生物分子荷质传递机理及其调控的理论研究

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生物分子荷质传递机理及其调控的理论研究

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英文题名：Studies on the Mechanisms of Proton and Electron Transport and Their Modulations in Biological Molecules
作者：陈效华
论文级别：博士
学科专业名称：理论与计算化学
中文关键词：质子耦合电子转移 ; 金属离子调控电子转移 ; 电子转移中继站 ; 三电子键 ; α-螺旋尾部
英文关键词：Proton-coupled electron transfer ; Metal ions regulating electron transfer ; Relay stations of electron transfer ; Three-electron bonds ; Tail ofα-helix
学位年度：2009
导师：步宇翔
学科代码：081704
学位授予单位：山东大学
论文提交日期：2009-04-16

摘要

电子转移、空穴转移和质子转移是生命科学的基本问题。许多生命过程都涉及到质子和电子的传递问题,例如,光合作用、呼吸作用、生物体内信号传导、酶促反应和基因复制及突变等等。那么电子在生物体内怎样有效传递,电子运动和质子运动的关系怎样,生物金属离子对二者的运动怎样调制,蛋白质能否导电,怎样有效参与电子传递?这一系列问题都是目前人们十分关注的生命问题,也是目前生命科学所遇到的难题。本文围绕这些问题,开展了一系列有意义的工作,取得了一些有价值的研究成果。主要成果和创新简述如下:
     (1)水合金属离子调控酰胺单元间的荷质传递:本文第一个突出贡献就是在氧化破坏的酰胺单元间可以通过七元环质子耦合电子转移机制有效地发生质子和电子交换,电子在两个氧原子间发生转移,同时一个质子在两个氮原子之间以相同方向发生转移。众所周知,酰胺单元是蛋白质肽链骨架的一个重要结构单元,同时也广泛存在于其他生物分子中,如天冬酰胺、谷氨酰胺、鸟嘌呤、胸腺嘧啶/尿嘧啶以及黄素等。我们进一步的研究发现这种有效的质子和电子转移反应机制也可以发生在这些生物分子间。更有趣的是金属离子及其水合物与其双氧位结合,能够有效地调节电子转移通道,从而导致不同的反应机制,使反应机制在单通道氢原子转移←→质子耦合双通道电子转移←→质子耦合单通道电子转移中变化,最终控制反应速率。这种调控性主要源自于不同结合能力的水合金属离子导致过渡态两个氧原子的结合强度的改变。总的来说,结合能力较小的水合金属离子支持质子耦合单通道电子转移,结合能力较大的支持氢原子转移,结合能力中等的支持质子耦合双通道电子转移。这是一个普遍的规律,任何一个水合金属离子与底物结合都会使反应机制坐落在这三个不同的区域。我们研究发现底物与金属离子的结合能、反应能垒、自旋密度分布、O...O的距离和水合金属离子的性质之间存在良好的相关性,这种相关性可以很好地解释酰胺单元间的质子/电子转移机制的变化。也就是说电子转移途径与水合物离子的结合能存在着高度的相关性。这一发现不仅为进一步理解生命过程中金属离子调节电子转移机制提供理论依据,而且还为设计纳米分子开关提供理论基础。
     (2)金属离子调控酰亚胺单元的自由基类型(σ或π)和电子通道(σ或π)对酰胺单元间的质子/电子交换反应另一个重大发现就是水合金属离子可以通过改变含酰亚胺单元分子的自由基的类型(σ-或π-自由基),使电子转移通道发生变化,从而调控反应机制。酰亚胺单元存在于许多生物化学物种内,例如,尿嘧啶、苯并尿嘧啶、萘并尿嘧啶、黄嘌呤、氧化黄素和胸腺嘧啶等等。这些生物化学物种可能会在分子探针和纳米电子装置上得到广泛应用;它的自由基是一些辅因子氧化还原活性中心的重要组成部分,是生物酶反应、DNA/蛋白质损伤过程中电子转移的中介。
     尿嘧啶是酰亚胺单元一种有代表性的物种,为此,我们利用密度泛函方法考察了尿嘧啶和N_3-脱氢尿嘧啶自由基耦合结构(UU)的质子/电子转移机理(UU是近平面顺式的结构),并且考察了水合金属离子对其的调控作用。UU是σ-自由基,没有其它影响时,此体系的PT/ET反应是通过七元环质子耦合σ-电子σ-通道转移机理(PC~σE~σT),反应能垒是3.8kcal/mol,质子是由N_3到N_(3')转移,电子是由O_4到O_(4')转移。水合金属离子结合到O_2/O_(2')或O_4/O_4位点会改变UU自由基的类型(σ-或π-自由基)和电子转移通道(σ-或π-通道),从而显著影响PT/ET协同反应,致使反应机理由PC~σE~σT到PC~πE~σT,再到PC~πE~πT变化。这种改变来自于结合水合金属离子导致UU体系的单占有轨道(SOMO)和最高双占居轨道(HOMO)能级发生交错,是三个因素协同变化的结果:反应物的非对称结构、电子云重新分配和金属离子对反应结构框架的固定作用。水合金属离子结合到O_2/O_(2')位点能够轻微促进UU PT/ET反应,并且没有改变自由基类型和PC~σE~σT机理,反应能垒在3.3kcal/mol到4.7kcal/mol之间。然而,水合金属离子结合在O_4/O_(4')位点会抑制反应,使体系自由基类型变为π-型,反应机理变为PC~πE~σT,相应的反应能垒升高(8.5～17.8kcal/mol)。在这种情况下,由于电子转移通道的变化,我们发现两种PC~πE~σT机理:依靠结合金属离子的结合能力,一种电子转移通道是由O_2到O_(2'),反应能垒较低(8.5～12.2kcal/mol);另一种电子转移通道是由O_4到O_(4'),反应能垒高(16.5～17.8kcal/mol)。两个水合金属离子同时结合到O_2/O_(2')和O_4/O_(4')部位也产生类似的抑制影响,反应能垒在8.3～15.4kcal/mol范围内变化。这儿,UU部分被转变为一个π-自由基,依靠水合离子的路易斯酸性不同,从而引起体系的PT/ET反应发生PC~πE~σT或PC~πE~πT机理。一般来说,弱的路易斯酸水合金属离子支持PC~πE~σT机理,电子转移经过O_4到O_(4');强的路易斯酸水合离子支持PC~πE~πT机理,电子通过π-通道发生转移(一个三电子π-键)。水合金属离子的结合能、反应能垒、与反应物的结合位点、水合金属离子的性质和数目存在良好的相关性,这些相关性可以用来解释UU PT/ET反应机理的变化。这一发现为更好地理解PT/ET协同反应机理提供了有价值的信息和为设计酰亚胺单元为基础的分子器件提供了方法,如,设计分子开关和分子导线等。
     (3)单或多质子耦合里德堡电子转移机理众所周知,-NH_2、-CH_2NH_2和-CH_2NHCH_2-是生物体内非常重要的片断,它们在一系列的生命过程中担任着非常重要的角色。在多数情况下,这些碱性片断很容易被质子化成为正电荷中心:-CH_2NH_3~+和-CH_2NH_2~+CH_2-。在生物电子传递过程中,这些质子化的胺单元一个基本的性质就是能够利用它们的里德堡轨道有效地捕获过剩电子。然而,这些电子富有的里德堡自由基片断是不稳定的并且容易向其它基团释放一个氢原子,从而引起蛋白质内的一系列质子/电子转移反应,这一过程与里德堡电子转移相关。研究这些里德堡片断参与电子/质子传递反应可以为进一步理解蛋白质内的电子转移提供有价值的信息。我们利用从头算法研究发现NH_4与NH_3之间发生单质子耦合里德堡电子转移反应,电子转移是通过环绕体系周围的里德堡轨道传递,同时质子在两个氮原子之间以相同方向的发生转移。CH_3NH_3与CH_3NH_2也通过类似机理发生反应。同时我们也考察了较大的胺分子束,NH_4(NH_3)_n(n=2,3)和CH_3NH_3·(NH_3)_n·NH_2CH_3(n=1,2,3),质子/电子沿着胺分子链传递是分步进行的,每一步都发生类似的单质子耦合里德堡电子转移机理,反应能垒都很小(小于5.0kcal/mol)。当CH_3NH_3和NH_2CH_3被水分子链连接,与单纯的胺分子束相比,CH_3NH_3和NH_2CH_3之间的质子/电子转移反应能垒明显升高。这可能是因为在此过程中,单电子的存在形式发生了变化,由里德堡态转化为溶剂化态,这种转化需要消耗一定的能量。更有趣的是溶剂化电子的运动促进两个或者三个质子同时沿着相同方向运动。这种反应机理可以被描述为多质子耦合里德堡电子转移。这一发现也证明了溶剂化电子的电荷传导性。
     (4)蛋白质内酪氨酸与色氨酸之间可能发生的电子转移机制理解酪氨酸与色氨酸之间分子内或分子间电子转移有非常重要的物理、化学和生物意义。因此,我们运用密度泛函和从头算法分子动力学模拟系统研究了酪氨酸到色氨酸之间所有可能的电子传递机理。研究表明,当这两个氨基酸芳香侧链相互靠近时,侧链发生相互碰撞,他们之间发生直接的质子耦合电子转移反应。在Trp~(·+)Gly_nTyrH(n=0,1,2,…)系统中,当酪氨酸和色氨酸的芳香侧链相互远离,并且有一个生物碱(以甲胺为模型)与苯酚以氢键相连接时,这样整个系统发生双向质子耦合长程电子跳跃机理反应。在这个反应中,酪氨酸是电子的给体,色氨酸是电子的受体,酪氨酸是质子的给体,甲胺是质子的受体,酪氨酸的一个电子发生跳跃传给远距离的色氨酸阳离子,同时苯酚的羟基释放一个质子,传给距离较近的甲胺,在这个过程中质子和电子传递的方向不同。更有趣的是,在Trp~(·+)Gly_nTyrH-A(n=0,1,2,…)系统中,甲胺作为质子受体协助从酪氨酸到色氨酸阳离子发生电子转移需要越过的反应能垒比较低(小于5.0 kcal/mol),并且反应能垒受中间甘氨酸的数目影响很小。这一结果能够很好地解释生物酶中酪氨酸与色氨酸之间的长程电子转移,为我们进一步理解蛋白质长程电子转移提供有价值的信息。
     (5)蛋白质中电子空穴迁移的中继站本论文的另一个重大贡献就是对蛋白质电子空穴有效传递的解释,我们提出了在蛋白质中凡是能够产生氧化还原势较低的区域都可能发挥空穴转移的中继站的功能,促进蛋白质内电子转移,这些区域包括一些弱相互作用结构和构成蛋白质的主要形式α-螺旋的尾部。由于以蛋白质为基础的电子转移反应在一系列的生命过程中扮演着十分重要的角色,因此电子空穴沿着肽链骨架的迁移已经是当今科研工作者最感兴趣的课题之一。最近,更多的工作表明一些特殊的弱相互作用可以担任化学和生物氧化还原反应的电子转移通道,这种弱相互作用包括孤电子对与π体系、π体系与π体系、阳离子与π体系、阴离子与π体系、氢键和两中心三电子键相互作用。
     对此,我们认为蛋白质导电与这些弱相互作用相关,这种可能性来源于在蛋白质空穴传递过程中产生的一系列中继站,其中一类就是形成三电子键。研究表明O∴O键(2.16～2.27(?))不仅能够产生于同一主链的两个相邻的肽键单元之间,也可以产生于两个靠近的不同主链上的肽键单元间。这种发现能够很好地解释电子空穴在蛋白质中从一个肽键到下一个肽键的传递过程。显然,这种O∴O键的稳定性强烈依赖于多肽的组成,当有体积大的氨基酸残基侧链出现在多肽时,这种三电子键的稳定性会降低。另外,由于多肽的成分不同,形成O∴O键又和形成其它种类的三电子键产生竞争。当有硫元素出现在多肽的侧链时,相对于形成O∴O键,热力学上更支持或有利于形成O∴S键。同样,当芳香基团出现在多肽侧链时,又容易在芳香基团和相邻的肽键单元间形成O∴π键。因此,我们推测,在蛋白质电子空穴沿着肽键骨架迁移过程中,这种三电子键能够被连续形成并且作为空穴转移的中继站来协助电子空穴传输。
     另外,构成蛋白质的主要形式α-螺旋的尾部区域也很容易形成电子空穴传递的中继站。我们对此做了系统的分析,发现随着α-螺旋的增长,它们的尾部区域的电离能越低,越容易失掉一个电子被氧化形成电子空穴,当α-螺旋的蛋白质残基大于8个时,它们尾部的电离能小于色氨酸侧链的电离能。不仅如此,我们也考虑真正的蛋白质环境下在尾部出现螺旋帽的情况,研究表明不同的螺旋帽会不同程度地影响α-螺旋尾部的电离势,但是总的来说,α-螺旋的电离势都会比蛋白质的其它区域偏低,容易产生电子空穴。而且,在蛋白质电子传递过程中,短时间内螺旋帽的离开螺旋尾部也为电子空穴的形成创造了机会,螺旋帽的恢复又促使着电子空穴的传出,最终导致蛋白质电子空穴有效传递。
Electron transfer,hole transfer and proton transfer are of the fundamental question in life science.Electron transfer and proton transfer take place in a range of biological processes,including photosynthesis,respiration,and signal transduction of biology,enzymatic reactions,gene replication and mutation and so on.Then how are electrons transferred effectively in these biological processes? What is the relationship between electron transfer and proton transfer? How do the biological metal ions regulate the movement of electron and proton? If the peptide chain is a good conductor of electron and how does the amino acid residues take part in the electron transfer in protein? All these questions are of fundamental importance to the unraveling of key biological processes and also are the main difficulties of life science encountered today. We carried out a series of significative work and obtained many valuable results on these issues,which may help us to understand the biological movement.The primary innovations can be described as follows.
     (1) The hydrated metal ions regulate the electron/proton transport in acylamide units.The first outstanding contribution of this paper is that the proton transfer(PT)/electron transfer(ET) in oxidated acylamide units can effectively occur via a seven-center cyclic proton-coupled electron transfer(PCET) mechanism with a N-→N PT and an O→O ET.The acylamide unit is found in many biological species, such as peptide bonds,asparagine,glutamine,guanine,thymine/uracil and Flavin etc.. Our further investigations indicate that the PT/ET reactions between these biological molecules may also occur via this kind of PCET.More interestingly,when different hydrated metal ions are bound to the two oxygen sites of FF,the PT/ET mechanism may significantly change.In addition to their inhibition of PT/ET rate,the hydrated metal ions can effectively regulate the FF PT/ET cooperative mechanism to produce a single pathway Hydrogen Atom Transfer(HAT) or a flexible Proton Coupled Electron Transfer(PCET) mechanism by changing the ET channel.The regulation essentially originates from the change in the O...O bond strength in the transition state,subject to the binding ability of the hydrated metal ions,In general,the high valent metal ions and those with large binding energies can promote HAT,and the low valent metal ions and those with small binding energies favor PCET.Hydration may reduce the Lewis acidity of cations,and thus favor PCET.Good correlations among the binding energies, barrier heights,spin density distributions,O...O contacts and hydrated metal ion properties have been found,which can be used to interpret the transition in the PT/ET mechanism.That is,there is a good correlation between the electron transfer pathway and the ability of hydrated metal ion.These findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide useful information for a greater understanding of PT/ET cooperative mechanisms,and a possible method for switching conductance in nano-electronic devices.
     (2) The hydrated metal ions regulate the radical type of imide units(σorπ) and electron channels(σorπ).Another outstanding finding on the proton/electron exchange reactions between the acylamide units is that the hydrated metal ions can regulate the radical type of the imide units in some biological molecules and change the type of electron channels among them,which controls the PT/ET mechanisms and reaction rate.Many biological and chemical molecules contain the imide unit,such as, uracil,benzo-fused uracil,naphtho-fused uracil,xanthine,thymine,and so on.These biological and chemical species may find application in molecular probes and nano-electronics.Its radicals are prominent redox-active cofactors and ET intermediates in enzyme reactions and in DNA/protein lesions.
     The mechanism of proton transfer(PT)/electron transfer(ET) in imide units,and its regulation by hydrated metal ions,was explored theoretically using density functional theory in a representative model(a nearly planar and cisoid complex between uracil and its N_3-dehydrogenated radical,UU).In UU(σ-radical),PT/ET normally occurs via a seven-center,cyclic proton-coupledσ-electronσ-channel transfer (PC~σE~σT) mechanism(3.8 kcal/mol barrier height) with a N_3→N_3 PT and an O_4→O_4 ET.Binding of hydrated metal ions to the dioxygen sites(O_2/O_2 or/and O_4/O_4) of UU may significantly affect its PT/ET cooperative reactivity by changing the radical type (σ-radical(?)π-radical) and ET channel(σ-channel(?)π-channel),leading to different mechanisms,ranging from PC~σE~σT,to proton-coupledπ-electronσ-channel transfer (PC~πE~σT) to proton-coupledπ-electronπ-channel transfer(PC~πE~πT).This change originates from an alteration of the ordering of the UU moiety SOMO/HOMO,induced by binding of the hydrated metal ions.It is a consequence of three associated factors:the asymmetric reactant structure,electron cloud redistribution,and fixing role of metal ions to structural backbone.Binding of a hydrated metal ion to the O_2/O_2,site of UU may slightly promote the UU PT/ET reaction without changing its radical type and PC~σE~σT mechanism(3.3-4.7 kcal/mol barrier heights).However, binding of a hydrated metal ion to the O_4/O_4,site may inhibit the reaction,with conversion of the UU moiety to aπ-radical,and a change of the PT/ET mechanism to PC~πE~σT,as characterized by their barrier heights(8,5～17.8 kcal/mol).Two PC~πE~σT mechanisms were observed in this situation,with different ET channels:the favorable O_2→O_2,mechanism,with 8.5-12.2 kcal/mol barrier heights vs.O_4→O_4.with 16.5-17.8 kcal/mol barrier heights,depending on the acidity of the binding metal ions. Synchronous binding of two hydrated metal ions to two dioxygen sites(O_2/O_2 and O_4/O_4.) of UU also yields similar inhibitive effects on the reaction(8.3-15.4 kcal/mol barrier heights).Here,the UU moiety is convened to aπ-radical,and causes the PT/ET reaction to occur via either a PC~πE~σT or PC~πE~πT mechanism,depending also on the Lewis acidity of the hydrated ions.In general,the weakly Lewis acidic hydrated metal ions favor the PC~πE~σT mechanism via the O_4→O_4,ET channel.The strongly acidic ones favor the PC~πE~πT mechanism,occurring via a three-electronπ-bond ET channel,from a doubly occupiedπ-orbital of the U moiety to the singly occupiedπ-orbital of the Ur moiety,in the same direction.Good correlations among the binding energies,barrier heights,the binding sites of substrate,and the properties and number of hydrated metal ions,were found,which can be used to interpret the transitions in the PT/ET mechanisms.The findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide valuable information for a greater understanding of PT/ET cooperative mechanisms,and an alternative way for designing imide-based molecular devices,such as molecular switches and molecular wires.
     (3) Single-/muli-proton coupled Rydberg state electron transfer mechanisms. It is well-known that -NH_2,-CH_2NH_2,and -CH_2NHCH_2- are the important fragments in biological bodies and play important roles in a range of biological progresses. In most cases,these basic fragments are inclined to be protonated and produce positive sites,-CH_2NH_3~+,and -CH_2NH_2~+CH_2-.A general property of these protonated amine fragments is their ability to efficiently trap excess electrons to form hypervalent radical(-CH_2NH_3~·,and -CH_2NH_2~·CH_2-) with their diffuse Rydberg orbitals during biological electron transfer progresses.However,these electron-rich Rydberg radical species are unstable and are ready to release an H-atom to other fragments,involving a series of proton/electron transfer reactions in proteins.Therefore,the study of these Rydberg species taking part in proton/electron transfer may provide useful information to understand electron transfer in proteins.Our ab initio calculations indicate that the proton/electron transfer from NH_4 to NH_3 via a single-proton-coupled Rydberg-state electron transfer mechanism with an Rydberg-state electron transfer pathway around the outside of the framework of system and a N-H~+→N proton migrating channel.A similar mechanism is found for the reactions between CH_3NH_3 and CH_3NH_2 for their two coupled modes:cis-CH_3NH_3NH_2CH_3 and trans-CH_3NH_3NH_2 CH_3.Besides,in the big amine clusters,NH_4(NH_3)_n(n=2,3) and CH_3NH_3·(NH_3)_n·NH_2CH_3(n=1,2,3),the proton/electron transfer along the amine wires is stepwise and every step takes place via a similar single-proton-coupled Rydberg-state electron transfer mechanism with low energy barrier(<5.0 kcal/mol). When a water chain(H_2O)_n,(n=1,2,3) lies between CH_3NH_3 and NH_2CH_3,the energy barriers(8.5～15.0 kcal/mol) of proton/electron transfer between CH_3NH_3 and NH_2CH_3 are raised significantly as compared to these of the pure amine wires(<5.0 kcal/mol).We attribute this fact to the transformation from a Rydberg orbital to a solvated orbital for the singly occupied molecular orbital of these systems,which consumes more energy.More interestingly,the movement of the solvated electron promotes two or three protons synchronously moving along the water wire at the same direction.This process can be described in terms of a multi-proton-coupled Rydberg-state electron transfer mechanism with two or three protons synchronously moving along the water wire and at the same time a Rydberg-state electron transfer- ring through a solvated molecular orbital in the middle of clusters.This finding also validates the charge conductibility of solvated electron.
     (4) The possible mechanisms for the electron transfer from Tyr to Trp in proteins.Understanding the intramolecular or intermolecular electron transfer between tyrosine and oxidized tryptophan residues has important physical,chemical, and biological implications.Therefore,we have systematically explored all the possible electron transfer mechanisms between them in proteins using density functional theory(DFT) and ab initio molecular dynamics(AIMD) methods.When the two aromatic side-chains of them are approximal,the aromatic tings collide with each other and a straightforward proton-coupled electron transfer reaction occurs between them.When the two aromatic side-chains of them are apart residing in the same main-chain of polypeptide cations(Trp~(·+)Gly_nTyrH,n=0,1,2,…) and an alkaloid(a methylamine) presents near the phenol moiety as a proton acceptor,the proton/electron transfer reactions of these systems take place via a didirectional proton -coupled electron hopping mechanism(dPCEH).For these reactions,the electron donor is tyrosine(TyrH),the electron acceptor is tryptophan cation(Trp~(·+)),the proton donor is TyrH,and the proton acceptor is methylamine(A).An electron of tyrosine hops over a long distance to tryptophan cation and at the same time the hydroxyl of phenol releases a proton to N-atom of methylamine over a short distance in the reverse direction.Not only the energy barriers for the dPCEH reactions in the Trp~(·+)Gly_nTyrH-A(n=0,1,2,…) systems is low but also the change of energy barriers with the increasing number of the center glycine is small,which may provide some significant information for understanding long-range electron transfer in proteins.
     (5) Relay station of electron hole migration in proteins Another outstanding finding of this paper is the interpretation of the electron hole migration in proteins.We have proposed that any region with a low reduction potential in proteins can act as the relay station of electron hole migration to promote electron transfer,which includes a series of weak interactions and tails ofα-helices.Electron hole migration along peptide backbone of proteins has become a general topic of substantial current interest, because the protein-based electron-transfer(ET) reactions play a fundamental role in a variety of biological processes.Recently,more efforts have suggested that some weakly special interactions may serve as electron transfer channels for the redox reactions in chemical and biological processes.There are many such kinds of weak interactions in proteins which includes noncovalent and weak-covalent interactions,such as lone pair…π(1p…π) interactions,π…πinteractions,cation…πinteractions,anion…πinteractions,hydrogen bonds(H-bonds),and two-center,three-electron(2c-3e) bonds
     So,we conjecture that the conduction of proteins has relation with these weak interactions and the possibility originates from the formations of a series of relay stations during the electron hole migration processes in proteins.One of relay stations is the three-electron bond.Our calculations found that the O∴O three-electron(3e) bonds(2.16～2.27(?)) can be formed not only between two neighboring peptide units in a main chain but also between two adjacent peptide units in two different main chains in proteins.This finding may address electron hole migration from one peptide unit to the next in proteins.Evidently,stability of the O∴O 3e bonded species is strongly dependent on the component of the oligopeptides and is reduced owing to the steric hindrance of the side chains when the big chains present in oligopeptides.Besides, formation of the O∴O 3e bonds competes with the formation of the other forms of three-electron bonds depending on the component of the polypeptides.Formation of the O∴S 3e bond is thermodynamically more favorable than that of the O∴O 3e bond for the oligopeptides containing sulfur atom in their side chains.Similarly,formation of the O∴π3e bond between aromatic ring of the side chain and the neighboring peptide unit is more stable than that of the O∴O 3e bond when the aromatic amino acids present in the oligopeptides.We infer that a series of three-electron bonds may be formed during the electron hole migration along the peptide backbone in proteins and assist electron hole transport as relay stations,supporting the peptide chain as a conduction wire.
     Besides,tails ofα-helices(α-helices are the main formations in most proteins) can easily form a new kind of relay station of electron hole migration in proteins.Our systemic analyses indicate that the longerα-helix is,the lower the reduction potential is.When the number of amino acid residues constitutingα-helix is more than eight, the ionization energy of the tail ofα-helix is lower than that of tryptophan residues.In this ease,the tail ofα-helix easily loses an electron to form an electron hole and facilitate the electron hole migration in proteins.Further more,we have also considered the effect of helical capping on the formation of electron hole in the tails ofα-helices. Our investigations indicate that the different helical cappings may increase the ionization energies of the tails ofα-helices in different degree.However,the ionization energies of the tails ofα-helices are lower than that of other fragment in proteins.Further more,the helical cappings may move away from the tails ofα-helices for a short time during proteins electron transfer processes,which can provide a chance for the formation of electron hole in these parts.The return of cappings to the tails can promote the transport of electron hole in proteins.

引文

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    [62]In formamide,both the N and O atoms satisfy the 8-electron rule for bonding.Dehydrogenation at the amino group may generate a stable ·NH-CH=O radical.But,this radical cannot form the cyclic coupling mode with formamide because the -HN-H...·NH- single electron H-bond is not as strong as its normal one,and the corresponding =O...O= interaction is repulsive.However,the ·NH-CH=O radical may be converted into the NH=CH-O·radical by intramolecular O→N electron transfer,favoring the formation of the cyclic coupling mode with formamide,resulting in a normal -HN-H...NH- two-electron H-bond and a O...O three-electron bond.
    [63]At the transition state FF~(ts),the HOMO is a two-electron π*-antibonding orbital,while the HOMO-2 is a two-electron g-bonding orbital.Both distribute over the whole molecular backbone and may be viewed as linear combinations of two local π orbitals located on two molecular fragments,respectively.The net contribution of their combination to the bonding between two molecular fragments is zero.
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    [65] Although the oligohydrates of the metal ions are not predominant species, we can use them to model the hydrated metal ions with large binding energies or Lewis acidity. The binding of these kinds of cations with FF favor HAT. To verify this conclusion, we also examined the effect of a trivalent cation Sc~(3+) hydrate, FF-Sc~(3+)(H_2O)_4 (FF+Sc~(3+)(H_2O)_6→FF-Sc~(3+)(H_2O)_4+2H_2O) on the FF PT/ET mechanism. Results (at the transition state, ρN3+N10=0.88, ρO2+O9=0.12) indicate that FF-Sc~(3+)(H_2O)_4 obeys the HAT mechanism.
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    [47] The binding of different hydrated metal ions to the O_4/O_4 site leads to lower the SOMO in different degree to HDMO-n because of the different binding ability of mental ions. For example, Na~+(H_2O)_2 and K~+(H_2O)2 make SOMO→HDMO-3; Mg~(2+)(H_2O)_4 and Ca~(2+)(H_2O)_4 make SOMO→HDMO-4.

    [48] For UU+2M~(Z+)(H_2O)_n systems, their reaction energies are in the range of -22 ～32 kcal/mol for the corresponding UU + 2M~(Z+)(H_2O)_n→ UU-2M(Z+)(H_2O)_(n-2)...4H_2O (M~(Z+)=Li~+, Na~+, Mg~(2+), Ca~(2+), Zn~(2+)) processes in which four inner-sphere water ligands of two hydrated metal ions are replaced by UU and move to the outer-sphere. Although the reaction energies are slightly positive and thermody-namically non-spontaneous for the divalent cation cases, the reaction processes mentioned above can really occur under normal thermodynamic conditions (heating or thermal fluctuation) (see Table S7 and remark).
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    [50] In the initial reactant complexes, the SOMO (π-orbital) is almost localized on the Ur fragment, while the corresponding HDMO (a π-orbital, too) is localized on the U fragment, indicating that no π-π conjugation exists between the two fragments. However, at the TS, the contraction produces a π-π interaction between these two fragments, and then the SOMO becomes delocalized equiva-lently on the two fragments, with a π~*-antibonding character, as does the HDMO, but with π-bonding character. Further combination of the SOMO and HDMO generates a three-electron π-bond between the two fragments. In addition, in both the initial reactant and transition state complexes, the π orbitals are always localized on the outside part of each U fragment (see Figure S14), and no atomic or- bital components of the atoms at the contact faces(ONO) are involved.Thus the actual π-π overlap distance is far larger than the O...O or N...N distances,the closest U...Ur contacts.As a result,this π-π overlap across their ONO contact zone is very small.
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