title: Hybrid QM/MM study of FMO complex with polarized protein-specific charge.
abstract: The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point calculations have been employed to predict the energy transfer pathways utilizing the polarized protein-specific charge (PPC), which provides a more realistic description of Coulomb interaction potential in the protein than conventional mean-field charge scheme. The recently discovered eighth pigment has also been included in this study. Comparing with the conventional mean-field charges, more stable structures of FMO complex were found under PPC scheme during molecular dynamic simulation. Based on the electronic structure calculations, an exciton model was constructed to consider the couplings during excitation. The results show that pigments 3 and 4 dominate the lowest exciton levels whereas the highest exciton level are mainly constituted of pigments 1 and 6. This observation agrees well with the assumption based on the spatial distribution of the pigments. Moreover, the obtained spectral density in this study gives a reliable description of the diverse local environment embedding each pigment.
authors.affiliation: State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Jia
authors.affiliation: State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Mei
authors.affiliation: State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.|Department of Chemistry, New York University, New York, NY 10003.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Mo
mesh_terms: D019414:Chlorobi / Q000737:chemistry* / Q000378:metabolism; D004735:Energy Transfer; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D045342:Light-Harvesting Protein Complexes