| 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 N3-dehydrogenated radical,UU).In UU(σ-radical),PT/ET normally occurs via a seven-center,cyclic proton-coupledσ-electronσ-channel transfer (PCσEσT) mechanism(3.8 kcal/mol barrier height) with a N3→N3 PT and an O4→O4 ET.Binding of hydrated metal ions to the dioxygen sites(O2/O2 or/and O4/O4) 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 PCσEσT,to proton-coupledπ-electronσ-channel transfer (PCπEσT) to proton-coupledπ-electronπ-channel transfer(PCπEπT).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 O2/O2,site of UU may slightly promote the UU PT/ET reaction without changing its radical type and PCσEσT mechanism(3.3-4.7 kcal/mol barrier heights).However, binding of a hydrated metal ion to the O4/O4,site may inhibit the reaction,with conversion of the UU moiety to aπ-radical,and a change of the PT/ET mechanism to PCπEσT,as characterized by their barrier heights(8,5～17.8 kcal/mol).Two PCπEσT mechanisms were observed in this situation,with different ET channels:the favorable O2→O2,mechanism,with 8.5-12.2 kcal/mol barrier heights vs.O4→O4.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(O2/O2 and O4/O4.) 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 PCπEσT or PCπEπT mechanism,depending also on the Lewis acidity of the hydrated ions.In general,the weakly Lewis acidic hydrated metal ions favor the PCπEσT mechanism via the O4→O4,ET channel.The strongly acidic ones favor the PCπEπT 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 -NH2,-CH2NH2,and -CH2NHCH2- 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,-CH2NH3+,and -CH2NH2+CH2-.A general property of these protonated amine fragments is their ability to efficiently trap excess electrons to form hypervalent radical(-CH2NH3·,and -CH2NH2·CH2-) 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 NH4 to NH3 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 CH3NH3 and CH3NH2 for their two coupled modes:cis-CH3NH3NH2CH3 and trans-CH3NH3NH2 CH3.Besides,in the big amine clusters,NH4(NH3)n(n=2,3) and CH3NH3·(NH3)n·NH2CH3(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(H2O)n,(n=1,2,3) lies between CH3NH3 and NH2CH3,the energy barriers(8.5～15.0 kcal/mol) of proton/electron transfer between CH3NH3 and NH2CH3 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·+GlynTyrH,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·+GlynTyrH-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) bondsSo,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.
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