, 10.1016/j.str.2014.09.007
Raszewski, 2008, Spectroscopic properties of reaction center pigments in photosystem II core complexes: revision of the multimer model, Biophys. J., 95, 105, 10.1529/biophysj.107.123935
Reppert, 2008, Low energy chlorophyll states in the CP43 antenna protein complex: simulation of absorbance and hole-burned spectra (II), J. Phys. Chem. B, 112, 9934, 10.1021/jp8013749
Hall, 2016, Circularly polarized luminescence spectroscopy reveals low-energy excited states and dynamic localization of vibronic transitions in CP43, Biochim. Biophys. Acta, 115-128
Abramavicius, 2010, Energy-transfer and charge-separation pathways in the reaction center of photosystem II revealed by coherent two-dimensional optical spectroscopy, J. Chem. Phys., 133, 10.1063/1.3493580
Renger, 2013, Structure-based modeling of energy transfer in photosynthesis, Photosynth. Res., 116, 367, 10.1007/s11120-013-9893-3
Kosugi, 2013, Arabitol provided by lichenous fungi enhances ability to dissipate excess light energy in a symbiotic green alga under desiccation, Plant Cell Physiol., 54, 1316, 10.1093/pcp/pct079
Reinot, 2016, On the conflicting estimations of pigment site energies in photosynthetic complexes: a case study of the CP47 complex, Anal. Chem. Insights, 1
Chen, 2015, Critical assessment of the emission spectra of various PSII Core Complexes (PSII-cc), Photosynth. Res., 124, 253, 10.1007/s11120-015-0128-7
Picorel, 2004, Isolation of CP43 and CP47 photosystem II proximal antenna complexes from plants, 129
Glaeser, 1999, Selective enrichment and characterization of Roseospirillum parvum, gen. nov. and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties, Arch. Microbiol., 171, 405, 10.1007/s002030050727
Permentier, 2000, Energy transfer and charge separation in the purple non-sulfur bacterium Roseospirillum parvum, Biochim. Biophys. Acta, 1460, 338, 10.1016/S0005-2728(00)00200-0
Madigan, 1984, A novel photosynthetic bacterium isolated from a Yellowstone hot spring, Science, 225, 313, 10.1126/science.225.4659.313
Permentier, 2001, A bacteriochlorophyll a antenna complex from purple bacteria absorbing at 963nm, Biochemistry, 40, 5573, 10.1021/bi0024308
Ma, 2015, The origin of the unusual Qy red shift in LH1–RC complexes from purple bacteria Thermochromatium tepidum as revealed by Stark absorption spectroscopy, Biochim. Biophys. Acta, 1847, 1479, 10.1016/j.bbabio.2015.08.007
Kimura, 2008, Calcium ions are involved in the unusual red shift of the light-harvesting 1 Qy transition of the core complex in thermophilic purple sulfur bacterium Thermochromatium tepidum, J. Biol. Chem., 283, 13867, 10.1074/jbc.M800256200
Sumi, 2004, Uphill energy trapping by reaction center in bacterial photosynthesis. 2. Unistep charge separation, virtually mediated by special pair, by photoexcitation in place of excitation transfer from the antenna system, J. Phys. Chem. B, 108, 11792, 10.1021/jp031341c
Niwa, 2014, Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0Å, Nature, 508, 228, 10.1038/nature13197
Yang, 2011, Effects of aggregation on the excitation dynamics of LH2 from Thermochromatium tepidum in aqueous phase and in chromatophores, J. Phys. Chem. B, 115, 7906, 10.1021/jp1097537
Timpmann, 2004, Emitting excitonic polaron states in core LH1 and peripheral LH2 bacterial light-harvesting complexes, J. Phys. Chem. B, 108, 10581, 10.1021/jp049165a
Owen, 1997, Excitonic interactions between the reaction center and antennae in purple photosynthetic bacteria, J. Phys. Chem. B, 101, 7197, 10.1021/jp9633759
Ferretti, 2014, The nature of coherences in the B820 bacteriochlorophyll dimer revealed by two-dimensional electronic spectroscopy, Phys. Chem. Chem. Phys., 16, 9930, 10.1039/c3cp54634a
Suzuki, 2007, Purification, characterization and crystallization of the core complex from thermophilic purple sulfur bacterium Thermochromatium tepidum, Biochim. Biophys. Acta, 1767, 1057, 10.1016/j.bbabio.2007.06.002
Ma, 2009, Specific Ca2+-binding motif in the LH1 complex from photosynthetic bacterium Thermochromatium tepidum as revealed by optical spectroscopy and structural modeling, FEBS J., 276, 1739, 10.1111/j.1742-4658.2009.06905.x
Ma, 2008, Excitation dynamics of two spectral forms of the core complexes from photosynthetic bacterium Thermochromatium tepidum, Biophys. J., 95, 3349, 10.1529/biophysj.108.133835
Georgakopoulou, 2002, Absorption and CD spectroscopy and modeling of various LH2 complexes from purple bacteria, Biophys. J., 82, 2184, 10.1016/S0006-3495(02)75565-3
Georgakopoulou, 2006, Investigation of the effects of different carotenoids on the absorption and CD signals of light harvesting 1 complexes, J. Phys. Chem. B, 110, 3354, 10.1021/jp0517955
Krausz, 2013, Selective and differential optical spectroscopies in photosynthesis, Photosynth. Res., 116, 411, 10.1007/s11120-013-9881-7
Ma, 2016, Temperature dependent LH1→RC energy transfer in purple bacteria Tch. tepidum with shiftable LH1-Q(y) band: a natural system to investigate thermally activated energy transfer in photosynthesis, Biochim. Biophys. Acta Bioenerg., 1857, 408, 10.1016/j.bbabio.2015.12.006
Hashimoto, 2015, Ultrafast time-resolved vibrational spectroscopies of carotenoids in photosynthesis, Biochim. Biophys. Acta, 1847, 69, 10.1016/j.bbabio.2014.09.001
Bautista, 1999, Singlet and triplet energy transfer in the peridinin−chlorophyll a−protein from Amphidinium carterae, J. Phys. Chem. A, 103, 2267, 10.1021/jp983943f
Zigmantas, 2002, Carotenoid to chlorophyll energy transfer in the peridinin–chlorophyll-a–protein complex involves an intramolecular charge transfer state, Proc. Natl. Acad. Sci. U. S. A., 99, 16760, 10.1073/pnas.262537599
Linden, 2004, Transient absorption study of peridinin and peridinin−chlorophyll a−protein after two-photon excitation, J. Phys. Chem. B, 108, 10340, 10.1021/jp031331b
Papagiannakis, 2005, Spectroscopic characterization of the excitation energy transfer in the fucoxanthin–chlorophyll protein of diatoms, Photosynth. Res., 86, 241, 10.1007/s11120-005-1003-8
Polívka, 2006, Energy transfer in the major intrinsic light-harvesting complex from Amphidinium carterae, Biochemistry, 45, 8516, 10.1021/bi060265b
Schulte, 2009, Identification of a single peridinin sensing Chl-a excitation in reconstituted PCP by crystallography and spectroscopy, Proc. Natl. Acad. Sci. U. S. A., 106, 20764, 10.1073/pnas.0908938106
Gildenhoff, 2010, Oligomerization and pigmentation dependent excitation energy transfer in fucoxanthin–chlorophyll proteins, Biochim. Biophys. Acta, 1797, 543, 10.1016/j.bbabio.2010.01.024
Gildenhoff, 2010, The excitation energy transfer in the trimeric fucoxanthin–chlorophyll protein from Cyclotella meneghiniana analyzed by polarized transient absorption spectroscopy, Chem. Phys., 373, 104, 10.1016/j.chemphys.2010.02.012
Polívka, 2010, Molecular factors controlling photosynthetic light harvesting by carotenoids, Acc. Chem. Res., 43, 1125, 10.1021/ar100030m
Kosumi, 2012, Excitation energy-transfer dynamics of brown algal photosynthetic antennas, J. Phys. Chem. Lett., 3, 2659, 10.1021/jz300612c
Kosumi, 2014, Elucidation and control of an intramolecular charge transfer property of fucoxanthin by a modification of its polyene chain length, J. Phys. Chem. Lett., 5, 792, 10.1021/jz5000287
Kosumi, 2014, Characterization of the intramolecular transfer state of marine carotenoid fucoxanthin by femtosecond pump–probe spectroscopy, Photosynth. Res., 121, 61, 10.1007/s11120-014-9995-6
Kosumi, 2011, Ultrafast excited state dynamics of fucoxanthin: excitation energy dependent intramolecular charge transfer dynamics, Phys. Chem. Chem. Phys., 13, 10762, 10.1039/c0cp02568b
Kosumi, 2011, Ultrafast S1 and ICT state dynamics of a marine carotenoid probed by femtosecond one- and two-photon pump-probe spectroscopy, J. Lumin., 131, 515, 10.1016/j.jlumin.2010.09.018
Kosumi, 2009, One- and two-photon pump–probe optical spectroscopic measurements reveal the S1 and intramolecular charge transfer states are distinct in fucoxanthin, Chem. Phys. Lett., 483, 95, 10.1016/j.cplett.2009.10.077
Huo, 2011, Theoretical study of coherent excitation energy transfer in cryptophyte phycocyanin 645 at physiological temperature, J. Phys. Chem. Lett., 2, 825, 10.1021/jz200301j
Rivera, 2013, Influence of site-dependent pigment-protein interactions on excitation energy transfer in photosynthetic light harvesting, j. phys. chem. b, 117, 5510, 10.1021/jp4011586
Hashimoto, 1989, Raman spectra of all-trans-β-carotene in the S1 and T1 states produced by direct photoexcitation, Chem. Phys. Lett., 163, 251, 10.1016/0009-2614(89)80045-4
Hashimoto, 1993, Isolation by high-pressure liquid chromatography of the cis-trans isomers of beta-apo-8'-carotenal. Determination of their S0-state configurations by NMR spectroscopy and prediction of their S1- and T1-state configurations by transient Raman spectroscopy, J. Am. Chem. Soc., 115, 9216, 10.1021/ja00073a042
Hashimoto, 1988, Time-resolved resonance Raman spectroscopy of triplet .beta.-carotene produced from all-trans, 7-cis, 9-cis, 13-cis, and 15-cis isomers and high-pressure liquid chromatography analyses of photoisomerization via the triplet state, J. Phys. Chem., 92, 2101, 10.1021/j100319a004
Niedzwiedzki, 2006, Femtosecond time-resolved transient absorption spectroscopy of xanthophylls, J. Phys. Chem. B, 110, 22872, 10.1021/jp0622738
Lasorne, 2008, Controlling S1/S0 decay and the balance between photochemistry and photostability in benzene: a direct quantum dynamics study, J. Phys. Chem. A, 112, 13017, 10.1021/jp803740a
Perveaux, 2015, Intramolecular charge transfer in 4‐aminobenzonitrile does not need the twist and may not need the bend, J. Phys. Chem. Lett., 6, 1316, 10.1021/acs.jpclett.5b00162
Lukes, 2011, Electronic ground state conformers of beta-carotene and their role in ultrafast spectroscopy, Chem. Phys. Lett., 506, 122, 10.1016/j.cplett.2011.02.060
Quick, 2015, β-Carotene revisited by transient absorption and stimulated raman spectroscopy, ChemPhysChem, 16, 3824, 10.1002/cphc.201500586
Balevicius, 2015, Vibronic energy relaxation approach highlighting deactivation pathways in carotenoids, Phys. Chem. Chem. Phys., 17, 19491, 10.1039/C5CP00856E
Gradinaru, 2001, An unusual pathway of excitation energy deactivation in carotenoids: singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic antenna, Proc. Natl. Acad. Sci. U. S. A., 98, 2364, 10.1073/pnas.051501298
Kosumi, 2012, Ultrafast excited state dynamics of spirilloxanthin in solution and bound to core antenna complexes: identification of the S* and T-1 states, J. Chem. Phys., 137, 064505, 10.1063/1.4737129
Papagiannakis, 2006, Excited-state dynamics of carotenoids in light-harvesting complexes. 1. Exploring the relationship between the S-1 and S* states, J. Phys. Chem. B, 110, 5727, 10.1021/jp054633h
Hauer, 2013, Explaining the temperature dependence of spirilloxanthin's S* signal by an inhomogeneous ground state model, J. Phys. Chem. A, 117, 6303, 10.1021/jp4011372
Niedzwiedzki, 2007, Ultrafast dynamics and excited state spectra of open-chain carotenoids at room and low temperatures, J. Phys. Chem. B, 111, 5984, 10.1021/jp070500f
Burgie, 2014, Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome, Proc. Natl. Acad. Sci. U. S. A., 111, 10179, 10.1073/pnas.1403096111
Tronrud, 2009, The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria, Photosynth. Res., 100, 79, 10.1007/s11120-009-9430-6
Fenna, 1975, Chlorophyll arrangement in a bacteriochlorophyll protein from Chlorobium limicola, Nature, 258, 573, 10.1038/258573a0
Louwe, 1997, Toward an integral interpretation of the optical steady-state spectra of the FMO-complex of Prosthecochloris aestuarii. 2. Exciton simulations, J. Phys. Chem. B, 101, 11280, 10.1021/jp9722162
Adolphs, 2006, How proteins trigger excitation energy transfer in the FMO complex of green sulfur bacteria, Biophys. J., 91, 2778, 10.1529/biophysj.105.079483
Wen, 2009, Membrane orientation of the FMO antenna protein from Chlorobaculum tepidum as determined by mass spectrometry-based footprinting, Proc. Natl. Acad. Sci. U. S. A., 106, 6134, 10.1073/pnas.0901691106
Cho, 2005, Exciton analysis in two-dimensional electronic spectroscopy, J. Phys. Chem. B, 109, 10542, 10.1021/jp050788d
Ishizaki, 2009, Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature, Proc. Natl. Acad. Sci. U. S. A., 106, 17255, 10.1073/pnas.0908989106
Pachón, 2011, Physical basis for long–lived electronic coherence in photosynthetic light–harvesting systems, J. Phys. Chem. Lett., 2, 2778-2732, 10.1021/jz201189p
Ritschel, 2011, Absence of quantum oscillations and dependence on site energies in electronic excitation transfer in the Fenna–Matthews–Olson Trimer, J. Phys. Chem. Lett., 2, 2912, 10.1021/jz201119j
Kell, 2014, On destabilization of the Fenna–Matthews–Olson complex of Chlorobaculum tepidum, Photosynth. Res., 120, 323, 10.1007/s11120-014-9990-y
Kell, 2014, On the controversial nature of the 825nm exciton band in the Fmo protein complex, J. Phys. Chem. Lett., 5, 1450, 10.1021/jz5001165
Herascu, 2014, Modeling of various optical spectra in the presence of slow excitation energy transfer in dimers and trimers with weak interpigment coupling: FMO as an example, J. Phys. Chem. B, 118, 2032, 10.1021/jp410586f
Müh, 2007, α-Helices direct excitation energy flow in the Fenna–Matthews–Olson protein, Proc. Natl. Acad. Sci. U. S. A., 104, 16862, 10.1073/pnas.0708222104
Adolphs, 2008, Calculation of pigment transition energies in the FMO protein, Photosynth. Res., 95, 197, 10.1007/s11120-007-9248-z
Busch, 2011, The eighth bacteriochlorophyll completes the excitation energy funnel in the FMO Protein, J. Phys. Chem. Lett., 2, 93, 10.1021/jz101541b
Blina, 2013, Chemical oxidation of the FMO antenna protein from Chlorobaculum tepidum, Photosynth. Res., 116, 11, 10.1007/s11120-013-9878-2
Renger, 2012, Normal mode analysis of the spectral density of the Fenna–Matthews–Olson light-harvesting protein: how the protein dissipates the excess energy of excitons, J. Phys. Chem. B, 116, 14565, 10.1021/jp3094935
Suryanarayanan, 2015, 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, 10.1021/acs.jpcb.5b03654
Jurinovich, 2014, The Fenna–Matthews–Olson protein revisited: a fully polarizable (TD)DFT/MM description, ChemPhysChem, 15, 3194, 10.1002/cphc.201402244
König, 2013, Protein effects on the optical spectrum of the Fenna–Matthews–Olson complex from fully quantum chemical calculations, J. Chem. Theory Comput., 9, 1808, 10.1021/ct301111q
Jia, 2015, Hybrid QM/MM study of FMO complex with polarized protein-specific charge, Sci. Rep., 5, 17096, 10.1038/srep17096
Hayes, 2011, Extracting the excitonic Hamiltonian of the Fenna-Matthews-Olson complex using three-dimensional third-order electronic spectroscopy, Biophys. J., 100, 2043, 10.1016/j.bpj.2010.12.3747
Brixner, 2005, Two-dimensional spectroscopy of electronic couplings in photosynthesis, Nature, 434, 625, 10.1038/nature03429
Renger, 2012, Theory of excitonic couplings in dielectric media – foundation of Poisson-TrEsp method and application to photosystem I trimers, Photosynth. Res., 111, 47, 10.1007/s11120-011-9685-6
Rätsep, 2007, Unusual temperature quenching of bacteriochlorophyll a fluorescence in FMO antenna protein trimers, Chem. Phys. Lett., 434, 306, 10.1016/j.cplett.2006.12.013
Vulto, 1998, Exciton simulations of optical spectra of the FMO complex from the green sulfur bacterium Chlorobium tepidum at 6K, J. Phys. Chem. B, 102, 9577, 10.1021/jp982095l
Wendling, 2002, The quantitative relationship between structure and polarized spectroscopy in the FMO complex of Prosthecochloris aestuarii: refining experiments and simulations, Photosynth. Res., 71, 99, 10.1023/A:1014947732165
Rätsep, 2007, Electron–phonon and vibronic couplings in the FMO bacteriochlorophyll a antenna complex studied by difference fluorescence line narrowing, J. Lumin., 127, 251, 10.1016/j.jlumin.2007.02.053
Kell, 2016, effect of spectral density shapes on the excitonic structure and dynamics of the Fenna-Matthews-Olson trimer from Chlorobaculum tepidum, J. Phys. Chem. A, 10.1021/acs.jpca.6b03107
Fuller, 2014, Vibronic coherence in oxygenic photosynthesis, Nat. Chem., 6, 706, 10.1038/nchem.2005
Perlík, 2015, Vibronic coupling explains the ultrafast carotenoid-to-bacteriochlorophyll energy transfer in natural and artificial light harvesters, J. Chem. Phys., 142, 212434, 10.1063/1.4919548
Lao, 1995, Higher-Order Stark Spectroscopy: Polarizability of Photosynthetic Pigments, J. Phys. Chem., 99, 496, 10.1021/j100002a007
Steffen, 1994, Dielectric asymmetry in the photosynthetic reaction centre, Science, 264, 810, 10.1126/science.264.5160.810
Rätsep, 2003, Resonant emission from the B870 exciton state and electron-phonon coupling in the LH2 antenna chromoprotein, Chem. Phys. Lett., 377, 371, 10.1016/S0009-2614(03)01193-X
Jankowiak, 2011, Site selective and single complex laser-based spectroscopies: a window on excited state electronic structure, excitation energy transfer, and electron–phonon coupling of selected photosynthetic complexes, Chem. Rev., 111, 4546, 10.1021/cr100234j
Gräslund, 2010
Rätsep, 2011, Demonstration and interpretation of significant asymmetry in the low-resolution and high-resolution Qy fluorescence and absorption spectra of bacteriochlorophyll a, J. Chem. Phys., 134, 10.1063/1.3518685
Rao, 2016, DOX: a new computational protocol for accurate prediction of the protein–ligand binding structures, J. Comput. Chem., 37, 336, 10.1002/jcc.24217
Goerigk, 2014, Recommending Hartree–Fock Theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures, J. Phys. Chem. B, 118, 14612, 10.1021/jp510148h
Goerigk, 2013, Efficient methods for the quantum chemical treatment of protein structures: the effects of London-dispersion and basis-set incompleteness on peptide and water-cluster geometries, J. Chem. Theory Comput., 9, 3240, 10.1021/ct400321m
Goerigk, 2012, First Steps Towards Quantum Refinement of Protein X-Ray Structures, 87
Cai, 2006, Density-functional theory for charge-transfer: the nature of the N-bands of porphyrins and chlorophylls revealed through CAM-B3LYP, CASPT2, and SAC-CI calculations, J. Phys. Chem. B, 110, 15624, 10.1021/jp063376t
Pedone, 2010, Environmental effects in computational spectroscopy: accuracy and Interpretation, ChemPhysChem, 11, 1812
Barone, 2009, Fully integrated approach to compute vibrationally resolved optical spectra: from small molecules to macrosystems, J. Chem. Theory Comput., 5, 540, 10.1021/ct8004744
Barone, 2014, A multifrequency virtual spectrometer for complex bio-organic systems: vibronic and environmental effects on the UV/Vis spectrum of chlorophylla, ChemPhysChem, 15, 3355, 10.1002/cphc.201402300
Ren, 2015, Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Foerster theory, J. Comput. Chem., 36, 137, 10.1002/jcc.23770
Ren, 2013, Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Foerster theory, J. Comput. Chem., 34, 1005, 10.1002/jcc.23221
Huo, 2010, Iterative linearized density matrix propagation for modelling coherent excitation energy transfer in photosynthetic light harvesting, J. Chem. Phys., 133, 184108, 10.1063/1.3498901
Frankcombe, 2010, Converged quantum dynamics with modified Shepard interpolation and Gaussian wave packets, Chem. Phys. Lett., 489, 242, 10.1016/j.cplett.2010.02.068
Koch, 2013, Basis expansion leaping: a new method to solve the time-dependent Schrödinger equation for molecular quantum dynamics, Phys. Rev. Lett., 110, 263202, 10.1103/PhysRevLett.110.263202
Richings, 2015, Quantum dynamics simulations using Gaussian wavepackets: the vMCG method, Int. Rev. Phys. Chem., 34, 269, 10.1080/0144235X.2015.1051354
Römer, 2013, Towards a variational formulation of mixed quantum-classical molecular dynamics, Mol. Phys., 111, 3618, 10.1080/00268976.2013.844371
Wang, 2003, Multilayer formulation of the multiconfiguration time-dependent Hartree theory, J. Chem. Phys., 119, 1289, 10.1063/1.1580111
Rancova, 2015, Probing environment fluctuations by 2DES of molecular systems at temperatures below T=5K, J. Chem. Phys., 142, 212428, 10.1063/1.4918584
Adolphs, 2016, Hole-burning spectroscopy on excitonically coupled pigments in proteins: theory meets experiment, J. Am. Chem. Soc., 138, 2993, 10.1021/jacs.5b08246