Proton assisted oxygen-oxygen bond splitting in cytochrome p450

Proton assisted O-O bond splitting of cytochromes' P450 hydroperoxo Compound 0 has been investigated by density functional theory, showing a barrier for the slightly endothermic formation of the iron-oxo Compound I. The barrier and the endothermicity increase with decreasing acidity of the distal proton source. Protonation of the proximal iron heme ligand favors the O-O bond scission and provides an important regulatory component in the catalytic cycle. The Compound 0 --> I conversion is slightly exothermic for the peroxidase and catalase models. Implications of the energetic relationship between the two reactive intermediates are discussed in terms of possible oxidative pathways.     

Evidence for an intramolecular charge transfer state in 12'-apo-beta-caroten-12'-al and 8'-apo-beta-caroten-8'-al: influence of solvent polarity and temperature

The ultrafast excited-state dynamics of two carbonyl-containing carotenoids, 12'-apo-beta-caroten-12'-al and 8'-apo-beta-caroten-8'-al, have been investigated by transient absorption spectroscopy in a systematic variation of solvent polarity and temperature. In most of the experiments, 12'-apo-beta-caroten-12'-al was excited at 430 nm and 8'-apo-beta-caroten-8'-al at 445 or 450 nm via the S0 --> S2 (11Ag- --> 11Bu+) transition. The excited-state dynamics were then probed at 860 nm for 12'-apo-beta-caroten-12'-al and at 890 or 900 nm for 8'-apo-beta-caroten-8'-al. The temporal evolution of all transient signals measured in this work can be characterized by an ultrafast decay of the S2 --> SN absorption at early times followed by the formation of a stimulated emission (SE) signal, which subsequently decays on a much slower time scale. We assign the SE signal to a low-lying electronic state of the apocarotenals with intramolecular charge-transfer character (ICT --> S0). This is the first time that the involvement of an ICT state has been detected in the excited-state dynamics of a carbonyl carotenoid in nonpolar solvents such as n-hexane or i-octane. The amplitude ratio of ICT-stimulated emission to S2 absorption was weaker in nonpolar solvents than in polar solvents. We interpret the results in terms of a kinetic model, where the S1 and ICT states are populated from S2 through an ultrafast excited-state branching reaction (tau2 < 120 fs). Delayed formation of a part of the stimulated emission is due to the transition S1 --> ICT (tau3 = 0.5-4.1 ps, depending on the solvent), which possibly involves a slower backward reaction ICT --> S1. Determinations of tau1 were carried out for a large set of solvents. Especially in 12'-apo-beta-caroten-12'-al, the final SE decay, assigned to the nonradiative relaxation ICT --> S0, was strongly dependent on solvent polarity, varying from tau1 = 200 ps in n-hexane to 6.6 ps in methanol. In the case of 8'-apo-beta-caroten-8'-al, corresponding values were 24.8 and 7.6 ps, respectively. This indicates an increasing stabilization of the ICT state with increasing solvent polarity, resulting in a decreasing ICT-S0 energy gap. Tuning the pump wavelength from the blue wing to the maximum of the S0 --> S2 absorption band resulted in no change of tau1 in acetone and methanol. Additional measurements in methanol after excitation in the red edge of the S0 --> S2 band (480-525 nm) also show an almost constant tau1 with only a 10% reduction at the largest probe wavelengths. The temperature dependence of the tau1 value of 12'-apo-beta-caroten-12'-al was well described by Arrhenius-type behavior. The extracted apparent activation energies for the ICT --> S0 transitions were in general small (on the order of a few times RT), which is in the range expected for a radiationless process.     

Modelling of Swelling Phenomena in Charged Hydrated Porous Media

Biological tissues like articular cartilage and geomaterials like clay have a multicomponent microstructure. The charged solid is saturated by a viscous fluid, which itself is composed of several components: the liquid solvent and the dissolved ions, namely, water, anions and cations. These charged multiphase materials exhibit a swelling behaviour under varying chemical conditions. The model describing such materials combines electrochemical and mechanical effects like osmosis and electrostatics within a macroscopic formulation. Starting from the Theory of Porous Media (TPM), a four component model is presented, wherein all constituents are materially incompressible and mass exchanges are excluded. This isothermal model leads to a set of equations which consists of three primary variables: the solid displacement u _S, the pore‐pressure p and the molar ion concentration c_m, since the ion concentrations always depend on each other because of the electroneutrality condition. For the numerical treatment, the weak formulations of governing equations are implemented in the FE tool PANDAS, wherein Taylor‐Hood elements are used for the spatial discretization. Finally, a simulation of a 3‐d swelling experiment is shown. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Localization Phenomena in Liquid-Saturatedand Empty Porous Solids

Localization phenomena occur as a result of local concentrations of plastic deformations in small bands of finite width (shear bands). Porous materials, as, for instance, soil, rock, concrete and sinter materials as well as polymeric and metallic foams exhibit a strong tendency towards shear banding caused by plastic dilatation in the brittle deformation range. This kind of behaviour is of great practical importance in engineering design, for example in the study and computation of failure mechanisms in soil mechanics (base failure, slope failure, etc.). From the mathematical point of view, the computation of localization phenomena, for example within the framework of the finite element method (FEM), yields an ill-posed problem, since each mesh refinement leads to smaller shear bands until one obtains (ideally) a singular surface. Following this, regularization mechanisms should be introduced to obtain reliable and robust results.In the present article, two natural regularization mechanisms for liquid-saturated and empty granular porous materials are discussed. These mechanisms are (1) the inclusion of additional independent degrees of freedom in the sense of the Cosserat brothers for the granular porous solid and (2) the inclusion of pore-fluid viscosity in the saturated case.     

Comparison of a biphasic and a multicomponent model describing viscoelastic swelling phenomena

Biological soft tissues like articular cartilage and their artificial replacement hydrogel have a multicomponent microstructure, consisting of a charged viscoelastic solid matrix saturated by a fluid, which is composed of the liquid solvent and the dissolved anions and cations. Such charged multiphasic materials exhibit a swelling behaviour under varying chemical conditions. These materials are best described by a macroscopic approach like the Theory of Porous Media (TPM). Starting from this point, a standard two-phase model is extended by dividing the fluid into the above mentioned components. Therein, the chemical relations describing the behaviour of the ions and their interaction with the other mixture constituents are incorporated. The resulting model covers mechanical as well as osmotic and electrostatic effects. For numerical and simplicity reasons, it is possible to describe the swelling phenomena by a simplified biphasic model, where the ions as a third degree of freedom and their time-dependent diffusion are neglected. Furthermore, the viscoelastic solid matrix can be replaced by an elastic material. Note that using the multicomponent model generally results in numerical problems, since the boundary conditions depend on the internal fixed charge density. It is shown that this problem can be solved by including the boundary conditions into the weak formulation. Finally, to compare the different behaviour of the above mentioned models by means of an swelling example, they are implemented into the FE tool PANDAS using stable Taylor-Hood elements for the spatial discretization. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)