几种生物光合色素分子体系电子激发光谱的理论研究
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摘要
研究高效、快速的光合作用反应机理对于开发利用太阳能，生物合理设计以光合作用系统为靶标的除草剂等具有重要的科学意义。捕光系统和光合反应中心是光合作用的两大主要场所，研究这些系统中电子激发的过程与性质是进一步深入探索电子转移机理的基础。目前针对捕光系统和光合反应中心的实验光谱研究已经取得了较大进展，但其光谱内在的性质必须通过相关的理论研究才能得到准确信息，因此，本论文综合运用各种现代分子模拟方法对高等植物光合作用的模型系统(蓝藻捕光系统和紫细菌光合反应中心)的电子激发光谱进行系统的理论归属研究。具体研究内容如下：
本论文第一章主要对高等植物的光合系统Ⅱ、藻类捕光系统和紫细菌光合反应中心的研究进展，以及论文中所涉及到的理论方法进行了概述性的介绍。
第二章以卟吩自由基为研究对象，对TDDFT，ZINDO和INDO／S三种方法计算的电子激发态光谱进行了比较研究，并考察了TDDFT方法下基组效应对卟吩自由基理论光谱的影响。为了进一步检验TDDFT方法的精确度，我们将TDDFT方法扩展到两种典型的卟啉类衍生物(四氧卟啉阳离子TOPDC和卟啉烯Porphycene)紫外吸收光谱的理论归属研究中，结合极化连续介质模型(PCM)有效考察了溶剂化效应对基态的电子结构和激发态能量的影响。采用TDDFT-PCM模型计算的理论光谱与溶液中实验吸收光谱的较好吻合证明了这一模型的合理性，也说明溶剂化效应对溶液中的吸收光谱的理论研究是相当重要的。
第三章以蓝藻捕光系统中的藻蓝蛋白为研究对象，运用含时的密度泛函理论(TDDFT)方法，结合极化连续介质模型(PCM)，对藻蓝蛋白的三个藻蓝素(α-84、β-84、β-155)在具有生理活性时的分子状态，紫外吸收光谱和CD光谱进行了深入系统的理论研究。并结合分子动力学模拟(MD)技术以及ONIOM方法，研究了藻蓝素中吡咯环之间的二面角与其最大吸收峰之间的定性关系。通过一系列模型化学的理论比较研究，阐明了藻蓝蛋白中三类藻蓝素在生理状态时都是以质子化的形式存在及其质子化可能的反应途径，并定量分析和归属了紫外吸收光谱和圆二色光谱。
第四章主要基于色素分子簇模型，运用TDDFT和ZINDO方法对紫细菌(Rps．viridis和Rb．sphaeroides)光合反应中心的紫外吸收光谱和CD光谱重新进行了理论计算与定量解析归属，并有效考察了色素分子间相互作用对电子激发态的影响。TDDFT的计算结果对紫细菌光合反应中心的P发色团被氧化后的实验CD光谱的合理解释表明：色素分子之间的相互作用不可忽视，只基于单个色素分子(或其模型分子)的理论计算进行光谱归属是不合理的。与TDDFT计算结果的比较再次证明，ZINDO半经验分子轨道理论方法对这两类紫细菌光合反应中心的低能带激发态的解析和归属已经具备了一定的精度。
在第五章中，同时考虑了C=O键长伸缩振动和H-C-H键角弯曲振动对H_2CO分子光电子能谱峰形的影响。同时考虑上述两种正则振动模式的情况下，在SAC-CI-GR／D95~*理论级别下对H_2CO分子的基态(1~1A_1)及三个阳离子激发态(1~2B_2，1~2B_1，1~2A_1)进行了势能面扫描，并拟合得到势能函数，最后采用从头算Franck-Condon因子计算程序解析了这三个激发态的实验光电子能谱的精细结构。
The studies of high efficiency photosynthesis mechanism play a crucial role indeveloping the novel pesticides targeting the photosynthesis systems, and rational usingsolar energy. Light-harvesting system and reaction center are the two fundamentalpigment-protein complexes in the plant photosynthesis system. To make clear theelementary processes of electronic transfer in photosynthesis, knowledge of theelectronic excited characters of light-harvesting system and reaction center is aprerequisite. The theoretical studies of the electronic excitations of light-harvestingsystem and reaction center can provide a sophisticated understanding and theassignments of UV/vis absorption and circular dichroism spectra of these two systems. Inthis thesis, the electronic excitation spectra of the model systems (light-harvesting systemof alga and photosynthetic reacting center (PSRC) of purple bacteria) of photosynthesishave been investigated by using modem molecular simulation methods. The presentthesis is organized as follows:
The previous studies about light-harvesting system of alga and photosyntheticreacting center of purple bacteria have been reviewed in chapter one. Furthermore, thetheoretical methods used in this thesis have been introduced.
In chapter two, the electronic ground and singlet vertical excited states of Free-BasePorphyrin (FBP) have been investigated by using TDDFT, ZINDO and INDO/S methods,the basis sets effects have been examined at TDDFT theoretical level. In order to furtherexamine the precision of TDDFT method, the UV/Vis spectra of tetraoxaporphyrindication (TOPDC) and Porphycene have been investigated by using TDDFT method. Thesolvent effects on excitation spectra also have been taken into account by usingpolarizable continuum model (PCM). TDDFT-PCM calculations lead to a closeragreement with the measured values of experimental absorption spectra in solutions,which demonstate the importance of considering the solvent effects for interpretingexperimental absorption spectra in solutions.
In chapter three, the optical characteristics of UV/Vis spectra and CircularDichroism (CD) spectra ofαandβsubunit of C-phycocyanin (C-PC) were investigatedby using TDDFT method combined with the PCM model. Combining the MolecularDynamic (MD) Simulation and ONIOM methods, the effects of the torsion of thepyrrolic rings in phycocyanobilin (PCB) on the absorption maximum also have been taken into account in this chapter. The electronic excitation at the various levels of modelchemistry demonstrate that, protonation is most likely existing in three PCBs (α-84、β-84、β-155) in C-PC in environmental protein moiety, and the reaction pathway forprotonation of PCBs also have been verified.
Using the super molecule cluster models, the excitation spectra of PSRC from Rps.viridis and Rb. sphaeroides have been investigated by using TDDFT method in chapterfour. The effects of the interactions of pigment-pigment on the electronic excitation alsohave been examined. The calculation results show that the interactions ofpigment-pigment play an important role in reasonably assigning the UV/Vis spectra andcircular dichroism (CD) spectra of PSRC from Rps. virids and Rb. sphaeroides. Bycomparing with TDDFT calculation, the agreeable assignment of the experimentalUV/Vis and CD spectra were achieved by using the ZINDO method.
In chapter five, the effects of both C=O stretch and H-C-H scissor models on thephotoelectron spectrum of formaldehyde have been taken into account simultaneously.The potential energy surface of the ground state (1~1A_1) and the first three excited states(1~2B_2, 1~2B_1, 1~2A_1) of formaldehyde have been scanned at SAC-CI-GR/D95* level. Byfitting the potential energy surfaces of these states, the fine structures of the experimentalphotoelectron spectrum of formaldehyde have been accurately assigned by using ab initiofranck-condon factor program.
本论文第一章主要对高等植物的光合系统Ⅱ、藻类捕光系统和紫细菌光合反应中心的研究进展，以及论文中所涉及到的理论方法进行了概述性的介绍。
第二章以卟吩自由基为研究对象，对TDDFT，ZINDO和INDO／S三种方法计算的电子激发态光谱进行了比较研究，并考察了TDDFT方法下基组效应对卟吩自由基理论光谱的影响。为了进一步检验TDDFT方法的精确度，我们将TDDFT方法扩展到两种典型的卟啉类衍生物(四氧卟啉阳离子TOPDC和卟啉烯Porphycene)紫外吸收光谱的理论归属研究中，结合极化连续介质模型(PCM)有效考察了溶剂化效应对基态的电子结构和激发态能量的影响。采用TDDFT-PCM模型计算的理论光谱与溶液中实验吸收光谱的较好吻合证明了这一模型的合理性，也说明溶剂化效应对溶液中的吸收光谱的理论研究是相当重要的。
第三章以蓝藻捕光系统中的藻蓝蛋白为研究对象，运用含时的密度泛函理论(TDDFT)方法，结合极化连续介质模型(PCM)，对藻蓝蛋白的三个藻蓝素(α-84、β-84、β-155)在具有生理活性时的分子状态，紫外吸收光谱和CD光谱进行了深入系统的理论研究。并结合分子动力学模拟(MD)技术以及ONIOM方法，研究了藻蓝素中吡咯环之间的二面角与其最大吸收峰之间的定性关系。通过一系列模型化学的理论比较研究，阐明了藻蓝蛋白中三类藻蓝素在生理状态时都是以质子化的形式存在及其质子化可能的反应途径，并定量分析和归属了紫外吸收光谱和圆二色光谱。
第四章主要基于色素分子簇模型，运用TDDFT和ZINDO方法对紫细菌(Rps．viridis和Rb．sphaeroides)光合反应中心的紫外吸收光谱和CD光谱重新进行了理论计算与定量解析归属，并有效考察了色素分子间相互作用对电子激发态的影响。TDDFT的计算结果对紫细菌光合反应中心的P发色团被氧化后的实验CD光谱的合理解释表明：色素分子之间的相互作用不可忽视，只基于单个色素分子(或其模型分子)的理论计算进行光谱归属是不合理的。与TDDFT计算结果的比较再次证明，ZINDO半经验分子轨道理论方法对这两类紫细菌光合反应中心的低能带激发态的解析和归属已经具备了一定的精度。
在第五章中，同时考虑了C=O键长伸缩振动和H-C-H键角弯曲振动对H_2CO分子光电子能谱峰形的影响。同时考虑上述两种正则振动模式的情况下，在SAC-CI-GR／D95~*理论级别下对H_2CO分子的基态(1~1A_1)及三个阳离子激发态(1~2B_2，1~2B_1，1~2A_1)进行了势能面扫描，并拟合得到势能函数，最后采用从头算Franck-Condon因子计算程序解析了这三个激发态的实验光电子能谱的精细结构。
The studies of high efficiency photosynthesis mechanism play a crucial role indeveloping the novel pesticides targeting the photosynthesis systems, and rational usingsolar energy. Light-harvesting system and reaction center are the two fundamentalpigment-protein complexes in the plant photosynthesis system. To make clear theelementary processes of electronic transfer in photosynthesis, knowledge of theelectronic excited characters of light-harvesting system and reaction center is aprerequisite. The theoretical studies of the electronic excitations of light-harvestingsystem and reaction center can provide a sophisticated understanding and theassignments of UV/vis absorption and circular dichroism spectra of these two systems. Inthis thesis, the electronic excitation spectra of the model systems (light-harvesting systemof alga and photosynthetic reacting center (PSRC) of purple bacteria) of photosynthesishave been investigated by using modem molecular simulation methods. The presentthesis is organized as follows:
The previous studies about light-harvesting system of alga and photosyntheticreacting center of purple bacteria have been reviewed in chapter one. Furthermore, thetheoretical methods used in this thesis have been introduced.
In chapter two, the electronic ground and singlet vertical excited states of Free-BasePorphyrin (FBP) have been investigated by using TDDFT, ZINDO and INDO/S methods,the basis sets effects have been examined at TDDFT theoretical level. In order to furtherexamine the precision of TDDFT method, the UV/Vis spectra of tetraoxaporphyrindication (TOPDC) and Porphycene have been investigated by using TDDFT method. Thesolvent effects on excitation spectra also have been taken into account by usingpolarizable continuum model (PCM). TDDFT-PCM calculations lead to a closeragreement with the measured values of experimental absorption spectra in solutions,which demonstate the importance of considering the solvent effects for interpretingexperimental absorption spectra in solutions.
In chapter three, the optical characteristics of UV/Vis spectra and CircularDichroism (CD) spectra ofαandβsubunit of C-phycocyanin (C-PC) were investigatedby using TDDFT method combined with the PCM model. Combining the MolecularDynamic (MD) Simulation and ONIOM methods, the effects of the torsion of thepyrrolic rings in phycocyanobilin (PCB) on the absorption maximum also have been taken into account in this chapter. The electronic excitation at the various levels of modelchemistry demonstrate that, protonation is most likely existing in three PCBs (α-84、β-84、β-155) in C-PC in environmental protein moiety, and the reaction pathway forprotonation of PCBs also have been verified.
Using the super molecule cluster models, the excitation spectra of PSRC from Rps.viridis and Rb. sphaeroides have been investigated by using TDDFT method in chapterfour. The effects of the interactions of pigment-pigment on the electronic excitation alsohave been examined. The calculation results show that the interactions ofpigment-pigment play an important role in reasonably assigning the UV/Vis spectra andcircular dichroism (CD) spectra of PSRC from Rps. virids and Rb. sphaeroides. Bycomparing with TDDFT calculation, the agreeable assignment of the experimentalUV/Vis and CD spectra were achieved by using the ZINDO method.
In chapter five, the effects of both C=O stretch and H-C-H scissor models on thephotoelectron spectrum of formaldehyde have been taken into account simultaneously.The potential energy surface of the ground state (1~1A_1) and the first three excited states(1~2B_2, 1~2B_1, 1~2A_1) of formaldehyde have been scanned at SAC-CI-GR/D95* level. Byfitting the potential energy surfaces of these states, the fine structures of the experimentalphotoelectron spectrum of formaldehyde have been accurately assigned by using ab initiofranck-condon factor program.
引文
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