Sebastien N. Kerisit

The roles of outer membrane cytochromes of Shewanella and Geobacter in extracellular electron transfer

As key components of the electron transfer (ET) pathways used for dissimilatory reduction of solid iron [Fe(III)] (hydr)oxides, outer membrane multihaem c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 and OmcE and OmcS of Geobacter sulfurreducens mediate ET reactions extracellularly. Both MtrC and OmcA are at least partially exposed to the extracellular side of the outer membrane and their translocation across the outer membrane is mediated by bacterial type II secretion system. Purified MtrC and OmcA can bind Fe(III) oxides, such as haematite (α-Fe2 O3 ), and directly transfer electrons to the haematite surface. Bindings of MtrC and OmcA to haematite are probably facilitated by their putative haematite-binding motifs whose conserved sequence is Thr-Pro-Ser/Thr. Purified MtrC and OmcA also exhibit broad operating potential ranges that make it thermodynamically feasible to transfer electrons directly not only to Fe(III) oxides but also to other extracellular substrates with different redox potentials. OmcE and OmcS are proposed to be located on the Geobacter cell surface where they are believed to function as intermediates to relay electrons to type IV pili, which are hypothesized to transfer electrons directly to the metal oxides. Cell surface-localized cytochromes thus are key components mediating extracellular ET reactions in both Shewanella and Geobacter for extracellular reduction of Fe(III) oxides.

Molecular dynamics simulations of the interactions between water and inorganic solids

Molecular dynamics simulations of three solid surfaces, namely, the (00.1) and (01.2) hematite surfaces and the (10.4) calcite surface, in contact with an aqueous solution have been performed and the structure of water near the interface investigated. We initially calculated the hydration and hydroxylation energies of the two hematite surfaces using static calculations to determine the adsorbed state of water on these surfaces before studying hydration using molecular dynamics. The dynamics simulations show that, in each case, the water density exhibits a damped oscillatory behaviour up to a distance of at least 15 A from the surface. Next, we investigated the adsorption of ions on the (10.4) calcite surface by calculating their free energy profile. These profiles show a strong correlation with the water structure at the interface. This implies that the adsorption of water at the surface of the solid causes the density fluctuations, which in turn control further adsorption. Further analysis revealed that, in each case, the solid surface had a strong effect on the self-diffusion coefficient and the orientation order parameter of water near the interface. Finally, to consider the effect of the crystal size on the solid/water interface, we modelled a calcite nanoparticle in vacuum and immersed in water. We found that the nanoparticle undergoes a phase change in vacuum but that, in the presence of water, the calcite structure was stabilised. Also, the water residence time in the first hydration shell of the surface calcium ions suggested that the dynamics of water in the vicinity of the nanoparticle resemble that around an isolated calcium ion.

Kinetic Monte Carlo model of charge transport in hematite (α-Fe2O3)

The mobility of electrons injected into iron oxide minerals via abiotic and biotic electron transfer processes is one of the key factors that control the reductive dissolution of such minerals. Building upon our previous work on the computational modeling of elementary electron transfer reactions in iron oxide minerals using ab initio electronic structure calculations and parametrized molecular dynamics simulations, we have developed and implemented a kinetic Monte Carlo model of charge transport in hematite that integrates previous findings. The model aims to simulate the interplay between electron transfer processes for extended periods of time in lattices of increasing complexity. The electron transfer reactions considered here involve the IIIII valence interchange between nearest-neighbor iron atoms via a small polaron hopping mechanism. The temperature dependence and anisotropic behavior of the electrical conductivity as predicted by our model are in good agreement with experimental data on hematite single crystals. In addition, we characterize the effect of electron polaron concentration and that of a range of defects on the electron mobility. Interaction potentials between electron polarons and fixed defects (iron substitution by divalent, tetravalent, and isovalent ions and iron and oxygen vacancies) are determined from atomistic simulations, based on the same model used to derive the electron transfer parameters, and show little deviation from the Coulombic interaction energy. Integration of the interaction potentials in the kinetic Monte Carlo simulations allows the electron polaron diffusion coefficient and density and residence time around defect sites to be determined as a function of polaron concentration in the presence of repulsive and attractive defects. The decrease in diffusion coefficient with polaron concentration follows a logarithmic function up to the highest concentration considered, i.e., approximately 2% of iron(III) sites, whereas the presence of repulsive defects has a linear effect on the electron polaron diffusion. Attractive defects are found to significantly affect electron polaron diffusion at low polaron to defect ratios due to trapping on nanosecond to microsecond time scales. This work indicates that electrons can diffuse away from the initial site of interfacial electron transfer at a rate that is consistent with measured electrical conductivities, but that the presence of certain kinds of defects will severely limit the mobility of donated electrons.

Computer simulation of electron thermalization in CsI and CsI(Tl)

A Monte Carlo (MC) model was developed and implemented to simulate the thermalization of electrons in inorganic scintillator materials. The model incorporates electron scattering with both longitudinal optical and acoustic phonons. In this paper, the MC model was applied to simulate electron thermalization in CsI, both pure and doped with a range of thallium concentrations. The inclusion of internal electric fields was shown to increase the fraction of recombined electron-hole pairs and to broaden the thermalization distance and thermalization time distributions. The MC simulations indicate that electron thermalization, following γ-ray excitation, takes place within approximately 10 ps in CsI and that electrons can travel distances up to several hundreds of nanometers. Electron thermalization was studied for a range of incident γ-ray energies using electron-hole pair spatial distributions generated by the MC code NWEGRIM (NorthWest Electron and Gamma Ray Interaction in Matter). These simulations revealed ...

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

In this work, molecular simulation techniques were employed to gain insight into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO2(2+)) in aqueous solution. The simulations made use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff [J. Mol. Struct. (THEOCHEM) 1996 , 366 , 55 - 63]. Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficient were also calculated and analyzed. Finally, a combination of metadynamics and transition path sampling simulations was employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states were also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.

Molecular dynamics simulations of the interaction between the surfaces of polar solids and aqueous solutions

Molecular dynamics (MD) simulations were performed on the interaction of two solid surfaces, namely the (00.1) hematite and (10.4) calcite surfaces, in contact with aqueous electrolyte solutions containing different concentrations of dissolved NaCl. The structure and a number of properties of the interface were investigated. The size and amount of statistics needed for convergence of these calculations required the use of high performance computers. The two surfaces show different bonding mechanisms with the water, but both result in a distinctive layering of the water, which in turn modifies a range of surface behaviour including diffusivity and charge distribution. We find that the resulting charge distribution from the solvent has a greater control of the disposition of dissolved ions than either surface charge or ionic strength, within reasonable limits. Thus we see a characteristic double layer at neutral surfaces and the charge distribution oscillates into the bulk. Finally, preliminary work on calculating the free energy of dissolution of ions from the surface to the aqueous solution suggests that the presence of dissolved ions makes a small but significant reduction to the dissolution free energies.

Effects of Oxygen-Containing Functional Groups on Supercapacitor Performance

Molecular dynamics (MD) simulations of the interface between graphene and the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (BMIM OTf) were carried out to gain molecular-level insights into the performance of graphene-based supercapacitors and, in particular, determine the effects of the presence of oxygen-containing defects at the graphene surface on their integral capacitance. The MD simulations predict that increasing the surface coverage of hydroxyl groups negatively affects the integral capacitance, whereas the effect of the presence of epoxy groups is much less significant. The calculated variations in capacitance are found to be directly correlated to the interfacial structure. Indeed, hydrogen bonding between hydroxyl groups and SO3 moieties prevents BMIM(+) and OTf(-) ions from interacting favorably in the interfacial layer and restrains the orientation and mobility of OTf(-) ions, thereby reducing the interfacial permittivity of the ionic liquid. The results of the simulations can facilitate the rational design of electrode materials for supercapacitors.

Transition path sampling of water exchange rates and mechanisms around aqueous ions

The rates and mechanisms of water exchange around two aqueous ions, namely, Na(+) and Fe(2+), have been determined using transition path sampling. In particular, the pressure dependence of the water exchange rates was computed to determine activation volumes. A common approach for calculating water exchange rates, the reactive flux method, was also employed and the two methods were compared. The water exchange rate around Na(+) is fast enough to be calculated by direct molecular dynamics simulations, thus providing a reference for comparison. Both approaches predicted exchange rates and activation volumes in agreement with the direct simulation results. Four additional sodium potential models were considered to compare the results of this work with the only activation volume for Na(+) previously determined from molecular simulation [D. Spangberg et al., Chem. Phys. Lett. 276, 114 (1997)] and provide the best possible estimate of the activation volume based on the ability of the models to reproduce known properties of the aqueous sodium ion. The Spangberg and Hermansson [D. Spangberg and K. Hermansson, J. Chem. Phys. 120, 4829 (2004)] and X-Plor/Charmm-22 [M. Patra and M. Karttunen, J. Comput. Chem. 25, 678 (2004)] models performed best and predicted activation volumes of -0.22 and -0.78 cm(3) mol(-1), respectively. For water exchange around Fe(2+), transition path sampling predicts an activation volume of +3.8 cm(3) mol(-1), in excellent agreement with the available experimental data. The potential of mean force calculation in the reactive flux approach, however, failed to sufficiently sample appropriate transition pathways and the opposite pressure dependence of the rate was predicted as a result. Analysis of the reactive trajectories obtained with the transition path sampling approach suggests that the Fe(2+) exchange reaction takes place via an associative interchange mechanism, which goes against the conventional mechanistic interpretation of a positive activation volume. Collectively, considerable insight was obtained not only for the exchange rates and mechanisms for Na(+) and Fe(2+) but also for identifying the most robust modeling strategy for these purposes.

Computer simulation of the light yield nonlinearity of inorganic scintillators

To probe the nature of the physical processes responsible for the nonlinear scintillation light yield of inorganic scintillators, we have combined an ab initio based Monte Carlo code for calculating the microscopic spatial distributions of electron-hole pairs with an atomistic kinetic Monte Carlo (KMC) model of energy-transfer processes. In the present study, we focus on evaluating the contribution of an annihilation mechanism between self-trapped excitons (STE) to the scintillation response of pure CsI and Ce-doped LaBr3. A KMC model of scintillation mechanisms in pure CsI was developed previously and we introduce in this publication a similar model for Ce-doped LaBr3. We show that the KMC scintillation model is able to reproduce both the kinetics and efficiency of the scintillation process in Ce-doped LaBr3. Relative light output curves were generated at several temperatures for both scintillators from simulations carried out at incident γ-ray energies of 2, 5, 10, 20, 100, and 400 keV. These simulation...

Atomistic Simulations of Uranium Incorporation into Iron (Hydr)Oxides

Atomistic simulations were carried out to characterize the coordination environments of U incorporated in three Fe-(hydr)oxide minerals: goethite, magnetite, and hematite. The simulations provided information on U-O and U-Fe distances, coordination numbers, and lattice distortion for U incorporated in different sites (e.g., unoccupied versus occupied sites, octahedral versus tetrahedral) as a function of the oxidation state of U and charge compensation mechanisms (i.e., deprotonation, vacancy formation, or reduction of Fe(III) to Fe(II)). For goethite, deprotonation of first shell hydroxyls enables substitution of U for Fe(III) with a minimal amount of lattice distortion, whereas substitution in unoccupied octahedral sites induced appreciable distortion to 7-fold coordination regardless of U oxidation states and charge compensation mechanisms. Importantly, U-Fe distances of ∼3.6 Å were associated with structural incorporation of U and cannot be considered diagnostic of simple adsorption to goethite surfaces. For magnetite, the octahedral site accommodates U(V) or U(VI) with little lattice distortion. U substituted for Fe(III) in hematite maintained octahedral coordination in most cases. In general, comparison of the simulations with available experimental data provides further evidence for the structural incorporation of U in iron (hydr)oxide minerals.