Theoretical Study Of Energy Transfer Pathways Between Pigments In Light-Harvesting Complex Ⅱ

Photosynthesis is the most important biological process in the Earth’s ecosystem,which is of great significance for energy conversion,carbon-oxygen balance in the atmosphere,and organic matter manufacturing.In the primary reaction stage of photosynthesis,the photon is absorbed by the pigment-protein complex,converted into electronic excitation energy,and efficiently transferred to the reaction center through the pigment molecules network.Such an efficient energy transfer process has attracted a lot of attention in many fields such as bioengineering,physics,and materials science.With the development of ultrafast spectroscopy,people have reached a consensus on many energy transfer pathways involved.However,due to the complexity of the structure and function of Light-Harvesting Complex II,there are still some problems that need to be further explored.In the Light-Harvesting Complex II of higher plants,lutein is the only carotenoid that appears in pairs,and whether there is an energy transfer pathway between them has not been determined.At the same time,whether the energy transfer process between the two will affect the energy transfer between them and chlorophyll-a remains unknown.The conclusion of these problems will affect the understanding of the energy transfer process between the primary and accessory LightHarvesting pigments.The main innovations in our work are as follows:(I)For two identical luteins,due to the influence of different local environments,there is a problem of switching the order of excited state energy levels.To accurately describe the influence of the environment on the excited state,we proposed a set of electrostatic iterative fitting scheme based on a multi-scale model,obtained the consistent convergence of the environmental charge,and accurately reproduced the energy level order of the excited state of the pigment molecule.It lays an important foundation for further simulation of energy transfer dynamics of excited states.(II)The energy transfer process involves multiple pigment molecules,and the Frenkel exciton model is an effective means to simulate the delocalization excitation behavior of the aggregate.However,when constructing the multi-order Frenkel exciton model of pigment molecules,the random introduction of the non-diagonal element phase of the matrix will directly affect the kinetic results.In this paper,we develop a set of phase correction methods based on principal component analysis,obtain the nondiagonal element value of phase matching,and solve the error problem caused by inaccurate phase.(III)A large number of quantum chemical calculations are unavoidable to obtain statistically significant ensemble results.To save calculation costs,based on the data characteristics of the finite resonance energy transfer system,we propose a " stochastic exciton Hamiltonian" model,which reduces the statistical error and improves the accuracy of the simulation.The model can be applied to statistical simulation of other similar systems.(IV)Through theoretical simulation,we proved for the first time that there is an energy transfer pathway between the two luteins,and found that the energy transfer process between pigment molecules is independent,and the energy transfer process between luteins does not affect the energy transfer process between lutein and chlorophyll-a,and there is no necessary site for the energy transfer process between the two types of pigment molecules.Our work gives a complete picture of the resonance energy transfer between the two luteins and the surrounding chlorophyll-a.The structure of this paper is as follows:Chapter 1 briefly describes the background of photosynthesis.The LightHarvesting Complex system,various pigment molecules,and energy relaxation pathways between two kinds of pigment molecules involved in photosynthesis were introduced,and the development of theoretical simulation and experimental methods for studying photosynthesis were also introduced.Finally,the research idea of this paper is introduced.Chapter 2 introduces the main theoretical knowledge and calculation methods involved in this work according to the contents and objectives of the study.The main contents include(1)time-dependent Schrodinger equation and Born-Oppenheimer approximation;(2)Multi-scale models for the calculation of biological macromolecular systems;(3)Construct molecular force field and molecular dynamics simulation;(4)Energy transfer processes within and between molecules;(5)electronic coupling between pigment molecules;(6)Construct Frenkel exciton model and phase correction.In Chapter 3,the effects of the photo-trapping complex and its environment on pigments were introduced.Firstly,the system model for our research goal is introduced.The importance of the simulated environment and some limitations of the environment are introduced.Finally,the self-consistent convergent charge developed by us to simulate the Light-Harvesting Complex environment is introduced,and the influence of the environment on the excited state energy levels of each pigment molecule is defined,and the main factors affecting the level order of lutein are found out.In Chapter 4,the energy transfer process between two luteins is studied in detail.Using a large number of configurations obtained from the simulation trajectories of molecular dynamics,the time evolution is carried out to obtain a statistically average energy transfer process of the system.The results show that there is a resonance energy transfer pathway between the two luteins.However,the energy transfer has certain requirements for the configuration of the two luteins,and it can only occur when the excited states of the two are very close to each other.Such a configuration is not common,which may be the reason why the energy transfer between luteins is controversial.For the theoretical simulation results,to obtain a smoother curve,we further proposed a new " stochastic exciton Hamiltonian model " according to the statistical characteristics of the calculated data,which can be used to quickly obtain the exciton model and energy transfer curve.Chapter 5 further explores the energy transfer process between the two luteins and the surrounding chlorophyll based on Chapter 4.Through the flexible use of the multiorder Frenkel exciton model for time evolution,the obtained results further clarify the energy transfer pathway between two types of pigment molecules involving two luteins at the same time.The results show that lutein and chlorophyll-a also follow the resonance energy transfer mechanism.However,there is no necessary site in the process of energy transfer between the two types of pigment molecules,and the energy transfer between lutein does not affect the energy transfer process of each other and the surrounding chlorophyll-a.In addition,the quantum time evolution program we developed to simulate the energy transfer process between pigment molecules in lighttrapping complexes is also presented.Summary and prospect are given in Chapter 6.