Investigation Of Molecular Mechanism Of Efficient Excitation Energy Transfer In Natural Photosynthetic Systems

During photosynthesis,the natural light-harvesting complexes capture sunlight and direct the excitation energy to the reaction center with nearly-unity quantum efficiency.Understanding the underlying mechanism on a molecular-level may provide a blueprint for the characterization,optimization,and design of artificial light-harvesting devices.The fact that the dynamic protein plays an important role in promoting the efficient transfer of excitation energy is wellunderstood.But how the protein environment influences the excitation energy transfer and the detailed molecular mechanism underlying has not been elucidated yet.Due to the complexity of the photosynthetic pigment-protein complex,which is composed of tens and hundreds of pigments/cofactors and multi-protein subunits,the dynamical changes of the conformation of pigments and proteins can not be observed directly in experiments.Therefore,it is highly desirable to reveal the molecular mechanism by combining structural-based theoretical calculations with experimental observations.However,it is not realistic to perform full quantum calculations for the whole system.Nowadays,the common theoretical method is introducing an exciton picture combined with quantum master approaches.Thus,the question is approximated in terms of how to accurately assess the site energies of pigments,the electronic couplings among pigments,and the spectral density.This thesis will follow this framework,to balance the accuracy and computationally expensive,the exciton model of the photosynthetic complex is constructed by combining the electrostatic-embedding quantum-mechanics/molecular-mechanics calculations with molecular dynamics simulations,for elucidating the relationship between structural characteristics and functions and revealing the molecular mechanism of excitation energy transfer.Firstly,based on the high-resolution crystal structure of the pigment-protein complex,the polarized protein-specific charges(PPC)are fitting by molecular fractionation with conjugate caps.The PPC scheme can provide a realistic description of the protein polarization and pigment-protein electrostatic interactions.The all-atom molecular dynamics simulation is performed by adopting the PPC scheme,it can solve the insufficient of traditional mean-field charge scheme in describing the polarization effect of protein environment.Thereby,we can get a more reasonable structural sampling of complex,and this may reduce the quantization calculation error caused by the unreasonable configurations.Then,a hybrid electrostatic–embedding QM/MM method with PPC is employed for elucidating how the protein environment influences the excitation energy transfer from both the pigment-protein interactions and the structure of pigments.The exciton model of the system is constructed by calculating the site energies of pigments and the corresponding electronic couplings among them.Finally,the spectral density is obtained based on an optimal construction of biexponential Drude bath correlation function,then the absorption spectrum and exciton dynamics are simulated by the dissipaton equation of motion(DEOM)approach.The DEOM theory is well-capable of treating the strong-correlated quantum dissipative systems,such as the natural light-harvesting system.The molecular mechanism of excitation energy transfer in the pigment-protein complex is elucidated based on the above analysis.In chapter one,we will start from the research background of natural photosynthetic systems,and elucidate the key issues to be solved.In chapter two,the structural characteristics of natural photosynthetic complexes will be introduced,as well as the detailed description of Phycoerythrin 545(PE545)and Fenna-MathewsOlson(FMO)complex which this thesis concerned.In chapter three,the methods used in the thesis for understanding the excitation energy transfer in pigment-protein complexes,PPC charge fitting and quantum dissipative theory will be introduced in detail.In chapter four,for PE545 complex,the exciton model was constructed by combining QM/MM calculations and all-atom MD simulation,to elucidate how the protein environment influences the excitation energy transfer and reveal the molecular mechanism of EET.The polarized protein–specific charge was adopted in both QM/MM calculations and MD simulation.Besides,the absorption spectrum and excitation dynamics of the pigment-protein complex were simulated by DEOM approach.In chapter five,for C type and P type FMO complex,their exciton models were built by adopting PPC scheme in both MD simulation and QM/MM calculations,respectively.Their absorption spectrum were simulated based on their own exciton models using DEOM approach to elucidate the relationship between their structural differences and spectral features,as well as the role of newly discovered BChla-8 in EET.In chapter six,it is the conclusions and prospects of this thesis.