Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II

ABSTRACT

QM(UB3LYP)/MM(AMBER) calculations were performed for the locations of the transition structure (TS) of the oxygen–oxygen (O–O) bond formation in the S₄ state of the oxygen-evolving complex (OEC) of photosystem II (PSII). The natural orbital (NO) analysis of the broken-symmetry (BS) solutions was also performed to elucidate the nature of the chemical bonds at TS on the basis of several chemical indices defined by the occupation numbers of NO. The computational results revealed a concerted bond switching (CBS) mechanism for the oxygen–oxygen bond formation coupled with the one-electron transfer (OET) for water oxidation in OEC of PSII. The orbital interaction between the σ-HOMO of the Mn(IV)₄–O₍₅₎ bond and the π*-LUMO of the Mn(V)₁=O₍₆₎ bond plays an important role for the concerted O–O bond formation for water oxidation in the CaMn₄O₆ cluster of OEC of PSII. One electron transfer (OET) from the π-HOMO of the Mn(V)₁=O₍₆₎ bond to the σ*-LUMO of the Mn(IV)₄–O₍₅₎ bond occurs for the formation of electron transfer diradical, where the generated anion radical [Mn(IV)₄–O₍₅₎]^-? part is relaxed to the ?Mn(III)₄?…?O₍₅₎^- structure and the cation radical [O₍₆₎=Mn(V)₁]⁺ ? part is relaxed to the ⁺O₍₆₎–Mn(IV)₁? structure because of the charge-spin separation for the electron-and hole-doped Mn–oxo bonds. Therefore, the local spins are responsible for the one-electron reductions of Mn(IV)₄->Mn(III)₄ and Mn(V)₁->Mn(IV)₁. On the other hand, the O₍₅₎^- and O₍₆₎⁺ sites generated undergo the O–O bond formation in the CaMn₄O₆ cluster. The Ca(II) ion in the cubane- skeleton of the CaMn₄O₆ cluster assists the above orbital interactions by the lowering of the orbital energy levels of π*-LUMO of Mn(V)₁=O₍₆₎ and σ*-LUMO of Mn(IV)₄–O₍₅₎, indicating an important role of its Lewis acidity. Present CBS mechanism for the O–O bond formation coupled with one electron reductions of the high-valent Mn ions is different from the conventional radical coupling (RC) and acid-base (AB) mechanisms for water oxidation in artificial and native photosynthesis systems. The proton-coupled electron transfer (PC-OET) mechanism for the O–O bond formation is also touched in relation to the CBS-OET mechanism.     

水斗非定常自由水膜流三维贴体数值模拟

本研究采用水斗三维非正交贴体坐标系进行了非定常自由水膜流动的数值解析。对不规则水斗内表面采用三维非正交贴体坐标系下离散点进行拟合,推导了曲面离散点的法向矢量和曲面微元面高斯曲率、平均曲率等几何特征量的计算公式,进而导出流体粒子在运动方向上曲率计算式。在水斗三维贴体坐标系中,还推导了流体粒子在水斗曲面上的运动控制方程。最后对某水轮机水斗内表面非定常自由水膜流进行了数值模拟,得到其非定常水膜流态分布。     

Influence of Azimuthal Structure of Surface Waves on Efficiency of their Excitation by Tubular Electron Beams

The excitation of eigen surface waves by tubular electron beams in cylindrical discharge devices is studied. The influence of the wave‐field azimuthal structure on the excitation efficiency and nonlinear stage of the plasmabeam instability is investigated both numerically and analytically. Analytical expressions for the saturation amplitude and excitation efficiency of the wave under study are derived. They are found to agree well with results obtained by numerical modelling of the plasma‐beam interaction presented in this paper. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Numerical solutions of the shallow water equations with discontinuous bed topography

A simple scheme is developed for treatment of vertical bed topography in shallow water flows. The effect of the vertical step on flows is modelled with the shallow water equations including local energy loss terms. The bed elevation is denoted with z_b^‐ for the left and z_b⁺ for the right values at each grid point, hence exactly representing a discontinuity in the bed topography. The surface gradient method (SGM) is generalized to reconstruct water depths at cell interfaces involving a vertical step so that the fluxes at the cell interfaces can accurately be calculated with a Riemann solver. The scheme is verified by predicting a surge crossing a step, a tidal flow over a step and dam‐break flows on wet/dry beds. The results have shown good agreements compared with analytical solutions and available experimental data. The scheme is efficient, robust, and may be used for practical flow calculations. Copyright © 2002 John Wiley & Sons, Ltd.     

THE QUALITATIVE CONTENT OF RENEWABLE RESOURCE MODELS

This paper analyzes the extent to which standard dynamic renewable resource models possess refutable implications. Both the steady state comparative static and local comparative dynamic properties of the standard model are studied. A unified framework is developed which enables one to analyze the qualitative properties of any standard renewable resource model. This is achieved by explicitly linking the local stability, steady state comparative static, and local comparative dynamic properties of the model.     

瓣形均匀带电面在其直径处的电势分布

从点电荷的电势计算公式出发推导出了瓣形均匀带电面在其直径处的电势分布.进一步讨论了均匀带电半球面在其底面以及均匀带电球面内部和外部的电势分布.     

Constructing Invariant Fairness Measures for Surfaces

The paper proposes a rational method to derive fairness measures for surfaces. It works in cases where isophotes, reflection lines, planar intersection curves, or other curves are used to judge the fairness of the surface. The surface fairness measure is derived by demanding that all the given curves should be fair with respect to an appropriate curve fairness measure. The method is applied to the field of ship hull design where the curves are plane intersections. The method is extended to the case where one considers, not the fairness of one curve, but the fairness of a one parameter family of curves. Six basic third order invariants by which the fairing measures can be expressed are defined. Furthermore, the geometry of a plane intersection curve is studied, and the variation of the total, the normal, and the geodesic curvature and the geodesic torsion is determined.     

Simulation of viscous water column collapse using adapting hierarchical grids

An adaptive hierarchical grid‐based method for predicting complex free surface flows is used to simulate collapse of a water column. Adapting quadtree grids are combined with a high‐resolution interface‐capturing approach and pressure‐based coupling of the Navier–Stokes equations. The Navier–Stokes flow solution scheme is verified for simulation of flow in a lid‐driven cavity at Re=1000. Two approaches to the coupling of the Navier–Stokes equations are investigated as are alternative face velocity and hanging node interpolations. Collapse of a water column as well as collapse of a water column and its subsequent interaction with an obstacle are simulated. The calculations are made on uniform and adapting quadtree grids, and the accuracy of the quadtree calculations is shown to be the same as those made on the equivalent uniform grids. Results are in excellent agreement with experimental and other numerical data. A sharp interface is maintained at the free surface. The new adapting quadtree‐based method achieves a considerable saving in the size of the computational grid and CPU time in comparison with calculations made on equivalent uniform grids. Copyright © 2005 John Wiley & Sons, Ltd.     

Energy Spectrum Width and Nonequilibrium Energy of Rayleigh Waves Scattered on a Two-Dimensional Near-Surface Electron Layer

We obtain expressions for the energy spectrum widths of Rayleigh waves corresponding to their deformational coupling to Fermi and Boltzmann electrons in a two-dimensional layer near the surface of a semibounded solid. We evaluate the nonequilibrium energy of Rayleigh waves that depends on these widths and is caused by the same coupling to the corresponding hot electrons. We show that this energy is independent of the degeneracy degree of the electrons and is given by the mean energy of free Rayleigh waves heated up to temperature of the electrons. We find conditions under which the thermodynamics is determined by this nonequilibrium energy of Rayleigh waves in films of a certain thickness with Fermi electrons near the surface and by the equilibrium energy of bulk phonons in thicker samples. All the results are obtained using the Keldysh diagram technique applied to the case of semibounded media.