光合反应中心原初电子转移机理的理论研究

用量子化学密度泛函B3LYP方法在3-21G水平上计算细菌光合反应中心原初电子给体P960和绿色植物PSⅡ光合反应中心原初电子给体P680的电子结构,然后研究轴向配位的组氨酸残基和周围蛋白质环境的影响,最后探讨其原初电子转移机理。计算结果表明：(1)细菌光合作用反应中心原初电子给体P960-h的HOMO主要是由与M分支相连的组成单元上原子的原子轨道组成,而它的LUMO则两个组成单元上原子的原子轨道都有贡献;PSⅡ反应中心中原初电子给体P680的HOMO和LUMO均主要由与D1蛋白相连的组成单元上原子的原子轨道组成。这些计算结果能够从反应中心最核心的部分-原初电子给体的电子结构方面解释Rps.uiridis反应中心和PSⅡ反应中心原初电子转移只沿一个分支进行的的途径选择性。(2)虽然与细菌反应中心原初电子给体超分子P960的两个细菌叶绿素分子形成轴向配位的组氨酸残基His并未参与超分子P960-h的HOMO和LUMO的组成,但是由于其轴向配位,使得P960-h的ELUMO显著地升高到高于辅助细菌叶绿素和去镁细菌叶绿素的相应值,使得原初电子转移反应能够顺利进行。否则原初电子转移反应很难进行。PSⅡ反应中心的情况,与细菌反应中心十分相似。(3)细菌反应中心辅助细菌叶绿素(ABChlb)中的Mg离子与最近的组氨酸残基His中的N原子的距离和原初电子给体P960中的相应的Mg-N的距离相似,因此同样应该考虑此轴向配位的组氨酸残基,此时原初电子转移反应是沿L分支从P960-h经ABChlb到去镁细菌叶绿素(BPheob)的两步电子转移过程。而PSⅡ反应中心的辅助叶绿素不存在His的轴向配位,这应是与细菌反应中心的重要区别之一,此时原初电子转移应是沿Dl分支从P680-h到Pheoa的一步电子转移过程,但同时也不能完全排除从P680-h到AChla到Pheoa的二步电子转移过程。     

细菌光合反应中心Q~A和Q~B间电子转移反应的量子化学研究

用量子化学半经验的AM1和密度泛函DFT(BELYP/6-31G(d))方法分别优化了质体醌MQ1(Q~A)、泛醌UQ1(Q~B)及其阳离子自由基的结构。用Nelsen方法计算了电子转移反应MQ1-UQ1→MQ1UQ^-~1的内重组能λi。用线性反应坐标方法构造了该电子转移反应的双势阱,两透热势能面在反应坐标R≈0.30处相交。对该电子转移体系进行闭壳层的单点计算,并用Koopmans定理计算了体系的分裂能△,得到△随线性反应坐标R的变化关系。结果表明,在R=0.342处△有一极小值,从而得到该电子转移反应的电子转移矩阵元Vrp,并由此确定了反应的过渡态。在此基础上,用两球模型计算了反应的溶剂重组能λ0。本文还计算了该电子转移反应的活化自由能△G。最后,根据Marcus电子转移理论计算了该反应的速率常数ket为5.93×10^4s^-^1,由此得到该反应的半衰期与文献报道的结果一致。     

紫细菌反应中心色素蛋白复合膜电子转移研究

采用自组装单层膜方法在金电极表面形成单分子层的2,3－双巯基丁二酸（DMSA）,聚二甲基二丙烯氯化铵（PDDA）及紫细菌（Rhodobacter Sphaeroides)反应中心色素蛋白复合体的有序复合膜,使用方波估安法研究了该蛋白复合膜的电化学行为,成功地检测到该蛋白内多电对的可逆或准可逆电子转移过程,探讨了紫细菌反应中心蛋白内容各电子受体的氧化还原电位及外加电位驱动对各受体电位的影响,同时,通过对方波信号的非线形拟合,获得了该蛋白复合膜内主要电对的电子转移速率常数及电子迁移数等相关参数。     

Rps. viridis光合反应中心分子间相互作用对电子转移机理影响的理论研究

基于晶体结构并经QM/MM优化后的结构数据, 用量子化学密度泛函(DFT, B3LYP)方法, 在6-31G基组水平上, 对紫色光合细菌Rhodopseudomonas(Rps.)viridis 反应中心内, 色素分子与蛋白质环境中氨基酸残基以及水分子间的配位及氢键等相互作用对反应中心原初电子转移反应机理的影响进行了探讨. 结果表明: 组氨酸残基的轴向配位使色素分子的ELUMO显著升高, 这对电子转移能够进行极为重要; 而氢键作用使色素分子的E_LUMO有所降低, 有利于说明电子转移由原初电子给体P沿L分支进行. 文中结果支持电子转移反应为不经过辅助细菌叶绿素的一步过程. 只将色素分子周围的蛋白质环境作为具有一定介电常数的均匀介质来处理是远远不够的.     

有机取代反应的电子转移机理

有机取代反应的电子转移机理贾志胜（兰州大学化学系甘肃７３００００）在有机化学中，取代反应占有非常重要的地位，对其反应机理的研究已公认相当成熟。最新的研究对该类反应机理有了新的认识。自７０年代末，对取代反应机理的研究，特别是对芳香取代反应、卤代烷的取代...     

用从头算研究Shilov反应的机理

Shilov反应在CH~4活化中占有中心地位,它有氧化加成和σ迁移两种可能的机理。本文用较大基组的从头算研究了这两种机理的反应过程,认为Shilov反应应按氧化加成机理进行。     

NH_3/NH_3~+体系电子转移性的黄金规则研究

用密度泛函理论(BEP86, B3LYP)在6-31G~*, 6-311+G~*基组水平上和从头算方 法[MP2(FULL)/6-311+G~*]优化了NH_3和NH_3~+以及复合物(NH_3…NH_3)~*的几何 构型，计算了体系稳定化能，然后用MP2（FULL）／6－311＋G”＊方法扫描势有面 找出不同N－N接触距离的活化志体系的能量、活化能、耦合矩阵元，利用黄金规则 计算出不同的N－N接触距离的电子转移速率。并讨论了活化态体系的能量、活化能 、耦合矩辄元和Franck-Condon因子及电子转移速率与接触距离的依赖关系。进一 步验证了黄金规则应用于电子转移反应的正确性。     

紫细菌光合反应中心电子激发态的理论研究

运用ZINDO和INDO/S两种量子化学理论方法, 对紫细菌(Rhodopseudomonas (Rps.) viridis) 光合反应中心色素分子簇的电子激发态进行了理论研究. 通过理论计算的电子激发态光谱与实验吸收光谱, Circular Dichroism光谱的比较, 对实验光谱重新进行了较为合理的归属. 考察了色素分子间相互作用、色素分子与蛋白质中氨基酸残基相互作用对激发态光谱的影响. 研究结果表明: Rps. viridis光合反应中心色素分子簇间的相互作用以及氨基酸残基与色素分子的作用, 对激发态光谱的性质具有一定的影响; 不考虑色素分子间相互作用以及色素分子与周围氨基酸残基的作用, 只基于单个色素分子(或其模型分子)理论计算进行光谱归属是不合理的.     

O~3＋NH→HNO＋O~2反应机理的量子化学研究

用密度泛函(DFT)的B3LYP方法(6－31++G^*^*)研究了臭氧与NH自由基反应的微观机理,优化得到反应途径上的反应物,过渡态,中间体和产物的构型,通过振动分析对过渡态和中间体进行了确认。对单点用QCISD(T)/6－31++G^*^*方法计算能量,同时进行零点能校正。研究结果表明：NH与O~3反应有两条不同的反应通道,且均表现为亲电反应特征,两条不同的反应均为强放热反应。     

四氯化苯醌-二苯撑体系的光诱导电子转移研究

用从头算方法对四氯化苯醌-二苯撑体系分子间相互作用进行了理论计算研究.用MP2/6-31G^**方法,分别优化电子给体二苯撑,受体四氯化苯醌的稳定构型,用同样的方法优化配合物的层间距得到其最稳定构型,并计算了BSSE校正后的电子给受体配合物的稳定化能.用CIS/6-31++G^**方法,计算了给体、受体及配合物的电子激发态.理论计算验证了给体和受体间能形成稳定的电子给受体配合物,该配合物受光激发能直接产生电荷转移态.在球孔穴近似和点偶极近似下,对电荷转移吸收的理论计算结果进行了非平衡溶剂化能校正.经非平衡溶剂化能校正的电荷转移跃迁能与实验值符合较好.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc     

Mechanism for the Nonadiabatic Photooxidation of Benzene to Phenol: Orientation‐Dependent Proton‐Coupled Electron Transfer

An efficient catalytic one‐step conversion of benzene to phenol was achieved recently by selective photooxidation under mild conditions with 2,3‐dichloro‐5,6‐dicyano‐p‐benzoquinone (DDQ) as the photocatalyst. Herein, high‐level electronic structure calculations in the gas phase and in acetonitrile solution are reported to explore the underlying mechanism. The initially populated ¹ππ* state of DDQ can relax efficiently through a nearby dark ¹nπ* doorway state to the ³ππ* state of DDQ, which is found to be the precursor state involved in the initial intermolecular electron transfer from benzene to DDQ. The subsequent triplet‐state reaction between DDQ radical anions, benzene radical cations, and water is computed to be facile. The formed DDQH and benzene‐OH radicals can undergo T₁→S₀ intersystem crossing and concomitant proton‐coupled electron transfer (PCET) to generate the products DDQH₂ and phenol. Two of the four considered nonadiabatic pathways involve an orientation‐dependent triplet PCET process, followed by intersystem crossing to the ground state (S₀). The other two first undergo a nonadiabatic T₁→S₀ transition to produce a zwitterionic S₀ complex, followed by a barrierless proton transfer. The present theoretical study identifies novel types of nonadiabatic PCET processes and provides detailed mechanistic insight into DDQ‐catalyzed photooxidation.     

肽链体系中的长程电子转移: 酪氨酸与色氨酸间电子转移的理论研究

用电子转移的半经典模型和量子化学半经验方法对色氨酸-酪氨酸二肽体系进行电子转移动力学参数计算.用AM1方法分别优化给体、受体和桥体几何构型,用线性反应坐标的构造了给体和受体分子间电子转移的双势阱,得到两透热势能面交叉处的反应坐标为R=(约等于)0.10,并确定了反应的内重组能及反应热.对色氨酰酪氨酸和酪氨酰色氨酸体系进行闭壳层HF自洽场计算,按Koopmans定理计算体系分子轨道分裂能值A(三角形),在R约为0处发现了A(三角形)的极小值,从而获得色氨酰酪氨酸及酪氨酰色氨酸体系分子内电子转移的电子转移矩阵元V~D~A分别为0.96kJ.mol^-^1和0.87kJ.mol^-^1.采用Marcus双球模型估算反应的溶剂重组能为64.60kJ.mol^-^1。     

Structural, kinetic, and theoretical studies on models of the zinc-containing phosphodiesterase active center: medium-dependent reaction mechanisms

Dinuclear zinc(II) complexes [Zn(2)(bpmp)(mu-OH)](ClO(4))(2) (1) and [Zn(2)(bpmp)(H(2)O)(2)](ClO(4))(3) (2) (H-BPMP=2,6-bis[bis(2-pyridylmethyl)aminomethyl]-4-methylphenol) have been synthesized, structurally characterized, and pH-driven changes in metal coordination observed. The transesterification reaction of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) in the presence of the two complexes was studied both in a water/DMSO (70:30) mixture and in DMSO. Complex 2 was not reactive whereas for 1 considerable rate enhancement of the spontaneous hydrolysis reaction was observed. A detailed mechanistic investigation by kinetic studies, spectroscopic measurements ((1)H, (31)P NMR spectroscopy), and ESI-MS analysis in conjunction with ab initio calculations was performed on 1. Based on these results, two medium-dependent mechanisms are presented and an unusual bridging phosphate intermediate is proposed for the process in DMSO.     

Electronic structures and long‐range electron transfer through DNA molecules

Quantum chemical calculation on an entire molecule of segments of native DNA was performed in an ab initio scheme with a simulated aqueous solution environment by overlapping dimer approximation and negative factor counting method. The hopping conductivity was worked out by random walk theory and compared with recent experiment. We conclude that electronic transport in native DNA molecules should be caused by hopping among different bases as well as phosphates and sugar rings. Bloch type transport through the delocalized molecular orbitals on the whole molecular system also takes part in the electronic transport, but should be much weaker than hopping. The complementary strand of the double helix could raise the hopping conductivity for more than 2 orders of magnitudes, while the phosphate and sugar ring backbone could increase the hopping conductivity through the base stacks for about 1 order of magnitude. DNA could transport electrons easily through the base stacks of its double helix but not its single strand. Therefore, the dominate factor that influences the electronic transfer through DNA molecules is the π stack itself instead of the backbone. The final conclusion is that DNA can function as a molecular wire in its double helix form with the conditions that it should be doped, the transfer should be a multistep hopping process, and the time period of the transfer should be comparable with that of an elementary chemical reaction. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 112–130, 2000     

Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis

All electron calculations were performed on the photosynthetic reaction center of Blastochloris viridis, using the fragment molecular orbital (FMO) method. The protein complex of 20,581 atoms and 77,754 electrons was divided into 1398 fragments, and the two‐body expansion of FMO/6‐31G* was applied to calculate the ground state. The excited electronic states of the embedded electron transfer system were separately calculated by the configuration interaction singles approach with the multilayer FMO method. Despite the structural symmetry of the system, asymmetric excitation energies were observed, especially on the bacteriopheophytin molecules. The asymmetry was attributed to electrostatic interaction with the surrounding proteins, in which the cytoplasmic side plays a major role. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010