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.     

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.     

Reference values for drag and lift of a two‐dimensional time‐dependent flow around a cylinder

This paper presents a numerical study of a two‐dimensional time‐dependent flow around a cylinder. Its main objective is to provide accurate reference values for the maximal drag and lift coefficient at the cylinder and for the pressure difference between the front and the back of the cylinder at the final time. In addition, the accuracy of these values obtained with different time stepping schemes and different finite element methods is studied. Copyright © 2004 John Wiley & Sons, Ltd.     

Robust handling of non‐linear constraints for GA optimization of aerodynamic shapes

A new approach to the robust handling of non‐linear constraints for GAs (genetic algorithms) optimization is proposed. A specific feature of the approach consists of the change in the conventional search strategy by employing search paths which pass through both feasible and infeasible points (contrary to the traditional approach where only feasible points may be included in a path). The method (driven by full Navier–Stokes computations) was applied to the problem of multiobjective optimization of aerodynamic shapes subject to various geometrical and aerodynamic constraints. The results demonstrated that the method retains high robustness of conventional GAs while keeping CFD computational volume to an acceptable level, which allowed the algorithm to be used in a demanding engineering environment. Copyright © 2004 John Wiley & Sons, Ltd.     

Least‐squares meshfree method for incompressible Navier–Stokes problems

A least‐squares meshfree method based on the first‐order velocity–pressure–vorticity formulation for two‐dimensional incompressible Navier–Stokes problem is presented. The convective term is linearized by successive substitution or Newton's method. The discretization of all governing equations is implemented by the least‐squares method. Equal‐order moving least‐squares approximation is employed with Gauss quadrature in the background cells. The boundary conditions are enforced by the penalty method. The matrix‐free element‐by‐element Jacobi preconditioned conjugate method is applied to solve the discretized linear systems. Cavity flow for steady Navier–Stokes problem and the flow over a square obstacle for time‐dependent Navier–Stokes problem are investigated for the presented least‐squares meshfree method. The effects of inaccurate integration on the accuracy of the solution are investigated. Copyright © 2004 John Wiley & Sons, Ltd.     

On a resolvent estimate of the Stokes equation with Neumann–Dirichlet‐type boundary condition on an infinite layer

This paper is concerned with the standard Lp estimate of solutions to the resolvent problem for the Stokes operator on an infinite layer with ‘Neumann–Dirichlet‐type’ boundary condition. Copyright © 2004 John Wiley & Sons, Ltd.     

Continuation of travelling‐wave solutions of the Navier–Stokes equations

An efficient way of obtaining travelling waves in a periodic fluid system is described and tested. We search for steady states in a reference frame travelling at the wave phase velocity using a first‐order pseudospectral semi‐implicit time scheme adapted to carry out the Newton's iterations. The method is compared to a standard Newton–Raphson solver and is shown to be highly efficient in performing this task, even when high‐resolution grids are used. This method is well suited to three‐dimensional calculations in cylindrical or spherical geometries. Copyright © 2006 John Wiley & Sons, Ltd.     

A complete boundary integral formulation for compressible Navier–Stokes equations

A complete boundary integral formulation for compressible Navier–Stokes equations with time discretization by operator splitting is developed using the fundamental solutions of the Helmholtz operator equation with different order. The numerical results for wall pressure and wall skin friction of two‐dimensional compressible laminar viscous flow around airfoils are in good agreement with field numerical methods. Copyright © 2004 John Wiley & Sons, Ltd.