On the formation, nature, stability and biological relevance of the primary reaction intermediates of myoglobins with hydrogen peroxide

The reaction between hydrogen peroxide and myoglobin (or haemoglobin) ferric haem is a two-electron redox process, yet the stable product is ferryl haem, retaining only one oxidizing equivalent. We have used SVD (singular value decomposition) and global spectroscopic analysis to examine the transient primary spectral intermediates in this reaction, which have been reported as either "compound 0"(ferric peroxide) or "compound I"(ferryl and porphyrin cation radical) types and which may precede the formation of ferrylmyoglobin. To test the hypothesis that the distal histidine facilitates ferryl formation we studied the myoglobin-like haemoglobin from the gastropod mollusc Aplysia fasciata, where this histidine is replaced by valine and its hydrogen bonding role is taken up by a non-homologous arginine. In this protein, consistent with the distal histidine hypothesis, a compound 0 intermediate is formed identified by an EPR spectrum typical of low spin ferric haem complexes. It is significantly more stable than any species seen with mammalian myoglobin. Thirdly, as ferryl haems and associated free radicals may play a role in disease, we have studied the action of myoglobin-peroxide mixtures towards external reductants. Even at a low pH, where ferrylmyoglobin is protonated and in its most reactive state, pre-incubation with reducing donors, including one-electron donors such as ferrocyanide, prior to peroxide addition renders both oxidizing equivalents available. The physiological antioxidant vitamin, ascorbate, is also able to trap both reactive species. Myoglobin can therefore act as a true ascorbate peroxidase. Ascorbate in vivo may be critical in controlling and preventing toxic side reactions of this and related haem proteins.     

The reaction of Ru3(CO)12 with HC9PPh2)3. Characterisation of Ru3(CO)9[HC(PPh2)3], and crystal and molecular structure of Ru3(CO)9[HC(PPh2)(PhPC6H4PPh)]·CHCl3

Reaction of Ru₃(CO)₁₂ with HC(PPh₂)₃ leads to a variety of products, two of which have been characterised. One is the symmetrically capped product Ru₃(CO)₉[HC(PPh₂)₃], which was characterised spectroscopically. The second product was characterised crystallographically as Ru₃(CO)₉[HC(PPh₂)-(PhPC₆H₄PPh)]-CHCl₃.     

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

This article describes a number of algorithms that are designed to improve both the efficiency and accuracy of finite difference solutions to the Poisson-Boltzmann equation (the FDPB method) and to extend its range of application. The algorithms are incorporated in the DelPhi program. The first algorithm involves an efficient and accurate semianalytical method to map the molecular surface of a molecule onto a three-dimensional lattice. This method constitutes a significant improvement over existing methods in terms of its combination of speed and accuracy. The DelPhi program has also been expanded to allow the definition of geometrical objects such as spheres, cylinders, cones, and parallelepipeds, which can be used to describe a system that may also include a standard atomic level depiction of molecules. Each object can have a different dielectric constant and a different surface or volume charge distribution. The improved definition of the surface leads to increased precision in the numerical solutions of the PB equation that are obtained. A further improvement in the precision of solvation energy calculations is obtained from a procedure that calculates induced surface charges from the FDPB solutions and then uses these charges in the calculation of reaction field energies. The program allows for finite difference grids of large dimension; currently a maximum of 571(3) can be used on molecules containing several thousand atoms and charges. As described elsewhere, DelPhi can also treat mixed salt systems containing mono- and divalent ions and provide electrostatic free energies as defined by the nonlinear PB equation.     

Boundary perturbation methods for high-frequency acoustic scattering: shallow periodic gratings

Despite significant recent advances in numerical methodologies for simulating rough-surface acoustic scattering, their applicability has been constrained by the limitations of state-of-the-art computational resources. This has been particularly true in high-frequency applications where the sheer size of the full-wave simulations render them impractical, and engineering processes must therefore rely on asymptotic models [e.g., Kirchhoff approximation (KA)]. However, the demands for high precision can make the latter inappropriate, thus efficient, error-controllable methodologies must be devised. This paper presents a computational strategy that combines the virtues of rigorous solvers (error control) with those of high-frequency asymptotic models (frequency-independent computational costs). These methods are based on high-order "boundary perturbations," which display high precision and unparalleled efficiency. This is accomplished by incorporating asymptotic phase information to effect a significant decrease in computational effort, simultaneously retaining the full-wave nature of the approach. The developments of this contribution are constrained to configurations that preclude multiple scattering; it is further explained how the schemes can be made applicable to general scattering scenarios, though implementation details are left for future work. Even for single-scattering configurations, the approach presented here gives significant gains in accuracy when compared to asymptotic theories (e.g., KA) with modest additional computational cost.     

Joint Analyticity and Analytic Continuation of Dirichlet–Neumann Operators on Doubly Perturbed Domains

In this paper we take up the question of analyticity properties of Dirichlet–Neumann operators (DNO) which arise in boundary value and free boundary problems from a wide variety of applications (e.g., fluid and solid mechanics, electromagnetic and acoustic scattering). More specifically, we consider DNO defined on domains inspired by the simulation of ocean waves over bathymetry, i.e. domains perturbed independently at both the top and bottom. Our analysis shows that the DNO, when perturbed from an arbitrary smooth domain, is parametrically analytic (as a function of deformation height/slope) for profiles of finite smoothness. Additionally, we extend these results to joint spatial and parametric analyticity when the perturbations are real analytic. This analysis is novel not only in that it accounts for the doubly perturbed nature of the geometry, but also in that the technique of proof establishes the full joint analyticity from an arbitrary smooth profile simultaneously.      

Spontaneous Magnetization in the Plane

The Arak process is a solvable stochastic process which generates coloured patterns in the plane. Patterns are made up of a variable number of random non-intersecting polygons. We show that the distribution of Arak process states is the Gibbs distribution of its states in thermodynamic equilibrium in the grand canonical ensemble. The sequence of Gibbs distributions forms a new model parameterised by temperature. We prove that there is a phase transition in this model, for some non-zero temperature. We illustrate this conclusion with simulation results. We measure the critical exponents of this off-lattice model and find they are consistent with those of the Ising model in two dimensions.