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1.
The coupling of proton and electron transfers is a key part of the chemistry of photosynthesis. The oxidative side of photosystem II (PS II) in particular seems to involve a number of proton-coupled electron transfer (PCET) steps in the S-state transitions. This mini-review presents an overview of recent studies of PCET model systems in the authors’ laboratory. PCET is defined as a chemical reaction involving concerted transfer of one electron and one proton. These are thus distinguished from stepwise pathways involving initial electron transfer (ET) or initial proton transfer (PT). Hydrogen atom transfer (HAT) reactions are one class of PCET, in which H+ and e are transferred from one reagent to another: AH+B→A+BH, roughly along the same path. Rate constants for many HAT reactions are found to be well predicted by the thermochemistry of hydrogen transfer and by Marcus Theory. This includes organic HAT reactions and reactions of iron-tris(α-diimine) and manganese-(μ-oxo) complexes. In PS II, HAT has been proposed as the mechanism by which the tyrosine Z radical (YZ) oxidizes the manganese cluster (the oxygen evolving complex, OEC). Another class of PCET reactions involves transfer of H+ and e in different directions, for instance when the proton and electron acceptors are different reagents, as in AH–B+C+→A–HB++C. The oxidation of YZ by the chlorophyll P680 + has been suggested to occur by this mechanism. Models for this process – the oxidation of phenols with a pendent base – are described. The oxidation of the OEC by YZ could also occur by this second class of PCET reactions, involving an Mn–O–H fragment of the OEC. Initial attempts to model such a process using ruthenium-aquo complexes are described. An erratum to this article can be found at  相似文献   

2.
The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (Wn) and protonated water clusters (TAH+Wn, n?=?1???6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n?=?1 and 2) and linear (n?=?1 – 6) types of water clusters. Further, the geometries of TAWn clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H3O+ also called Eigen cation) formation in both TAWn and protonated TAWn clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAWn and TAH+Wn clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.  相似文献   

3.
A stochastic exploration of the quantum conformational spaces in the microsolvation of divalent cations with explicit consideration of up to six solvent molecules [Mg (H 2 O) n )]2+, (n?=?3, 4, 5, 6) at the B3LYP, MP2, CCSD(T) levels is presented. We find several cases in which the formal charge in Mg2+ causes dissociation of water molecules in the first solvation shell, leaving a hydroxide ion available to interact with the central cation, the released proton being transferred to outer solvation shells in a Grotthus type mechanism; this particular finding sheds light on the capacity of Mg2+ to promote formation of hydroxide anions, a process necessary to regulate proton transfer in enzymes with exonuclease activity. Two distinct types of hydrogen bonds, scattered over a wide range of distances (1.35–2.15 Å) were identified. We find that in inner solvation shells, where hydrogen bond networks are severely disturbed, most of the interaction energies come from electrostatic and polarization+charge transfer, while in outer solvation shells the situation approximates that of pure water clusters.
Figure
Water dissociation in the first solvation shell is observed only for [Mg(H2O)n]2+ clusters. The dissociated proton is then transferred to higher solvation shells via a Grotthus type mechanism  相似文献   

4.
The reaction mechanism of the hydration of acetylene to acetaldehyde catalyzed by [WIVO(mnt)2]2− (where mnt2− is 1,2-dicyanoethylenedithiolate) is studied using density functional theory. Both the uncatalyzed and the catalyzed reaction are considered to find out the origin of the catalysis. Three different models are investigated, in which an aquo, a hydroxo, or an oxo coordinates to the tungsten center. A first-shell mechanism is suggested, similarly to recent calculations on tungsten-dependent acetylene hydratase. The acetylene substrate first coordinates to the tungsten center in an η2 fashion. Then, the tungsten-bound hydroxide activates a water molecule to perform a nucleophilic attack on the acetylene, resulting in the formation of a vinyl anion and a tungsten-bound water molecule. This is followed by proton transfer from the tungsten-bound water molecule to the newly formed vinyl anion intermediate. Tungsten is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Three other mechanisms are also considered, but the associated energetic barriers were found to be very high, ruling out those possibilities.  相似文献   

5.
The stability constant of the complex of tRNA with 50S subunits of ribosomes was compared in ordinary and heavy water. A considerable effect (about fourfold) was observed, showing the importance of hydrogen bonds in this interaction. In addition, the isotope effect of complementary polynucleotide interaction was measured for two examples. In the case of the binary complex of heptainosinic acid oligomers with poly(C) in the presence of 10?3 M MgCl2, the transfer from ordinary to heavy water gave an increase of the stability constant of about 5%. But in the case of a ternary complex of hexaadenylic acid with poly(U) under the same conditions, the stability constant in D2O increased threefold. The isotope effect depends strongly on magnesium ion concentration and is possibly due to some specific mechanism of magnesium ion complexing involving water molecules.  相似文献   

6.
This minireview is an attempt to summarize our current knowledge on oxidative water splitting in photosynthesis. Based on the extended Kok model (Kok, Forbush, McGloin (1970) Photochem Photobiol 11:457–476) as a framework, the energetics and kinetics of two different types of reactions comprising the overall process are discussed: (i) P680+• reduction by the redox active tyrosine YZ of polypeptide D1 and (ii) Yzox induced oxidation of the four step sequence in the water oxidizing complex (WOC) leading to the formation of molecular oxygen. The mode of coupling between electron transport (ET) and proton transfer (PT) is of key mechanistic relevance for the redox turnover of YZ and the reactions within the WOC. The peculiar energetics of the oxidation steps in the WOC assure that redox state S1 is thermodynamically most stable. This is a general feature in all oxygen evolving photosynthetic organisms and assumed to be of physiological relevance. The reaction coordinate of oxidative water splitting is discussed on the basis of the available information about the Gibbs energy differences between the individual redox states S i+1 and S i and the data reported for the activation energies of the individual oxidation steps in the WOC. Finally, an attempt is made to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O–O bond and on the active role of the protein in tuning the local proton activity that depends on time and redox state S i . The O–O linkage is assumed to take place at the level of a complexed peroxide.  相似文献   

7.
Thirteen different polypeptide subunits, each in one copy, five phosphatidyl ethanolamines and three phosphatidyl glycerols, two hemes A, three Cu ions, one Mg ion, and one Zn ion are detectable in the crystal structure of bovine heart cytochrome c oxidase in the fully oxidized form at 2.8 Å resolution. A propionate of hems a, a peptide unit (–CO–NH–), and an imidazole bound to CuA are hydrogen-bonded sequentially, giving a facile electron transfer path from CuA to heme a. The O2 binding and reduction site, heme a 3, is 4.7 Å apart from CuB. Two possible proton transfer paths from the matrix side to the cytosolic side are located in subunit I, including hydrogen bonds and internal cavities likely to contain randomly oriented water molecules. Neither path includes the O2 reduction site. The O2 reduction site has a proton transfer path from the matrix side possibly for protons for producing water. The coordination geometry of CuB and the location of Tyr244 in subunit I at the end of the scalar proton path suggests a hydroperoxo species as the two electron reduced intermediate in the O2 reduction process.  相似文献   

8.
The rate constants k12n for isomerization of the E1H isomer (pKa 8 in H2O) of ribonuclease-A to the E2H isomer (pKa = 6.1 in H2O), determined from proton-uptake measurements by the temperature-jump technique, in mixtures of protium and deuterium oxides (atom fraction of deuterium n), are described by the equation k12n = (733 ± 16)(1 − n + [0.46 ± 0.04]n)(1 − n + 0.69n)2sec−1 at 25°C. On the basis of the absolute magnitude of the rate constant, the magnitude of the solvent isotope effect and the proton inventory, it appears that the rate-determining step is proton transfer to a water molecule from the imidazolium form of a histidine residue, with a product-like activated complex resembling a hydronium ion. The subsequent motion of the protein structure to generate the new isomer (conformation change) must then occur in a time approaching a vibrational period. Alternative but less likely mechanisms include rate-limiting protein reorganization concerted with proton transfer to water, rate-limiting diffusion of hydronium ion away from the enzyme, or “solvation catalysis” of protein reorganization.  相似文献   

9.
Wang  Meng  Liu  Chao  Li  Qibin  Xu  Xiaoxiao 《Journal of molecular modeling》2015,21(11):1-10

The antioxidant properties of some phenolic Schiff bases in the presence of different reactive particles such as OH, OOH, (CH2=CH−O−O), and -•O2 were investigated. The thermodynamic values, ΔH BDE, ΔH IP, and ΔH PA, were used for this purpose. Three possible mechanisms for transfer of hydrogen atom, concerted proton−electron transfer (CPET), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) were considered. These mechanisms were tested in solvents of different polarity. On the basis of the obtained results it was shown that SET-PT antioxidant mechanism can be the dominant mechanism when Schiff bases react with radical cation, while SPLET and CPET are competitive mechanisms for radical scavenging of hydroxy radical in all solvents under investigation. Examined Schiff bases react with the peroxy radicals via SPLET mechanism in polar and nonpolar solvents. The superoxide radical anion reacts with these Schiff bases very slowly.

  相似文献   

10.
The approach of CO2 to a series of active site model complexes of human carbonic anhydrase II (HCAII) and its catalytic hydration to bicarbonate anion have been investigated using semiempirical MO theory (AM1). The results show that direct nucleophilic attack of zinc-bound hydroxide to the substrate carbon occurs in each model system. Further rearrangement of the bicarbonate complex thus formed via a rotation-like movement of the bicarbonate ligand can only be found in active site model systems that include at least one additional water molecule. Further refinement of the model complex by adding a methanol molecule to mimic Thr-199 makes this process almost activationless. The formation of the final bicarbonate complex by an internal (intramolecular) proton transfer is only possible in the simplest of all model systems, namely {[Im3Zn(OH)]+·CO2}. The energy of activation for this process, however, is 36.8 kcal·mol–1 and thus too high for enzymatic catalysis. Therefore, we conclude that within the limitations of the model systems presented and the level of theory employed, the overall mechanism for the formation of the bicarbonate complex comprises an initial direct nucleophilic attack of zinc-bound hydroxide to carbon dioxide followed by a rotation-like rearrangement of the bicarbonate ligand via a penta-coordinate Zn2+ transition state structure, including the participation of an extra active site water molecule.Electronic Supplementary Material available.  相似文献   

11.
Rate constants for C(α)-proton transfer from racemic 2-(1-hydroxyethyl)-3,4-dimethylthi-oazolium ion catalyzed by lyoxide ion and various oxygen-containing and amine buffers were determined by iodination at 25°C and ionic strength 1.0 in H2O. Thermodynamically unfavorable C(α)-proton transfer to oxygen-containing and amine bases shows general base catalysis with a Brønsted β value of ≥0.92 for bases of pKa ≤ 15; this indicates that the thermodynamically favorable protonation reaction in the reverse direction has a Brønsted α value ≤0.08, which is consistent with diffusion-controlled reprotonation of the C(α)-enamine by most acids. General base catalysis is detectable because there is an 85-fold negative deviation from the Brønsted correlation by hydroxide ion. Primary kinetic isotope effects of (kH/kD)obsd = 1.0 for thermodynamically unfavorable proton transfer to buffer bases and hydroxide ion (ΔpKa ≤ −6) and a secondary solvent isotope effect of kDO/kHO = 2.3 for C(α)-proton transfer are consistent with a very late, enamine-like transition state and rate-limiting diffusional separation of buffer acids from the C(α)-enamine in the rate-limiting step, as expected for a “normal” acid. The second-order rate constants for catalysis by buffer bases were used to calculate a pKa of 21.8 for the C(α)-proton assuming a rate constant of 3 × 109 −1 s−1 for the diffusion-controlled reprotonation of the C(α)-enamine by buffer acids in the reverse direction. It is concluded (i) that C(α)-proton removal occurs at the maximum possible rate for a given equilibrium constant, and (ii) that C(α)-enamines can have a significant lifetime in aqueous solution and on thiamin diphosphate-dependent enzymes.  相似文献   

12.
The nature of hydrogen bonds formed between carboxylic acid residues and histidine residues in proteins is studied by ir spectroscopy. Poly(glutamic acid) [(Glu)n] is investigated with various monomer N bases. The position of the proton transfer equilibrium OH…?N ? O?…?H+N is determined considering the bands of the carboxylic group. It is shown that largely symmetrical double minimum energy surfaces are present in the OH…?N ? O?…?H+N bonds when the pKa of the protonated N base is two values larger than that of the carboxylic groups of (Glu)n. Hence OH…?N ? O?…?H+N bonds between glutamic and aspartic acid residues and histidine residues in proteins may be easily polarizable proton transfer hydrogen bonds. The polarizability of these bonds is one to two orders of magnitude larger than usual electron polarizabilities; therefore, these bonds strongly interact with their environment. It is demonstrated that water molecules shift these proton transfer equilibria in favor of the polar proton boundary structure. The access of water molecules to such bonds in proteins and therefore the position of this proton transfer equilibrium is dependent on conformation. The amide bands show that (Glu)n is α-helical with all systems. The only exception is the (Glu)n-n-propylamine system. When this system is hydrated (Glu)n is α-helical, too. When it is dried, however, (Glu)n forms antiparallel β-structure. This conformational transition, dependent on degree of hydration, is reversible. An excess of n-propylamine has the same effect on conformation as hydration.  相似文献   

13.
A systematic investigation of the proton transfer in the keto-amino/enol tautomerization of imidazolone was undertaken. Calculations in aqueous solution were performed using both combined discrete/self-consistent reaction field (SCRF) and SCRF methods. Complexes containing one to three water molecules around the hydrophilic site of imidazolone were used for the combined discrete/SCRF calculations. The DFT results predict that the barrier height for non-water-assisted intramolecular proton transfer is very high (214.8 kJmol–1). Hydrogen bonding between imidazolone and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process through a eight-member ring formed by imidazolone and two water molecules is found to be more efficient and the calculated barrier height is ca. 61 kJmol–1.Figure DFT calculations in aqueous solution predict the H-bonding between imidazolone(IZ) and the water molecule(s) will dramatically lower the tautomeric barrier by a concerted multiple proton transfer mechanism, in which an eight-member ring structure formed by IZ and 2H2O is found to be more efficient and the barrier is 60.8 kJ mol–1, much less than 214.8 kJ mol–1 in the non-water-assisted mechanism.  相似文献   

14.
Six oxygen-associated resonance Raman bands were identified for intermediates in the reaction of bovine cytochrome c oxidase with O2 at room temperature. The primary intermediate, corresponding to Compound A of cryogenic measurements, is an O2 adduct of heme a 3 and its isotope frequency shifts for 16O18O have established that the binding is of an end-on type. This is followed by two oxoheme intermediates, and the final intermediate appearing around 3 ms is the Fe–OH heme. The reaction rate between the two oxoheme intermediates is significantly slower in D2O than in H2O, suggesting that the electron transfer is regulated by proton translocations at this step. It is noted that the reaction intermediates of oxidized enzyme with hydrogen peroxide yield the same three sets of oxygen isotope-sensitive bands as those of oxoheme intermediates seen for O2 reduction and that the O–O bond has already been cleaved in the so-called peroxy form (or 607 nm form).  相似文献   

15.
The proton/hydroxide (H+/OH) permeability of phospholipid bilayer membranes at neutral pH is at least five orders of magnitude higher than the alkali or halide ion permeability, but the mechanism(s) of H+/OH transport are unknown. This review describes the characteristics of H+/OH permeability and conductance through several types of planar phospholipid bilayer membranes. At pH7, the H+/OH conductances (G H/OH) range from 2–6 nS cm–2, corresponding to net H+/OH permeabilities of (0.4–1.7)×10–5 cm sec–1. Inhibitors ofG H/OH include serum albumin, phloretin, glycerol, and low pH. Enhancers ofG H/OH include chlorodecane, fatty acids, gramicidin, and voltages >80 mV. Water permeability andG H/OH are not correlated. The characteristics ofG H/OH in fatty acid (weak acid) containing membranes are qualitatively similar to the controls in at least eight different respects. The characteristics ofG H/OH in gramicidin (water wire) containing membranes are qualitatively different from the controls in at least four different respects. Thus, the simplest explanation for the data is thatG H/OH in unmodified bilayers is due primarily to weakly acidic contaminants which act as proton carriers at physiological pH. However, at low pH or in the presence of inhibitors, a residualG H/OH remains which may be due to water wires, hydrated defects, or other mechanisms.  相似文献   

16.
The uptake of glutamate in nerve synapses is carried out by the excitatory amino acid transporters (EAATs), involving the cotransport of a proton and three Na+ ions and the countertransport of a K+ ion. In this study, we use an EAAT3 homology model to calculate the pKa of several titratable residues around the glutamate binding site to locate the proton carrier site involved in the translocation of the substrate. After identifying E374 as the main candidate for carrying the proton, we calculate the protonation state of this residue in different conformations of EAAT3 and with different ligands bound. We find that E374 is protonated in the fully bound state, but removing the Na2 ion and the substrate reduces the pKa of this residue and favors the release of the proton to solution. Removing the remaining Na+ ions again favors the protonation of E374 in both the outward- and inward-facing states, hence the proton is not released in the empty transporter. By calculating the pKa of E374 with a K+ ion bound in three possible sites, we show that binding of the K+ ion is necessary for the release of the proton in the inward-facing state. This suggests a mechanism in which a K+ ion replaces one of the ligands bound to the transporter, which may explain the faster transport rates of the EAATs compared to its archaeal homologs.  相似文献   

17.
The uptake of glutamate in nerve synapses is carried out by the excitatory amino acid transporters (EAATs), involving the cotransport of a proton and three Na+ ions and the countertransport of a K+ ion. In this study, we use an EAAT3 homology model to calculate the pKa of several titratable residues around the glutamate binding site to locate the proton carrier site involved in the translocation of the substrate. After identifying E374 as the main candidate for carrying the proton, we calculate the protonation state of this residue in different conformations of EAAT3 and with different ligands bound. We find that E374 is protonated in the fully bound state, but removing the Na2 ion and the substrate reduces the pKa of this residue and favors the release of the proton to solution. Removing the remaining Na+ ions again favors the protonation of E374 in both the outward- and inward-facing states, hence the proton is not released in the empty transporter. By calculating the pKa of E374 with a K+ ion bound in three possible sites, we show that binding of the K+ ion is necessary for the release of the proton in the inward-facing state. This suggests a mechanism in which a K+ ion replaces one of the ligands bound to the transporter, which may explain the faster transport rates of the EAATs compared to its archaeal homologs.  相似文献   

18.
Proton transfer involving internal water molecules that provide hydrogen bonds and facilitate proton diffusion has been identified in some membrane proteins. Arg-94 in cytochrome b of the Rhodobacter sphaeroides bc1 complex is fully conserved and is hydrogen-bonded to the heme propionate and a chain of water molecules. To further elucidate the role of Arg-94, we generated the mutations R94A, R94D, and R94N. The wild-type and mutant bc1 complexes were purified and then characterized. The results show that substitution of Arg-94 decreased electron transfer activity and proton pumping capability and increased O2˙̄ production, suggesting the importance of Arg-94 in the catalytic mechanism of the bc1 complex in R. sphaeroides. This also suggests that the transport of H+, O2, and O2˙̄ in the bc1 complex may occur by the same pathway.  相似文献   

19.
《Journal of molecular biology》2019,431(14):2554-2566
Proton transfer through membrane-bound ion channels is mediated by both water and polar residues of proteins, but the detailed molecular mechanism is challenging to determine. The tetrameric influenza A and B virus M2 proteins form canonical proton channels that use an HxxxW motif for proton selectivity and gating. The BM2 channel also contains a second histidine (His), H27, equidistant from the gating tryptophan, which leads to a symmetric H19xxxW23xxxH27 motif. The proton-dissociation constants (pKa's) of H19 in BM2 were found to be much lower than the pKa's of H37 in AM2. To determine if the lower pKa's result from H27-facilitated proton dissociation of H19, we have now investigated a H27A mutant of BM2 using solid-state NMR. 15N NMR spectra indicate that removal of the second histidine converted the protonation and tautomeric equilibria of H19 to be similar to the H37 behavior in AM2, indicating that the peripheral H27 is indeed the origin of the low pKa's of H19 in wild-type BM2. Measured interhelical distances between W23 sidechains indicate that the pore constriction at W23 increases with the H19 tetrad charge but is independent of the H27A mutation. These results indicate that H27 both accelerates proton dissociation from H19 to increase the inward proton conductance and causes the small reverse conductance of BM2. The proton relay between H19 and H27 is likely mediated by the intervening gating tryptophan through cation–π interactions. This relayed proton transfer may exist in other ion channels and has implications for the design of imidazole-based synthetic proton channels.  相似文献   

20.
The oxygen evolution reaction (OER) is of prime importance in multiple energy storage devices. Perovskite oxides involving lattice‐oxygen oxidation are generally regarded as highly active OER catalysts, but the deprotonation of surface‐bound intermediates limit the further activity improvement. Here, it is shown that this kinetic limitation can be removed by introducing Sr3B2O6 (SB) which activates a proton‐acceptor functionality to boost OER activity. As a proof‐of‐concept example, an experimental validation is conducted on the extraordinary OER performance of a Sr(Co0.8Fe0.2)0.7B0.3O3?δ (SCFB‐0.3) hybrid catalyst, made using Sr0.8Co0.8Fe0.2O3?δ as active component and SB as a proton acceptor. This smart hybrid exhibits an exceptionally ultrahigh OER activity with an extremely low overpotential of 340 mV in 0.1 m KOH and 240 mV in 1 m KOH required for 10 mA cm?2 which is the top‐level catalytic activity among metal oxides reported so far, while maintaining excellent durability. The correlation of pH and activity study reveals that this enhanced activity mainly originates from the improved interfacial proton transfer. Such a strategy further demonstrated to be universal, which can be applied to enhance the OER activity of other high covalent oxides with close O 2p‐band centers relative to Fermi energy.  相似文献   

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