A tetrameric iron superoxide dismutase from the eucaryote Tetrahymena pyriformis.

Abstract An iron-containing superoxide dismutase has been purified from the protozoan Tetrahymena pyriformis. It has a molecular weight of 85,000 and is composed of four subunits of equal size. The tetramer contains 2.5 g atoms of ferric iron. Visible absorption and electron spin resonance spectra closely resemble those of other iron-containing superoxide dismutases. The amino acid sequence of the iron superoxide dismutase was determined. Each subunit is made up of 196 residues, corresponding to a molecular weight of 22,711. Comparison of the primary structure with the known sequences of other iron-containing superoxide dismutases reveals a relatively low degree of identity (33-34%). However, a higher percentage identity is found with mammalian manganese-containing superoxide dismutases (41-42%). The amino acid sequence is discussed in consideration of residues that may distinguish iron from manganese or dimeric from tetrameric superoxide dismutases

Percolation transition of hydration water at hydrophilic surfaces

An analysis of water clustering is used to study the quasi-2D percolation transition of water adsorbed at planar hydrophilic surfaces. Above the critical temperature of the layering transition (quasi-2D liquid-vapor phase transition of adsorbed molecules) a percolation transition occurs at some threshold surface coverage, which increases with increasing temperature. The location of the percolation line is consistent with the existence of a percolation transition at the critical point. The percolation threshold at a planar surface is weakly sensitive to the size of the system when its lateral dimension increases from 80 to 150 A. The size distribution of the largest water cluster shows a specific two-peaks structure in a wide range of surface coverage : the lower- and higher-size peaks represent contributions from non-spanning and spanning clusters, respectively. The ratio of the average sizes of spanning and non-spanning largest clusters is about 1.8 for all studied planes. The two-peak structure becomes more pronounced with decreasing size of the planar surface and strongly enhances at spherical surfaces.Comment: 17 pages, 11 figure

Molecular structural order and anomalies in liquid silica

The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water.Comment: 30 pages, 8 figure

Excitation and relaxation in atom-cluster collisions

Electronic and vibrational degrees of freedom in atom-cluster collisions are treated simultaneously and self-consistently by combining time-dependent density functional theory with classical molecular dynamics. The gradual change of the excitation mechanisms (electronic and vibrational) as well as the related relaxation phenomena (phase transitions and fragmentation) are studied in a common framework as a function of the impact energy (eV...MeV). Cluster "transparency" characterized by practically undisturbed atom-cluster penetration is predicted to be an important reaction mechanism within a particular window of impact energies.Comment: RevTeX (4 pages, 4 figures included with epsf

Static and Dynamic Properties of a Viscous Silica Melt Molecular Dynamics Computer Simulations

We present the results of a large scale molecular dynamics computer simulation in which we investigated the static and dynamic properties of a silica melt in the temperature range in which the viscosity of the system changes from O(10^-2) Poise to O(10^2) Poise. We show that even at temperatures as high as 4000 K the structure of this system is very similar to the random tetrahedral network found in silica at lower temperatures. The temperature dependence of the concentration of the defects in this network shows an Arrhenius law. From the partial structure factors we calculate the neutron scattering function and find that it agrees very well with experimental neutron scattering data. At low temperatures the temperature dependence of the diffusion constants $D$ shows an Arrhenius law with activation energies which are in very good agreement with the experimental values. With increasing temperature we find that this dependence shows a cross-over to one which can be described well by a power-law, D\propto (T-T_c)^gamma. The critical temperature T_c is 3330 K and the exponent gamma is close to 2.1. Since we find a similar cross-over in the viscosity we have evidence that the relaxation dynamics of the system changes from a flow-like motion of the particles, as described by the ideal version of mode-coupling theory, to a hopping like motion. We show that such a change of the transport mechanism is also observed in the product of the diffusion constant and the life time of a Si-O bond, or the space and time dependence of the van Hove correlation functions.Comment: 30 pages of Latex, 14 figure

A New Method for the Generation of Realistic Atomistic Models of Siliceous MCM-41

A new method is outlined for constructing realistic models of the mesoporous amorphous silica adsorbent, MCM-41. The procedure uses the melt-quench molecular dynamics technique. Previous methods are either computationally expensive or overly simplified, missing key details necessary for agreement with experimental data. Our approach enables a whole family of models spanning a range of pore widths and wall thicknesses to be efficiently developed and yet sophisticated enough to allow functionalisation of the surface – necessary for modelling systems such as self-assembled monolayers on mesoporous supports (SAMMS), used in nuclear effluent clean-up. The models were validated in two ways. The first method involved the construction of adsorption isotherms from grand canonical Monte Carlo simulations, which were in line with experimental data. The second method involved computing isosteric heats at zero coverage and Henry law coefficients for small adsorbate molecules. The values obtained for carbon dioxide gave good agreement with experimental values. We use the new method to explore the effect of increasing the preparation quench rate, pore diameter and wall thickness on low pressure adsorption. Our results show that tailoring a material to have a narrow pore diameter can enhance the physisorption of gas species to MCM-41 at low pressure

Ion association in concentrated NaCI brines from ambient to supercritical conditions: results from classical molecular dynamics simulations

Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H(2)O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m) NaCl–water mixtures under ambient (25°C, 1 bar), hydrothermal (325°C, 1 kbar) and deep crustal (625°C, 15 kbar) conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757). With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (Na(n)Cl(m))(n-m )clusters in addition to simple NaCl ion pairs. Large polyatomic (Na(n)Cl(m))(n-m )clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions