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1.
We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z)() (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fe(d) at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(I) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(I)-Fe(I) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride. Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(I) species, but cannot bond with the Fe(I)-Fe(I) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2 pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (i) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2 pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(I)-Fe(I) complexes; and (iii) in the e(g)-2 pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).  相似文献   

2.
 A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways form rings in which the separated charges can be stabilized. Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000  相似文献   

3.
Concerted proton and electron transfers (CPET) currently attract considerable theoretical and experimental attention, notably in view of their likely involvement in many enzymatic reactions. Electrochemistry, through techniques such as cyclic voltammetry, can provide a quite effective access to CPET in terms of diagnosis and quantitative kinetic characterization. The relationships expressing the rate constant of an electrochemical CPET are given. Besides the CPET standard potential, it depends on two main factors. One is the reorganization energy, which appears as the sum of an intramolecular contribution and two solvent reorganization energies corresponding to proton and electron transfers, respectively. The other is the pre-exponential factor that mainly depends on proton tunneling through the activation barrier. Procedures for estimating these various factors as well as the H/D kinetic isotope effect are described. Application of the theory is illustrated by the experimental results obtained for the cyclic voltammetric reduction of the water-superoxide ion complex in dimethylformamide and acetonitrile.  相似文献   

4.
Proton-coupled electron transfers currently attract considerable attention in view of their likely involvement in many natural processes. Electrochemistry, through techniques such as cyclic voltammetry, is an efficient way of investigating the reaction mechanism of these reactions, and deciding whether proton and electron transfers are concerted or occur in a stepwise manner. The oxidation of an ortho-substituted 4,6-di (tert-butyl)-phenol in which the phenolic hydrogen atom is transferred during the reaction to the nitrogen atom of a nearby amine is taken as illustrative example. A careful analysis of the cyclic voltammetric responses obtained with this compound and its OD derivative allows, after estimation of the various thermodynamic parameters, ruling out the occurrence of the square scheme mechanism involving the proton-electron and electron-proton sequences. Simulation and comparison of the rate constant and H/D kinetic isotope effect with theoretical predictions show that the experimental value of the preexponential factor is ca. 1 order of magnitude larger than the theoretical value. Detailed calculations suggest that an electric field effect is responsible for this discrepancy.  相似文献   

5.
6.
Ceria based oxides are regarded as key oxide materials for energy and environmental applications, such as solid oxide fuel cells, oxygen permeation membranes, fuel cell electrodes, oxygen storage, or heterogeneous catalysis. This great versatility in applications is rendered possible by the fact that rare earth-doped ceria is a pure oxygen ion conductor while undoped ceria, CeO(2-δ), is a mixed oxygen ion-electron conductor. To get deeper insight into the mixed conduction mechanism of oxygen ions and electrons from atomistic and electronic level viewpoints we have applied first-principles density functional theory (DFT + U method). The calculation results show that oxygen vacancies strongly attract localized electrons, forming associates between them. The migration energy of an oxygen vacancy in such an associate is substantially lowered compared to the unassociated case due to the simultaneous positional rearrangement of localized electrons during the ionic jump process. Accordingly, we propose a concerted migration mechanism of oxygen vacancies and localized electrons in reduced ceria; this mechanism results in an increased diffusivity of oxygen vacancies supported by localized electrons compared with that in pure oxide ion conductors.  相似文献   

7.
The transition metal rhodium has been proved the effective catalyst to convert from NO(x) to N(2.) In the present work, we are mainly focused on the NO adsorption and decomposition reaction mechanism on the surface of the Rh(7)(+) cluster, and the calculated results suggest that the reaction can proceed via three steps. First, the NO can adsorb on the surface of the Rh(7)(+) cluster; second, the NO decomposes to N and O atoms; finally, the N atom reacts with the second adsorbed NO and reduces to a N(2) molecule. The N-O bond breaks to yield N and O atoms in the second step, which is the rate-limiting step of the whole catalytic cycle. This step goes over a relatively high barrier (TS(12)) of 39.6 kcal/mol and is strongly driven by a large exothermicity of 55.1 kcal/mol during the formation of stable compound 3, accompanied by the N and O atoms dispersed on the different Rh atoms of the Rh(7)(+) cluster. In addition, the last step is very complex due to the different possibilities of reaction mechanism. On the basis of the calculations, in contrast to the reaction path II that generates N(2) from two nitrogen atoms coupling, the reaction path I for the formation of intermediate N(2)O is found to be energetically more favorable. Present work would provide some valuable fundamental insights into the behavior of the nitric oxide adsorption and reduction reaction mechanism on the Rh(7)(+) cluster.  相似文献   

8.
The reduction chemistry of (mu-bridge)[Fe(CO)3]2 [bridge = propane-1,3-dithiolate (1) and ethane-1,2-dithiolate (2)] is punctuated by the formation of distinct products, resulting in a marked difference in CO inhibition of electrocatalytic proton reduction. The products formed following reduction of 2 have been examined by a range of electrochemical, spectroelectrochemical, and spectroscopic approaches. Density functional theory has allowed assessment of the relative energies of the structures proposed for the reduction products and agreement between the calculated spectra (IR and NMR) and bond distances with the experimental spectra and EXAFS-derived structural parameters. For 1 and 2, one-electron reduction is accompanied by dimerization, but the structure, stability, and reaction with CO of the dimer is different in the two cases, and this is responsible for the different CO inhibition response for electrocatalytic proton reduction. Calculations of the alternate structures of the two-electron, one-proton reduced forms of 2 show that the isomers with terminally bound hydrides are unlikely to play a significant role in the chemistry of these species. The hydride-transfer chemistry of the 1B species is more reasonably attributed to a hydride-bridged form. The combination of experimental and computational results provides a solid foundation for the interpretation of the reduction chemistry of dithiolate-bridged diiron compounds, and this will underpin translation of the diiron subsite of the [FeFe] hydrogenase H cluster into an abiological context.  相似文献   

9.
In NiFe hydrogenases, electrons are transferred from the active site to the redox partner via a chain of three Iron-Sulfur clusters, and the surface-exposed [4Fe4S] cluster has an unusual His(Cys)3 ligation. When this Histidine (H184 in Desulfovibrio fructosovorans) is changed into a cysteine or a glycine, a distal cubane is still assembled but the oxidative activity of the mutants is only 1.5 and 3% of that of the WT, respectively. We compared the activities of the WT and engineered enzymes for H2 oxidation, H+ reduction and H/D exchange, under various conditions: (i) either with the enzyme directly adsorbed onto an electrode or using soluble redox partners, and (ii) in the presence of exogenous ligands whose binding to the exposed Fe of H184G was expected to modulate the properties of the distal cluster. Protein film voltammetry proved particularly useful to unravel the effects of the mutations on inter and intramolecular electron transfer (ET). We demonstrate that changing the coordination of the distal cluster has no effect on cluster assembly, protein stability, active-site chemistry and proton transfer; however, it slows down the first-order rates of ET to and from the cluster. All-sulfur coordination is actually detrimental to ET, and intramolecular (uphill) ET is rate determining in the glycine variant. This demonstrates that although [4Fe4S] clusters are robust chemical constructs, the direct protein ligands play an essential role in imparting their ability to transfer electrons.  相似文献   

10.
Treating the phenylvinyldene manganese complex Cp(CO)2MnC1C2HPh, 1, with [Fe(CO)4] yields the binuclear μ-vinylidene complex Cp(CO)2MnFe(μ-C1C2HPh)(CO)4, 2, that further isomerizes to the carbonylated product η4-[Cp(CO)2MnC1(CO)C2HPh]Fe(CO)3, 3. In a computational study of the mechanism using a hybrid density functional method, we considered two stereoisomers for species 2 and 3 where the phenyl group at center C2 is oriented in cis (E form) or trans (Z form) fashion to the Cp(CO)2Mn unit. Isomers 2E and 2Z were calculated to be degenerate whereas the experimentally detected species 3E is 8 kcal/mol more stable than its isomer 3Z. The two-step pathway 1 → 2Z → 3E was calculated to be the lowest-energy route with the highest activation barrier at 12 kcal/mol. The activation energy of the alternative single-step pathway 1 → 3E is 19 kcal/mol. We rationalized the stabilization of the ground state of 3E and the transition states leading to or starting from isomer 2Z as conjugation effect between the Mn-CC metallaallene fragment and the co-planar phenyl ring.  相似文献   

11.
The electron capture dynamics of halocarbon and its water complex have been investigated by means of the full dimensional direct density functional theory molecular dynamics method in order to shed light on the mechanism of electron capture of a halocarbon adsorbed on the ice surface. The CF(2)Cl(2) molecule and a cyclic water trimer (H(2)O)(3) were used as halocarbon and water cluster, respectively. The dynamics calculation of CF(2)Cl(2) showed that both C-Cl bonds are largely elongated after the electron capture, while one of the Cl atoms is dissociated from CF(2)Cl(2) (-) as a Cl(-) ion. Almost all total available energy was transferred into the internal modes of the parent CF(2)Cl radical on the product state, while the relative translational energy of Cl(-) was significantly low due to the elongation of two C-Cl bonds. In the case of a halocarbon-water cluster system, the geometry optimization of neutral complex CF(2)Cl(2)(H(2)O)(3) showed that one of the Cl atoms interacts with n orbital of water molecules of trimer and the other Cl atom existed as a dangling Cl atom. After the electron capture, only one C-Cl bond (dangling Cl atom) was rapidly elongated, whereas the other C-Cl bond is silent during the reaction. The dangling Cl atom was directly dissociated from CF(2)Cl(2) (-)(H(2)O)(3) as Cl(-). The fast Cl(-) ion was generated from CF(2)Cl(2) (-)(H(2)O)(3) on the water cluster. The mechanism of the electron capture of halocarbon on water ice was discussed on the basis of the theoretical results.  相似文献   

12.
The mechanism of the Beckmann rearrangement (BR) catalyzed by the ZSM-5 zeolite has been investigated by both the quantum cluster and embedded cluster approaches at the B3LYP level of theory using the 6-31G(d,p) basis set. Single-point calculations were carried out at the MP2/6-311G(d,p) level of theory to improve energetic properties. The embedded cluster model suggests that the initial step of the Beckmann rearrangement is not the O-protonated oxime but the N-protonated oxime. The energy barriers derived from the proton shuttle of the N-bound to the O-bound isomer are determined to be approximately 99 and approximately 40 kJ/mol for the embedded cluster and quantum cluster approaches, respectively. The difference in the activation energy is due mainly to the effect of the Madelung potential from the zeolite framework. The next step is the rearrangement step, which is the transformation of the O-protonated oxime to be an enol-formed amide compound, formimidic acid. The activation energy, at the rearrangement step, is calculated to be approximately 125 and approximately 270 kJ/mol for the embedded cluster and quantum cluster approaches, respectively. The final step is the tautomerization step which transforms the enol-form to the keto-form, formamide compound. The energy barrier for tautomerization is calculated to be 123 and 151 kJ/mol for the embedded cluster and quantum cluster approaches, respectively. These calculated results suggest that the rate-determining step of the vapor phase of the Beckmann rearrangement on H-ZSM-5 is the rearrangement or tautomerization step.  相似文献   

13.
Using broken-symmetry density functional theory and spin-projection methods, we have examined the electronic structure and properties of a large mixed-valent Fe(III)-Fe(IV) diiron system that displays two bidentate carboxylates and a single mu-oxo moiety as bridging ligands. Two carboxylates and a single oxygen species have long been implicated as core elements of the elusive intermediate X in ribonucleotide reductase. Spectroscopic studies of X have also identified the presence of an additional terminal or bridging oxygen-based ligand. Introduction of a second oxygen and protonated variants thereof in the core of our structural model is favored as a bridging hydroxide based on the lowest energy structure. M?ssbauer measurements indicate clearly that the two iron sites of X are distinct and that there is significant electron delocalization onto the oxygen-based ligands. For several examined spin states of our model cluster, M?ssbauer parameters from density functional calculations are neither able to differentiate between the iron sites nor reproduce the strong spin delocalization onto the oxygen-based ligands observed experimentally. The combined comparison of the calculated geometries, spin states, spin densities, and M?ssbauer properties for our model clusters with available experimental data for X implies that intermediate X is significantly different from the diiron structural models examined herein.  相似文献   

14.
The infrared OH stretching frequencies of the various types of hydroxyl groups on MgO surfaces have been calculated by periodic (VASP) and cluster (Gaussian) DFT simulations. Surface irregularities (mono and diatomic steps, corners, step divacancies, and kinks) have been considered to model the IR spectra of hydroxylated MgO powders. A good correspondence between calculated and experimental frequencies is obtained with the B3LYP functional. Hydrogen-bonding is the parameter which influences most the IR frequency of OH groups, followed by location of OH groups in concave or convex areas of the surface and then oxygen coordination. The evolution of experimental IR spectra upon evacuation at increasing temperature can be rationalized on the basis of calculated thermal stabilities of each kind of OH groups. A new model is finally proposed to help assign the experimental bands, in terms of hydrogen-bonding, local topology of the hydroxylated sites, and coordination of oxygen.  相似文献   

15.
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess electron density with the frontier orbitals of the first-shell solvent molecules cannot explain the observed magnetic, vibrational, and electronic properties of this species. Despite the need for multielectron effects to explain these important properties, the ensemble-averaged radial wavefunctions and energetics of the highest occupied and three lowest unoccupied orbitals of the hydrated electrons in our hybrid model are close to the s- and p-like states obtained in one-electron models. Thus, one-electron models can provide a remarkably good approximation to the multielectron picture of the hydrated electron for many applications; indeed, the two approaches appear to be complementary.  相似文献   

16.
Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge8z(z=-6, -4, -2, 0, +2, +4) using nine initial geometries. For Ge8(2-) the D2d bisdisphenoid structure predicted by the Wade-Mingos rules is not computed to be the global minimum but instead lies 3.9 kcal mol-1 above the Td tetracapped tetrahedron global minimum predicted to exhibit spherical aromaticity. The hyperelectronic clusters Ge(8)4- and Ge8(6-) have nido B8H12 and square antiprism structures, respectively, as global minima in accord with the Wade-Mingos rules and experimental data on E(8)2+(E=Sb, Bi) cations. Hypoelectronic eight-vertex clusters isoelectronic and isolobal with Ge8, Ge8(2+) and Ge(8)4+ are not known experimentally. Their computed structures include smaller polyhedra having one or more capped triangular faces as well as more open non-polyhedral structures.  相似文献   

17.
Density functional theory transition structures were located for three concerted [6 + 4] cycloaddition reactions involving cis-hexatriene and butadiene, cyclopentadiene and cycloheptatriene, and cyclopentadiene and tropone. Geometries, energies, and entropies were computed at the Becke3LYP/6-31G* level. The activation energy of the concerted [6 + 4] cycloaddition of hexatriene and butadiene is 33.3 kcal/mol, about 8 kcal/mol above the activation energy of the butadiene plus ethylene [4 + 2] cycloaddition. The endo concerted [6 + 4] transition state is 1.1 kcal/mol higher than the exo. The [6 + 4] reaction of cyclopentadiene and cycloheptatriene has a barrier of 25.9 kcal/mol, while the cyclopentadiene–tropone barrier drops to 20.7 kcal/mol. Received: 3 December 1998 / Accepted: 18 February 1999 / Published online: 7 June 1999  相似文献   

18.
Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.  相似文献   

19.
Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge(9)(z) clusters (z = -6, -4, -3, -2, 0, +2, and +4) starting from three different initial configurations. Double-zeta quality LANL2DZ basis functions extended by adding one set of polarization (d) and one set of diffuse (p) functions were used. The global minimum for Ge(9)(2)(-) is the tricapped trigonal prism expected by Wade's rules for a 2n + 2 skeletal electron structure. An elongated tricapped trigonal prism is the global minimum for Ge(9)(4)(-) similar to the experimentally found structure for the isoelectronic Bi(9)(5+). However, the capped square antiprism predicted by Wade's rules for a 2n + 4 skeletal electron structure is only 0.21 kcal/mol above this global minimum indicating that these two nine-vertex polyhedra have very similar energies in this system. Tricapped trigonal prismatic structures are found for both singlet and triplet Ge(9)(6)(-), with the latter being lower in energy by 3.66 kcal/mol and far less distorted. The global minimum for the hypoelectronic Ge(9) is a bicapped pentagonal bipyramid. However, a second structure for Ge(9) only 4.54 kcal/mol above this global minimum is the C(2)(v)() flattened tricapped trigonal prism structure found experimentally for the isoelectronic Tl(9)(9)(-). For the even more hypoelectronic Ge(9)(2+), the lowest energy structure consists of an octahedron fused to two trigonal bipyramids. For Ge(9)(4+), the global minimum is an oblate (squashed) pentagonal bipyramid with two pendant Ge vertices.  相似文献   

20.
Electron-rich polyisocyano derivatives Fe(2)(S(2)C(n)H(2n)(CO)(6-x)(CNMe)(x) (x approximately 4) undergo oxidatively induced (FeCp(2)(+)) reaction with additional CNMe to give [Fe(2)(SR)(2)(CNMe)(7)](PF(6))(2), a new class of iron thiolates. Crystallographic characterization established that the 34 e(-) dinuclear core resembles the oxidized (H(2)-binding) form of the active sites of the Fe-only hydrogenases, key features being the face-sharing bioctahedral geometry, the mu-CX ligand, and an Fe-Fe separation of 2.61 A. Oxidation of the phenylthiolate Fe(2)(SPh)(2)(CO)(2)(CNMe)(4) led to mononuclear [Fe(SPh)(CNMe)(5)](PF(6)), which is analogous to [Fe(2)(SR)(2)(CNMe)(10)](PF(6))(2) formed upon treatment of [Fe(2)(S(2)C(3)H(6))(CNMe)(7)](PF(6))(2) with excess CNMe.  相似文献   

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