2009. "Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study." Langmuir 25(12):6841-6848. Abstract Replica Kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface non-uniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation do not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic non-uniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.
2009. "Long-Range Electron Transfer Across Cytochrome-Hematite (a-Fe2O3) Interfaces." Journal of Physical Chemistry C 113(6):2096-2103. Abstract Electrochemical scanning tunneling microscopy (EC-STM) was used to assess the distance dependence of electron tunneling facilitated by a bacterial multiheme cytochrome to a single crystal iron oxide surface. We measured tunneling current-distance (I-s) profiles across the nanoscale space between insulated Au STM tips and the basal (001) surface of a hematite (-Fe2O3) crystal, and compared them to the case in which an intervening small tetraheme cytochrome (STC) from Shewanella oneidensis covalently linked to the Au tip surface. Tunneling profiles were collected at constant surface potentials in solutions having a range of ionic strengths. At short tip-sample separation, the distance dependece of the tunneling current shows a quasi-linear behavior. At longer distances it shows an exponential decay. The different regions are discussed in terms of ordering of interfacial water and ion layers in the electrical double layer associated with the hematite surface. The effective tunneling range and its rate of decay are substantially increased when STC is present in the tunneling junction, suggesting that cytochrome molecules provide enhanced tunneling pathways and stronger electronic coupling to the hematite surface. Based on these results, cytochrome-mediated electron transfer during bacterial metal reduction may be possible at distances further than originally thought. Also, as multiheme cytochromes and other similar molecules gain attention for their promising role in fuel cells and molecular electronics, we show that the solution conditions and surface properties of the substrate must be carefully considered.
2009. "The Roles of Outer Membrane Cytochromes of Shewanella and Geobacter in Extracellular Electron Transfer." Environmental Microbiology Reports 1(4):220-227. doi:10.1111/j.1758-2229.2009.00035.x Abstract As key components of the electron transfer (ET) pathways used for dissimilatory reduction of solid iron [Fe(III)] and manganese [Mn(IV)] (hydr)oxides, outer membrane cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 and OmcE and OmcS of Geobacter sulfurreducens mediate ET reactions extracellularly. Cell surface-exposed MtrC and OmcA can transfer electrons directly to the metal oxides. S. oneidensis MR-1 cells also secrete flavins that can facilitate ET to the oxides. The secreted flavins are thought to serve either as chelators that form soluble Fe(III)/Mn(IV)-flavin complexes or as electron shuttles that ferry the electrons from cell-associated ET proteins to the metal oxides. Cell-surface localization may also permit MtrC and OmcA to transfer electrons extracellularly to either flavin-chelated Fe(III)/Mn(IV) or oxidized flavins. OmcE and OmcS are proposed to be located on the Geobacter cell surface where they are believed to function as the intermediates to relay electrons to type IV pili, which are then hypothesized to transfer electrons directly to the metal oxides. Thus, cell surface-localization positions these outer membrane cytochromes to transfer electrons to Fe(III)/Mn(IV) oxides external to the bacterial cells either directly, indirectly, or both, demonstrating a common strategy shared by Shewanella and Geobacter for extracellular reduction of the oxides.
2009. "Effect of Chemical Lithium Intercalation into Rutile TiO2 Nanorods." Journal of Physical Chemistry C 113(32):14567-14574. doi:10.1021/jp904148z Abstract Rutile TiO2 nanorods were synthesized by hydrolysis of TiCl4 followed by a hydrothermal method. Lithium insertion into the rutile nanorods was achieved by a chemical lithium intercalation process. The structural evolution of nano-structured rutile upon lithium intercalation was characterized by several experimental techniques, namely, XRD, TEM and 6Li MAS NMR. The XRD and TEM studies indicate the formation of a new lithium titanate phase (LixTiO2) during lithium intercalation. Additionally, SAED patterns show that the lithium titanate phase has cubic symmetry. Finally, ultra-high magnetic field (21.1T) 6Li MAS NMR reveals that the lithium titanate phase adopts two different structures depending on lithium content. Taken together, the three techniques consistently show that the intercalation of lithium into rutile TiO2 nanorods causes two consecutive structural phase transformations to lithium titanate phases with spinel (Fd m) and rocksalt (Fm m) structures at x=0.46 and 0.88, respectively. In addition, the broad line widths in the 6Li MAS NMR spectrum of the rocksalt phase are indicative of a disordered structure. Density functional theory calculations of the rutile, spinel and rocksalt bulk phases as a function of lithium content corroborate the observed phase transformations. These phase transitions could account for the large irreversible capacity loss of nano-structured rutile anodes observed in electrochemical cycling experiments.
2009. "Computer Simulation of the Light Yield Nonlinearity of Inorganic Scintillators." Journal of Applied Physics 105(11):Art. No. 114915. Abstract To probe the nature of the physical processes responsible for the nonlinear photon response of inorganic scintillators, we have combined a Monte Carlo (MC) code for calculating the microscopic spatial distributions of electron-hole pairs with a kinetic Monte Carlo (KMC) model of energy-transfer processes. In this publication, we focus on evaluating the contribution of an annihilation mechanism between self-trapped excitons (STE) to the photon 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 2, 5, 10, 20, 100, and 400 keV. These simulations suggest that STE-STE annihilation can account for the initial rise in relative light yield with increasing incident energy. This is due to the fact that the proportion of high-density regions decreases as the incident energy increases thus reducing the likelihood for STE-STE encounter. In addition, the simulations clearly show a lack of temperature dependence of the relative light output, in agreement with a majority of experimental work on the temperature dependence of nonlinearity in inorganic scintillators.
2009. "Role of Directed van der Waals Bonded Interactions in the Determination of the Structures of Molecular Arsenate Solids." Journal of Physical Chemistry A 113(4):736-749. Abstract Bond paths, local energy density properties, and Laplacian, L(r) = −2ρ(r), composite isosurfaces of the electron density distributions were calculated for the intramolecular and intermolecular bonded interactions for molecular solids of As2O3 and AsO2 composition, an As2O5 crystal, a number of arsenate molecules, and the arsenic metalloid, arsenolamprite. The directed intermolecular van der Waals As−O, O−O, and As−As bonded interactions are believed to serve as mainstays between the individual molecules in each of the molecular solids. As−O bond paths between the bonded atoms connect Lewis base charge concentrations and Lewis acid charge depletion domains, whereas the O−O and As−As paths connect Lewis base pair and Lewis acid pair domains, respectively, giving rise to sets of intermolecular directed bond paths. The alignment of the directed bond paths results in the periodic structures adopted by the arsenates. The arrangements of the As atoms in the claudetite polymorphs of As2O3 and the As atoms in arsenolamprite are similar. Like the As2O3 polymorphs, arsenolamprite is a molecular solid connected by relatively weak As−As intermolecular directed van der Waals bond paths between the layers of stronger As−As intramolecular bonded interactions. The bond critical point and local energy density properties of the intermolecular As−As bonded interactions in arsenolamprite are comparable with the As−As interactions in claudetite I. As such, the structure of claudetite I can be viewed as a stuffed derivative of the arsenolamprite structure with O atoms between pairs of As atoms comprising the layers of the structure. The cubic structure adopted by the arsenolite polymorph can be understood in terms of sets of directed acid−base As−O and base−base O−O pair domains and bond paths that radiate from the tetrahedral faces of its constituent molecules, serving as face-to-face key−lock mainstays in forming a periodic tetrahedral array of molecules rather than one based on some variant of close packing. The relatively dense structure and the corrugation of the layers in claudetite I can also be understood in terms of directed van der Waals As−O bonded interactions. Our study not only provides a new basis for understanding the crystal chemistry and the structures of the arsenates, but it also calls for a reappraisal of the concept of van der Waals bonded interactions, how the structures of molecular solids are viewed, and how the molecules in these solids are bonded in a periodic structure.
2009. "Bonded Interactions in Silica Polymorphs, Silicates and Siloxane Molecules ." American Mineralogist 94(8-9):1085-1102. Abstract Experimental model electron density distributions recorded for the silica polymorphs coesite and stishovite are comparable with electron density distributions calculated for a variety of silicates and siloxane molecules. The Si-O bond lengths and Si-O-Si angles calculated with first principles density functional theory methods as a function of pressure are also comparable with the bond lengths and angles observed for coesite and quartz within the experimental error. The similarity of the topological properties of the Si-O bonded interactions and the experimental and the geometry optimized structures for the silica polymorphs provides a basis for understanding the properties and crystal chemistry in terms of a molecular-based model. The agreement supports the argument that the bulk of the structural, physical and thermodynamic properties of the silica polymorphs are intrinsic properties of the molecular-like coordinated polyhedra such that the silica polymorphs can be pictured as ‘supermolecules’ of silica bound by the virtually same forces that bind the Si and O atoms in simple siloxane molecules. The topology of the electron density distribution is consistent with the assertion that the Si-O bonded interaction arises from the net electrostatic attraction exerted on the nuclei by the electron density accumulated between the Si and O atoms. The correlation between the Si-O bond length and Si-O-Si angle is ascribed to the progressive local concentration of the electron density in the nonbonded region of the O atom as the bond length increases and angle decreases rather then to bonded interactions involving the d-orbitals on Si. On the basis of the proximity of the bond critical point, rc, to the nodal surface of the Laplacian, 2(rc), and the values of (rc) and G(rc)/(rc), the Si-O bond qualifies as an intermediate bonded interaction. For bonded interactions of intermediate character, 2(rc) increases linearly as (rc) increases, the greater the shared character, the larger the value of 2(rc). In addition, a mapping of 2(r) serves to highlight those Lewis base domains that are susceptible to electrophilic attack by H like the O atom in coesite involved in bent Si-O-Si angles, the narrower the angle, the greater the affinity for H . On the basis of the net charges conferred on the Si and O atoms and the bonded radii of the two atoms, the Si-O bond of stishovite with six-coordinated Si and three-coordinated O is indicated to be more ionic in character than that in quartz with four-coordinated Si and two coordinated O. Unlike the conclusion reached for ionic and crystal radii (quantum mechanical unobservables), it is the bonded radius of the O atom that increases with the increasing coordination number of Si, not the radius of the Si atom. The modeling of the electron density distributions for quartz, coesite and beryl as a function of pressure indicates that the shared character of the bonded interactions in these minerals increases slightly with increasing pressure. The insight provided by the calculations and the modeling of the electron density distributions and the structures of the silica polymorphs bodes well for future Earth materials studies that are expected to improve and clarify our understanding of the connection between properties and structure within the framework of quantum mechanical observables, to find new and improved uses and to predict new properties for materials and to enhance our understanding of crystal chemistry and chemical reactions of materials in their natural environment at the atomic level
2009. "Bond-Valence Constraints on Liquid Water Structure." Journal of Physical Chemistry A 113(9):1847-1857. Abstract The recent controversy about the structure of liquid water pits a new model involving water molecules in relatively stable rings-and-chains structures against the standard model that posits water molecules in distorted tetrahedral coordination. Molecular dynamics (MD) simulations—both classical and ab initio—almost uniformly support the standard model, but since none of them can yet reproduce all the anomalous properties of water, they leave room for doubt. We argue that it is possible to evaluate these simulations by testing them against their adherence to the bond-valence model, a well known, and quantitatively accurate, empirical summary of the behavior of atoms in the bonded networks of inorganic solids. Here we use the results of ab initio molecular dynamics simulations of ice, water, and several solvated aqueous species to show that the valence sum rule (the first axiom of the bond-valence model,) is followed in both solid and liquid bond networks. We then test MD simulations of water, employing several popular potential models, against this criterion and the experimental O-O radial distribution function. It appears that most of those tested cannot satisfy both criteria well, except TIP4P and TIP5P. If the valence sum rule really can be applied to simulated liquid structures, then it follows that the bonding behaviors of atoms in liquids are in some ways identical to those in solids. We support this interpretation by showing that the simulations produce O-H…O geometries completely consistent with the range of geometries available in solids, and the distributions of instantaneous valence sums reaching the atoms in both the ice and liquid water simulations are essentially identical. Taken together, this is powerful evidence in favor of the standard distorted tetrahedral model of liquid water structure.
2008. "Linked Reactivity at Mineral-Water Interfaces Through Bulk Crystal Conduction." Science 320(5873):218-222. doi:10.1126/science.1154833 Abstract Chemical behavior at mineral-water interfaces is of fundamental importance to geochemistry, but for minerals that are natural semiconductors the pursuit of mechanistic understanding is uniquely challenging. We show that surface specific charge density accumulation reactions combined with bulk charge carrier diffusivity create conditions at which interfacial electron transfer reactions at one surface couple with those at another by a current through the crystal bulk. Using iron oxide as the example, we present measurements showing that chemically induced surface potential gradient across hematite (a-Fe2O3) crystals is sufficiently high and the bulk electrical resistivity is sufficiently low during reductive dissolution to link dissolution of edge surfaces to simultaneous growth of the basal plane. The finding defines a new characteristic of mineral-water interface behavior that is immediately generalizable to a host of naturally abundant semiconducting minerals playing varied key roles in soils, sediments, and the atmosphere.
2008. "Kinetics of Reduction of Fe(III) Complexes by Outer Membrane Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 74(21):6746-6755. doi:10.1128/AEM.01454-08 Abstract Shewanella Oneidensis MR-1 possesses up to 42 c-type cytochromes with heme content varying between 1 to as many as 37. Among them, the outer-membrane cytochromes, particularly MtrC and OmcA, are suspected to function as terminal reductases and are responsible for its enzymatic catalysis capability. So far, the mechanisms of metal reduction by these outer-membrane cytochromes are unknown. In this work, we report the study of reduction kinetics of a series of Fe(III) complexes with citrate, NTA and EDTA by abiotically reduced MtrC and OmcA using a stopped-flow technique in combination with theoretical computation methods within the framework of the electron transfer theory of Marcus and speciation calculations based on the current thermodynamic database. Stopped-flow kinetic data showed that the reaction was very fast and appeared to proceed in two stages, a fast stage that completes in much less than a second and a slower stage afterwards. For a given complex, the reaction is faster by reduction with MtrC than OmcA, while for a given protein, the reaction completes in the decreasing order of Fe-EDTA > Fe-NTA > Fe-citrate. All the stopped-flow kinetic curves could be modeled by two parallel second-order bimolecular redox reactions with second-order rate constants ranging from 0.872 µM-1s-1 for the fast reaction between MtrC with Fe-EDTA complex to 0.012 µM-1s-1 for the slow reaction between OmcA and Fe-citrate complex. Speciation calculations indicated that at both metal:ligand ratios, 1:1.5 and 1:10, a single dominant ferric complex was responsible for the observed reaction for each ligand and, therefore, the observed dual-reaction pathways was attributed to the differences in the reduction behavior among various heme groups within each protein. The results of redox potential calculations with known thermodynamic data show only small differences on the scale of a few millivolts among the three complexes, suggested that the observed differences in reaction rate cannot be explained by the overall redox reaction free energy. In contrast, reorganization energies () calculated based on DFT-COSMO model are substantially different between the complexes, with a larger reorganization energy and therefore a larger activation energy associated with the citrate complex, and progressively smaller ones for the NTA and EDTA complexes. In combination with approximate electronic coupling terms, the theoretical results show good agreement with the observed trend and implicate the reorganization energy as the key factor in the kinetic reaction.
2008. "A Spectroscopic Study of the effect of Ligand Complexation on the Reduction of Uranium(VI) by Anthraquinone-2,6-disulfonate (AH2DS)." Radiochimica Acta 96(9-11):599-605. doi:10.1524/ract.2008.1542 Abstract In this project, the reduction rate of uranyl complexes with hydroxide, carbonate, EDTA, and Desferriferrioxamine B (DFB) by anthraquinone-2,6-disulfonate (AH2DS), a potential electron shuttle for microbial reduction of metal ions (Newman and Kolter 2000), is studied by stopped-flow kinetics techniques under anoxic atmosphere. The apparent reaction rates varied with ligand type, solution pH, and U(VI) concentration. For each ligand, a single largest kobs within the studied pH range was observed, suggesting the influence of pH-dependent speciation on the U(VI) reduction rate. The maximum reaction rate found in each case followed the order of OH- > CO32- > EDTA > DFB, consistent with the same trend of the thermodynamic stability of the uranyl complexes and ionic sizes of the ligands. Increasing the stability of uranyl complexes and ligand size decreased the maximum reduction rate. The pH-dependent rates were modeled using a second-order rate expression that was assumed to be dependent on a single U(VI) complex and AH2DS species. By quantitatively comparing the calculated and measured apparent rate constants as a function of pH, species AHDS3- was suggested as the primary reductant in all cases examined. Species UO2CO3(aq) , UO2HEDTA-, and (UO2)2(OH)22+ were suggested as the principal electron acceptors among the U(VI) species mixture in carbonate, EDTA, and hydroxyl systems, respectively.
2008. "Thermodynamic Model for ThO2(am) Solubility in Alkaline Silica Solutions ." Journal of Solution Chemistry 37(12):1725-1746. doi:10.1007/s10953-008-9344-5 Abstract No thermodynamic data for Th complexes with aqueous Si are available. To obtain such data, extensive studies on ThO2(am) solubility were carried out as functions of: (1) a wide range of aqueous silica concentrations (0.0004 to 0.14 mol⋅L−1) at fixed pH values of about 10, 11, 12, and 13; and (2) and variable pH (ranging from 10 to 13.3) at fixed aqueous Si concentrations of about 0.006 mol⋅L−1 or 0.018 mol⋅L−1. The samples were equilibrated over long periods (ranging up to 487 days), and the data showed that steady-state concentrations were reached in < 29 days. X-ray diffraction, FTIR, and Raman analyses of the equilibrated solid phases showed that the Th solids were amorphous ThO2(am) containing some adsorbed Si. The solubility of ThO2(am) at pH values ranging from 10 to 13.3 at fixed 0.018 mol⋅L−1 aqueous Si concentrations decreases rapidly with an increase in pH, and increases dramatically with an increase in Si concentrations beyond about 0.003 mol⋅L−1 at fixed pH values > 10. The data were interpreted using both the Pitzer and SIT models, and required only the inclusion of one mixed-hydroxy-silica complex of Th [Th(OH)3(H3SiO4)32−]. Both models provided similar complexation constant values for the formation of this species. Density functional theory calculations predict complexes of this stoichiometry, having six-fold coordination of the Th cation, to be structurally stable. Predictions based on the fitted value of log 10 K 0=−18.5±0.7 for the ThO2(am) solubility reaction involving Th(OH)3(H3SiO4)32−[ThO2(am)+3H4SiO4+H2O↔Th(OH)3(H3SiO4)32−+2H+], along with the thermodynamic data for aqueous Si species reported in the literature, agreed closely with the extensive experimental data and showed that under alkaline conditions aqueous Si makes very strong complexes with Th.
2008. "Environmental Mobility of Pu(IV) in the presence of ethylenediaminetetraacetic acid: Myth or Reality." Journal of Solution Chemistry 37(7):957-986. doi:10.1007/s10953-008-9282-2 Abstract Ethylenediaminetetracetic acid (EDTA), which was co-disposed with Pu at several U. S. Department of Energy sites, has been reported to enhance the solubility and transport of Pu. It is generally assumed that this enhanced transport of Pu in geologic environments is a result of complexation of Pu(IV) with EDTA. However, the fundamental bases for this assumption have never been fully explored. Whether EDTA can mobilize Pu(IV) in geologic environments is dependent on many factors, chief among them are not only the complexation constants of Pu with EDTA and dominant oxidation state and the nature of Pu solids, but also 1) the complexation constants of environmentally important metal ions (e.g. Fe, Al, Ca, Mg) that compete with Pu for EDTA and 2) EDTA interactions with geomedia (e.g., adsorption, biodegradation) that reduce effective EDTA concentrations available for complexation. Extensive studies over a large range of pH values (1 to 14) and EDTA concentrations (0.0001 to 0.01 M) as a function of time were conducted on the solubility of 2-line ferrihydrite (Fe(OH)3(s)), PuO2(am) in the presence of different concentrations of Ca ions, and mixtures of PuO2(am) and Fe(OH)3(s). The solubility data were interpreted using Pitzer’s ion-interaction approach to determine/validate the solubility product of Fe(OH)3(s), the complexation constants of Pu(IV)-EDTA and Fe(III)-EDTA, and to determine the affect of EDTA in solubilizing Pu(IV) from PuO2(am) in the presence of Fe(III) compounds and aqueous Ca concentrations. Predictions based on these extensive fundamental data show that environmental mobility of Pu as a result of Pu(IV)-EDTA complexation as reported/implied in the literature is a myth rather than the reality.
2008. "Simple Kinetic Monte Carlo Models for Dissolution Pitting Induced by Crystal Defects." Journal of Chemical Physics 129(20):204106. doi:10.1063/1.3021478 Abstract The solid-on-solid kinetic Monte Carlo model of Lasaga and Blum for dislocation- controlled etch pit growth has been extended to the growth of etch pits under the control of multiple dislocations and point defects. This has required the development of algorithms that are 0(103) – O(104) times faster than primitive kinetic Monte Carlo models for surfaces with areas in the range 1024x1024 – 4096x4096 lattice sites. Simulations with multiple line defects indicate that the surface morphology coarsens with increasing time and that the coarsening is more pronounced for large bond-breaking activation energies. For small bond breaking activation energies dissolution enhanced by line defects perpendicular the dissolving surface results in pits with steep sides terminated by deep narrow hollow tubes (nanopipes). Larger bond breaking activation energies lead to shallow pits without deep nanopipes, and if the bond breaking activation energy is large enough, step flow is the primary dissolution mechanism, and pit formation is suppressed. Simplified models that neglect the far field strain energy density but include either a rapidly dissolving core or an empty core lead to results that are qualitatively similar to those obtained using models that include the effects of the far field stress and strain. Simulations with a regular array of line defects show that microscopic random thermal fluctuations play an important role in the coarsening process.
2008. "Kinetic Monte Carlo Model of Scintillation Mechanisms in CsI and CsI(Tl)." IEEE Transactions on Nuclear Science 55(3 Pt. 2):1251-1258. doi:10.1109/TNS.2008.922830 Abstract We have developed a computational model of energy transfer processes in scintillators using the kinetic Monte Carlo (KMC) approach. In this publication, we focus on the alkali halide compound CsI both pure and doped with a range of thallium concentrations. The KMC model makes use of an explicit atomistic representation of the crystal lattice, activator sites, defect sites, and individual electron-hole pairs. The probability of individual diffusion, recombination, and scintillation events is calculated from rate equations parameterized with data published in the literature. Scintillation decay curves, relative intensities of emission peaks, and light yields are computed and found to be in good agreement with experimental data for a range of temperatures and thallium concentrations. This demonstrates that the KMC scintillation model is capable of reproducing both the kinetics and the efficiency of the scintillation process in CsI. In addition, novel predictions emerge from our simulations such as the diffusion distance distributions of self-trapped holes and excitons. Finally, the KMC scintillation model provides a framework for probing possible physical processes responsible for the nonlinear relationship between scintillation light yield and incident gamma-ray energy.
2008. "A Shell Model for Atomistic Simulation of Charge Transfer in Titania." Journal of Physical Chemistry C 112(20):7678-7688. doi:10.1021/jp8007865 Abstract The derivation of atomistic potential parameters, based on electronic structure calculations, for modeling electron and hole polarons in titania polymorphs is presented. The potential model is a polarizable version of the Matsui and Akaogi model (Matsui, M.; Akaogi, M. Mol. Simul. 1991, 6, 239) that makes use of a shell model to account for the polarizability of oxygen ions. The -1 and +1 formal charges of the electron and hole polarons, respectively, are modeled by delocalizing the polaron’s charge over a titanium or oxygen ion, respectively, and its first nearest-neighbors. The charge distributions and the oxygen polarizability were fitted to the reorganization energies of a series of electron and hole polaron transfers in rutile and anatase obtained from electronic structure calculations at zero Kelvin and validated against lattice deformation due to both types of polaron. Good agreement was achieved for both properties. In addition, the potential model yields an accurate representation of a range of bulk properties of several TiO2 polymorphs as well as Ti2O3. The model thus derived enables us to consider systems large enough to investigate how the charge transfer properties at titania surfaces and interfaces differ from those in the bulk. For example, reorganization energies and free energies of charge transfer were computed as a function of depth below vacuum-terminated rutile (110) and anatase (001) surfaces using a two-state model based on Marcus theory. These calculations indicate that deviations from bulk values at the surface are substantial but limited to the first couple of surface atomic layers and that polarons are generally repelled from the surface. Moreover, attractive sub-surface sites may be found as is predicted for hole polarons at the rutile (110) surface. Finally, several charge transfers from under-coordinated surface sites were found to be in the so-called Marcus inverted-region.
2008. "Redox-Reactive Membrane Vesicles produced by Shewanella." Geobiology 6(3):232-241. doi:10.1111/j.1472-4669.2008.00158.x Abstract Dissimilatory iron reducing bacteria produce and release membrane vesicles with diameters ranging from 50 to 250 nm. The vesicles, which arise from the outer membrane of these Gram-negative bacteria, lack DNA but contain proteins that catalyze the reduction of ferric iron and other multivalent heavy metals and radionuclides. This enzymatic process results in the formation of nano-size biogenic mineral assemblages that resemble nanofossils. Under low-shear conditions, membrane vesicles are commonly tethered to intact cells by electrically conductive filaments known as bacterial nanowires. The functional role of membrane vesicles and associated nanowires is not known, but the potential for mineralized vesicles that morphologically resemble nanofossils to serve as paleontological indicators of early life on earth and as biosignatures of like on other planets is recognized.
2008. "Shared and closed-shell O-O interactions in silicates." Journal of Physical Chemistry A 112(16):3693-3699. Abstract A chemical bond is an interaction that should be detectable in the electron density distribution associated with a bonded pair of atoms. A common method for detecting the existence of a bond is to determine whether a bond path exists between the nuclei of the pair. However, especially for relatively weak secondary interactions, such as O-O bonded interaction, the existence of or non-existence of actual bond paths may be misleading. Other factors, external to the interactions between the atoms, may cause the appearance of a bogus bond path or may obliterate the existence of a bona fide path. For example, bond paths between O-O edge sharing equivalent and quasi-equivalent MOn coordinated polyhedra may well be artifacts due to the superposition of the electron density of nearby metal M atoms situated on opposite sides of the shared polyhedral edges. On the other hand, the bond path associated with a bona fide O-O bonded interaction may be disrupted by the electron density distribution of the nearby atoms. In fact, a disruption factor is defined that correctly separates the cases for which bond paths appear and for which they do not for a wide variety of O-O occurrences.
2008. "Experimental bond critical point and local energy density properties determined for Mn-O, Fe-O and Co-O bonded interactions for tephroite, Mn2SiO4, fayalite, Fe2SiO4 and Co2SiO4 olivine and selected organic metal complexes: Comparison with properties calculated for non-transition and transition metal M-O bonded interactions for silicates and oxides." Journal of Physical Chemistry A 112(37):8811-8823. doi:10.1021/jp804280j Abstract Bond critical point, bcp, and local energy density properties for the electron density, ED, distributions, calculated with first principle quantum mechanical methods for divalent transition metal Mn-, Co- and Fe-containing silicates and oxides are compared with experimental model ED properties for tephroite, Mn2SiO4, fayalite, Fe2SiO4 and Co2SiO4 olivine, each determined with high energy synchrotron single crystal X-ray diffraction data. Trends observed between the experimental bond lengths, R(M-O), (M = Mn, Fe, Co), and the calculated bcp properties are comparable with those observed for non-transition M-O bonded interactions. The bcp, local total energy density, H(rc), and bond length trends determined for the Mn-O, Co-O and Fe-O interactions are virtually identical. A comparison is also made with model experimental bcp properties determined for several Mn-O, Fe-O and Co-O bonded interactions for organometallic complexes and several oxides. Despite the complexities of the structures of the organometallic complexes, the agreement between the calculated and the model experimental bcp properties is good in several cases. The G(rc)/p(rc) vs. R(M-O) trends established for non-transition metal M-O bonded interactions hold for the given transition metal M O bonded interactions with the G(rc)/p(rc) ratio increasing in value as H(rc) becomes progressively more negative in value and the shared character of the interaction increases. As observed for the non-transition metal M-O bonded interactions, the Laplacian, 2p(rc), increases in value as p(rc) increases and as H(rc) decreases. The Mn-O, Fe-O, and Co-O bonded interactions are indicated to be of intermediate character with a substantial component of closed-shell character compared with Fe-S and Ni-S bonded interactions which show greater shared character based on the |V(rc)|/G(rc) bond character indicator. The atomic charges conferred on the transition metal atoms for the three olivines decrease with increasing atomic number from Mn to Fe to Co.
2008. "Bonded Interactions and the Crystal Chemistry of Minerals: A Review." Zeitschrift fur Kristallographie 223(1-2):1-40. doi:10.1524/zkri.2008.0002 Abstract Connections established during the 20th century between bond length, radii, bond strength, bond valence and crystal and molecular chemistry are briefly reviewed followed with a survey of the physical properties of the electron density distributions for a variety of minerals and representative molecules, recently generated with first-principles local density based quantum mechanical methods. The structures for several minerals, geometry-optimized at ambient conditions and at a variety of pressures, match those determined experimentally within several percent. The structures and the physical properties of model experimental electron density distributions determined with high resolution and high energy synchrotron single crystal X-ray diffraction data also closely match those calculated with first principles methods. As the electron density is progressively accumulated and locally concentrated between pairs of bonded atoms, the nuclei are progressively shielded and the bond lengths and the bonded radii of the atoms decrease. Concomitant with the decrease in bond length, the local kinetic density energy increases while the potential energy and the electronic energy densities both decrease for intermediate and shared interactions with the potential energy dominating the local energy for the shorter bonded interactions. The shorter the bonds, the more negative the local electronic energy density, the greater the stabilization and the greater the shared character of the bonded interactions.
2008. "Spectroscopic Characterization of Extracellular Polymeric Substances from Escherichia coli and Serratia marcescens: Suppression using Sub-Inhibitory Concentrations of Bismuth Thiols." Biomacromolecules 9(11):3079-3089. doi:10.1021/bm800600p Abstract Free and capsular EPS produced by Escherichia coli and Serratia marcescens were characterized in detail using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and Auger electron spectroscopy (AES). Total EPS production decreased upon treatment with sub-inhibitory concentrations of lipophilic bismuth thiols (bismuth dimercaptopropanol, BisBAL; bismuth ethanedithiol, BisEDT; and bismuth pyrithione, BisPYR), BisBAL being most effective. Bismuth thiols also influenced acetylation and carboxylation of polysaccharides in EPS from S. marcescens. Extensive homology between EPS samples in the presence and absence of bismuth was observed with proteins, polysaccharides, and nucleic acids varying predominantly only in the total amount expressed. Second derivative analysis of the amide I region of FTIR spectra revealed decreases in protein secondary structures in the presence of bismuth thiols. Hence, anti-fouling properties of bismuth thiols appear to originate in their ability to suppress O-acetylation and protein secondary structures in addition to total EPS secretion.
2008. "Bismuth Dimercaptopropanol (BisBAL) Inhibits the Expression of Extracellular Polysaccharides and Proteins by Brevundimonas diminuta: Implications for Membrane Microfiltration." Biotechnology and Bioengineering 99(3):634-643. doi:10.1002/bit.21615 Abstract A 2:1 molar ratio preparation of bismuth with a lipophilic dithiol (3-dimercapto-1-propanol, BAL)significantly reduced extracellular polymeric substances (EPS) expression by Brevundimonas diminuta in suspended cultures at levels just below the minimum inhibitory concentration (MIC). Total polysaccharides and proteins secreted by B. diminuta decreased by approximately 95% over a 5-day period when exposed to the bismuth-BAL chelate (BisBAL) at near MIC (12 μM). Fourier-transform infrared spectroscopy (FTIR) suggested that a possible mechanism of biofilm disruption by BisBAL is the inhibition of carbohydrate Oacetylation. FTIR also revealed extensive homology between EPS samples with and without BisBAL treatment, with proteins, polysaccharides, and peptides varying predominantly only in the amount expressed. EPS secretion decreased following BisBAL treatment as verified by atomic force microscopy and scanning electron microscopy. Without BisBAL treatment, a slime-like EPS matrix secreted by B. diminuta resulted in biofouling and inefficient hydrodynamic backwashing of microfiltration membranes.
2007. "Mechanisms of Electron Transfer in Two Decaheme Cytochromes from a Metal-Reducing Bacterium." Journal of Physical Chemistry B 111(44):12857-12864. doi:10.1021/jp0718698 Abstract Single-molecule current-voltage (I–V) spectra were collected using a scanning tunneling microscope for two decaheme c-type cytochromes, OmcA and MtrC, which are outer-membrane proteins from the dissimilatory metal-reducing bacterium Shewanella oneidensis. Although the two cytochromes are similar in heme count, charge-carrying amino-acid content, and molecular mass, their I–V spectra are significantly different. The I–V spectra for OmcA show smoothly varying symmetric exponential behavior. These spectra are well fit by a coherent tunneling model that is based on a simple square barrier description of the tunneling junction. In contrast, the I–V spectra for MtrC have pronounced breaks in slope in the positive tip bias range. Two large peaks in the normalized differential conductance spectra of MtrC were fit to a tunneling model that accounts for the possibility of transient population of empty states stabilized by vibrational relaxation. Reorganization energies deduced for the two features are similar to those normally assigned to metal centers in other metalloproteins. Work function measurements of the cytochrome films were used to convert the energies of these two spectral features to the normal hydrogen electrode scale for comparison with the midpoint potential measured using protein film voltammetry, which showed good correspondence. We conclude that MtrC mediates tunneling current by heme orbital participation. The difference in tunneling behavior between OmcA and MtrC suggests distinct physiological functions for the two cytochromes; in contrast to OmcA, MtrC appears to be tuned to a specific operating potential.
2007. "Electron tunneling properties of outer-membrane decaheme cytochromes from Shewanella oneidensis." Geochimica et Cosmochimica Acta 71(3):543-555. Abstract In this report, we describe the characterization of two outer-membrane decaheme cytochromes OmcA and MtrC purified from the metal-reducing bacterium Shewanella oneidensis using scanning tunneling microscopy (STM) and tunneling spectroscopy (TS). OmcA and MtrC were solubilized with a common detergent and irreversibly bound to Au (111) substrates as self-assembled cytochrome films. X-ray photoelectron spectroscopy (XPS) verified that OmcA and MtrC were covalently bound to the Au surface via thiol bonds to cysteine residues. Initial STM images show that a layer of detergent covers and protects the cytochrome films. Temporary application of high bias voltage causes the detergent film to reorganize around the tip, opening a window for direct STM imaging of the cytochrome layer underneath. The STM apparent sizes of both OmcA and MtrC are 58 nanometers in diameter consistent with expectations from their molecular masses. Current-voltage TS over individual cytochromes showed that OmcA and MtrC have different abilities to mediate the tunneling current, reflecting differences in their electronic structures. The data suggest that the two cytochromes could have different roles in the electron transport chain during metal reduction.
2007. "Structure and Charge Hopping Dynamics in Green Rust ." Journal of Physical Chemistry C 111(30):11414-11423. doi:10.1021/jp072762n Abstract Green rust is a family of mixed-valent iron phases formed by a number of abiotic and biotic processes under alkaline suboxic conditions. Due to its high Fe2+ content, green rust is a potentially important phase for pollution remediation by serving as a powerful electron donor for reductive transformation. However, mechanisms of oxidation of this material are poorly understood. An essential component of the green rust structure is a mixed-valent brucite-like Fe(OH)2 sheet comprised of a two dimensional network of edge-sharing iron octahedra. Room temperature Mössbauer spectra show a characteristic signature for intermediate valence on the iron atoms in this sheet, indicative of a Fe2+‑Fe3+ valence interchange reaction faster than approximately 107 s-1. Using Fe(OH)2 as structural analogue for reduced green rust, we performed Hartree-Fock calculations on periodic slab models and cluster representations to determine the structure and hopping mobility of Fe3+ hole polarons in this material, providing a first principles assessment of the Fe2+‑Fe3+ valence interchange reaction rate. The calculations show that among three possible symmetry unique iron-to-iron hops within a sheet, a hop to next-nearest neighbors at an intermediate distance of 5.6 Å is the fastest. The predicted rate is on the order of 1012 s-1 consistent the Mössbauer-based constraint. All other possibilities, including hopping across interlayer spaces, are predicted to be slower than 107 s-1. Collectively, the findings suggest the possibility of hole self-diffusion along sheets as a mechanism for regeneration of lattice Fe2+ sites, consistent with previous experimental observations of edge-inward progressive oxidation of green rust.
2007. "Chromium(III) Hydroxide Solubility in the Aqueous K+-H+-OH--CO2- HCO3-- CO32--H2O System: A Thermodynamic Model." Journal of Solution Chemistry 36(10):1261-1285. doi:10.1007/s10953-007-9179-5 Abstract Chromium(III)-carbonate reactions are expected to be important in managing high-level radioactive wastes. Extensive studies on the solubility of amorphous Cr(III) hydroxide solid in a wide range of pH (3-13), at two different fixed partial pressures of CO2(gas) (0.003 or 0.03 atm.), and as functions of K2CO3 concentrations (0.01 to 5.8 m) in the presence of 0.01 M KOH and KHCO3 concentrations (0.001 to 0.826 m) at room temperature (22 ± 2°C) were carried out to obtain reliable thermodynamic data for important Cr(III)-carbonate reactions. A combination of techniques (XRD, XANES, EXAFS, UV-Vis-NIR spectroscopy, thermodynamic analyses of solubility data, and quantum mechanical calculations) was used to characterize solid and aqueous species. The Pitzer ion-interaction approach was used to interpret the solubility data. Only two aqueous species [Cr(OH) (CO3)22-) and Cr(OH)4CO33-] are required to explain Cr(III)-carbonate reactions in a wide range of pH, CO2(gas) partial pressures, and bicarbonate and carbonate concentrations. Calculations based on density functional theory support the existence of these species. The log K0 values of reactions involving these species [{Cr(OH)3(am) + 2CO2(gas) = Cr(OH)(CO3)22- + 2H+}and {Cr(OH)3(am) + OH- + CO32- = Cr(OH)4(CO3)3-}] were found to be –(19.07 0.41), -(4.19 0.19), respectively. No other data on any Cr(III)-carbonato complexes are available for comparisons.
2007. "Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces." Journal of Physical Chemistry C 111(30):11363-11375. Abstract The interface between electron transfer proteins such as cytochromes and solid phase mineral oxides is central to the activity of dissimilatory-metal reducing bacteria. A combination of potential-based molecular dynamics simulations and ab initio electronic structure calculations are used in the framework of Marcus’ electron transfer theory to compute elementary electron transfer rates from a well-defined cytochrome model, namely the small tetraheme cytochrome (STC) from Shewanella oneidensis, to surfaces of the iron oxide mineral hematite (α-Fe2O3). Room temperature molecular dynamics simulations show that an isolated STC molecule favors surface attachment via direct contact of hemes I and IV at the poles of the elongated axis, with electron transfer distances as small as 9 Å. The cytochrome remains attached to the mineral surface in the presence of water and shows limited surface diffusion at the interface. Ab initio electronic coupling matrix element (VAB) calculations of configurations excised from the molecular dynamics simulations reveal VAB values ranging from 1 to 20 cm-1, consistent with nonadiabaticity. Using these results, together with experimental data on the redox potential of hematite and hemes in relevant cytochromes and calculations of the reorganization energy from cluster models, we estimate the rate of electron transfer across this model interface to range from 1 to 1000 s-1 for the most exothermic driving force considered in this work, and from 0.01 to 20 s-1 for the most endothermic. This fairly large range of electron transfer rates highlights the sensitivity of the rate upon the electronic coupling matrix element, which is in turn dependent on the fluctuations of the heme configuration at the interface. We characterize this dependence using an idealized bis-imidazole heme to compute from first principles the VAB variation due to porphyrin ring orientation, electron transfer distance, and mineral surface termination. The electronic matrix element and consequently the rate of electron transfer are found to be sensitive to all parameters considered. This work indicates that biomolecularly similar solvent-exposed bis-histidine hemes in outer-membrane cytochromes such as MtrC or OmcA are likely to have an affinity for the oxide surface in water governing the approach and interfacial conformation and, if allowed sufficient conformational freedom, will achieve distances and configurations required for direct interfacial electron transfer.
2007. "Kinetic Monte Carlo Model of Charge Transport in Hematite (α-Fe2O3)." Journal of Chemical Physics 127(12):Art. No. 124706. doi:10.1063/1.2768522 Abstract 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 parameterized 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 II/III 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., ~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.
2007. "Theoretical Electron Density Distributions for Fe- and Cu-Sulfide Earth Materials: A Connection between Bond Length, Bond Critical Point Properties, Local Energy Densities, and Bonded Interactions." Journal of Physical Chemistry B 111(8):1923-1931. doi:10.1021/jp065086i Abstract Bond critical point and local energy density properties together with net atomic charges were calculated for theoretical electron density distributions, F(r), generated for a variety of Fe and Cu metal-sulfide materials with high- and low-spin Fe atoms in octahedral coordination and high-spin Fe atoms in tetrahedral coordination. The electron density, F(rc), the Laplacian, 32F(rc), the local kinetic energy, G(rc), and the oxidation state of Fe increase as the local potential energy density, V(rc), the Fe-S bond lengths, and the coordination numbers of the Fe atoms decrease. The properties of the bonded interactions for the octahedrally coordinated low-spin Fe atoms for pyrite and marcasite are distinct from those for high-spin Fe atoms for troilite, smythite, and greigite. The Fe-S bond lengths are shorter and the values of F(rc) and 32F(rc) are larger for pyrite and marcasite, indicating that the accumulation and local concentration of F(r) in the internuclear region are greater than those involving the longer, high-spin Fe-S bonded interactions. The net atomic charges and the bonded radii calculated for the Fe and S atoms in pyrite and marcasite are also smaller than those for sulfides with high-spin octahedrally coordinated Fe atoms. Collectively, the Fe-S interactions are indicated to be intermediate in character with the low-spin Fe-S interactions having greater shared character than the highspin interactions. The bond lengths observed for chalcopyrite together with the calculated bond critical point properties are consistent with the formula Cu+Fe3+S2. The bond length is shorter and the F(rc) value is larger for the FeS4 tetrahedron displayed by metastable greigite than those displayed by chalcopyrite and cubanite, consistent with a proposal that the Fe atom in greigite is tetravalent. S-S bond paths exist between each of the surface S atoms of adjacent slabs of FeS6 octahedra comprising the layer sulfide smythite, suggesting that the neutral Fe3S4 slabs are linked together and stabilized by the pathways of electron density comprising S-S bonded interactions. Such interactions not only exist between the S atoms for adjacent S8 rings in native sulfur, but their bond critical point properties are similar to those displayed by the metal sulfides.
2007. "Structure, Magnetism and Conductivity in Epitaxial Ti-doped -Fe2O3 Hematite: Experiment and density functional theory calculations." Physical Review. B, Condensed Matter and Materials Physics 75(10):, doi:10.1103/PhysRevB.75.104412 Abstract We explore the feasibility of growing epitaxial Ti-doped -Fe2O3 in which Ti(IV) substitutes for Fe(III) preferentially in one magnetic sublattice, but not the other. Such a structure has been predicted by first-principles theory to be energetically likely, and is expected to yield interesting and useful magnetic and electronic properties. However, we find that a majority of Ti dopants disperse and occupy random cation sites in both magnetic sublattices. Density functional theory predicts that the magnetically ordered and magnetically random structures are nearly isoenergetic.
2007. "Molecular Dynamics Characterization of Rutile-Anatase Interfaces." Journal of Physical Chemistry C 111(26):9290-9298. doi:10.1021/jp0713211 Abstract We report molecular dynamics (MD) simulations of interfaces between rutile and anatase surfaces of TiO2. These interfaces are important for understanding mixed-phase catalysts, such as the Degussa P25 catalyst, and in particular as a first step toward characterizing electron/hole transport in these photo-active materials. Construction of these interfaces was possible with near-coincidence-site lattice (NCSL) theory. The results suggest adhesion energies for the most stable structures typically near -2 J/m2, and the interfaces appear energetically favorable due to an increase of six-coordinate Ti atoms (Ti6c). Two other notable observations emerge from this work. First, the interfaces are characterized as slightly disordered, with the disorder limited to a narrow region at the interface, in agreement with experiment. Second, formation of rutile octahedral structures was observed at the anatase side of the interface due to surface rearrangement. This appears as the beginning of an anatase-to-rutile phase transition. This work was supported by the Department of Energy, Office of Basic Energy Sciences. Computational resources were provided by the Molecular Science Computing Facility located at the Environmental Molecular Science Laboratory in Richland, WA. All work was performed at Pacific Northwest National Laboratory (PNNL). Battelle operates PNNL for the U.S. Department of Energy. KMR acknowledges the support of the Geosciences program of the DOE Office of Basic Energy Sciences, and the Stanford Environmental Molecular Sciences Institute jointly funded by the National Science Foundation (NSF) and the DOE Office of Biological and Environmental Research.
2007. "Potential protonation sites in the Al2SiO5 polymorphs based on polarized FTIR spectroscopy and properties of the electron density distribution ." Physics and Chemistry of Minerals 34(5):295-306. Abstract Potential protonation sites within the three aluminosilicate polymorphs, kyanite, sillimanite, and andalusite, have been examined through analysis of (3,-3) bond critical point information in comparison with polarized FTIR spectroscopy of single crystals of kyanite and sillimanite from previous studies and examination with the polarized infrared spectrum of andalusite from this study. Seven peaks were observed, four strong peaks at 3440 cm-1, 3460 cm-1, 3530 cm-1, and 3600 cm-1 and three weak peaks at 3480 cm-1, 3520 cm-1, and 3650 cm-1, when the electric vector is parallel with a, six peaks, three strong at 3440 cm-1, 3460 cm-1, and 3530 cm-1 and three weak peaks at 3480 cm-1, 3520 cm-1, and 3560 cm-1, when the electric vector is parallel with b, and no peaks when the electric vector is parallel with c. The results indicate that hydrogen is located in the (001) plane of andalusite and sillimanite and the (11-1) plane in kyanite as determined from the polarized FTIR spectrum of the three minerals. The concentration of water in the samples of andalusite examined varied between 10 and 15 ppm H20 by weight. Examination of the (3,-3) critical points in comparison with the polarized FTIR indicates that hydrogen will prefer bonding to the O1 and O2 oxygen atoms in andalusite and the O2 and O4 oxygens in sillimanite, which correspond to the oxygen with the highest Laplacian value and the underbonded oxygen in the two structures. In kyanite, comparison of the FTIR spectrum and the bond critical points indicate that hydrogen will bond to the two four-coordinated oxygens, O4 and O6.
2006. "Chemical Bonding in Sulfide Minerals." Chapter 5 in Sulfide Mineralogy and Geochemistry, Reviews in Mineralogy & Geochemistry, vol. 61, ed. Jodi J. Rosso, pp. 231-264. The Mineralogical Society of America, Chantilly, VA. Abstract An understanding of chemical bonding and electronic structure in sulfide minerals is central to any attempt at understanding their crystal structures, stabilities and physical properties. It is also an essential precursor to understanding reactivity through modeling surface structure at the molecular scale. In recent decades, there have been remarkable advances in first principles (ab initio) methods for the quantitative calculation of electronic structure. These advances have been made possible by the very rapid development of high performance computers. Several review volumes that chart the applications of these developments in mineralogy and geochemistry are available (Tossell and Vaughan, 1992; Cygan and Kubicki, 2001). An important feature of the sulfide minerals is the diversity of their electronic structures, as evidenced by their electrical and magnetic properties (see Pearce et al. 2006, this volume). Thus, sulfide minerals range from insulators through semiconductors to metals, and exhibit every type of magnetic behavior. This has presented problems for those attempting to develop bonding models for sulfides, and also led to certain misconceptions regarding the kinds of models that may be appropriate. In this chapter, chemical bonding and electronic structure models for sulfides are reviewed with emphasis on more recent developments. Although the fully ab initio quantitative methods are now capable of a remarkable degree of sophistication in terms of agreement with experiment and potential to interpret and predict behavior with varying conditions, both qualitative and more simplistic quantitative approaches will also be briefly discussed. This is because we believe that the insights which they provide are still helpful to those studying sulfide minerals. In addition to the application of electronic structure models and calculations to solid sulfides, work on sulfide mineral surfaces (Rosso and Vaughan 2006a,b) and solution complexes and clusters (Rickard and Luther, 2006) are discussed in detail later in this volume.
2006. "Computational molecular basis for improved silica surface complexation models." Chapter 13 in Surface Complexation Modeling, 11, ed. J Lutzenkirchen, pp. 359-396. Elsevier, Amsterdam, Netherlands. Abstract The acidity and reactivity of surface sites on amorphous and crystalline polymorphs of silica and other oxides control their thermodynamic stability and kinetic reactivity towards reactants in surface-controlled processes of environmental, industrial, biomedical and technological relevance. Recent advances in computational methodologies such as CPMD and increasing computer power combined with spectroscopic measurements are now making it possible to link, with an impressive degree of accuracy, the molecular-level description of these processes to phenomenological, surface complexation models The future challenge now lies in linking mesoscale properties at the nanometer scale to phenomenological models that will afford a more intuitive understanding of the systems under consideration.
2006. "Sulfide Mineral Surfaces." Chapter 9 in Sulfide Mineralogy and Geochemistry, Reviews in Mineralogy & Geochemistry, vol. 61, ed. Jodi J. Rosso, pp. 505-556. The Mineralogical Society of America, Chantilly, VA. Abstract The past twenty years or so have seen dramatic development of the experimental and theoretical tools available to study the surfaces of solids at the molecular (‘atomic resolution’) scale. On the experimental side, two areas of development well illustrate these advances. The first concerns the high intensity photon sources associated with synchrotron radiation; these have both greatly improved the surface sensitivity and spatial resolution of already established surface spectroscopic and diffraction methods, and enabled the development of new methods for studying surfaces. The second centers on the scanning probe microscopy (SPM) techniques initially developed in the 1980’s with the first scanning tunneling microscope (STM) and atomic force microscope (AFM) experiments. The direct ‘observation’ of individual atoms at surfaces made possible with these methods has truly revolutionized surface science. On the theoretical side, the availability of high performance computers coupled with advances in computational modeling has provided powerful new tools to complement the advances in experiment. Particularly important have been the quantum mechanics based computational approaches such as density functional theory (DFT), which can now be easily used to calculate the equilibrium crystal structures of solids and surfaces from first principles, and to provide insights into their electronic structure. In this chapter, we review current knowledge of sulfide mineral surfaces, beginning with an overview of the principles relevant to the study of the surfaces of all crystalline solids. This includes the thermodynamics of surfaces, the atomic structure of surfaces (surface crystallography and structural stability, adjustments of atoms at the surface through relaxation or reconstruction, surface defects) and the electronic structure of surfaces. We then discuss examples where specific crystal surfaces have been studied, with the main sulfide minerals organized by structure type (galena, sphalerite, wurtzite, pyrite, pyrrhotite, covellite and molybdenite types). Some examples of more complex phases, where fracture surfaces of unspecified orientation have been studied, are then discussed (millerite, marcasite, chalcopyrite, arsenopyrite, and enargite) before a brief summary of possible future developments in the field. In this chapter, the focus is on the nature of the pristine surface, i.e., the arrangement of atoms at the surface, and the electronic structure of the surface. This is an essential precursor to any fundamental understanding of processes such as dissolution, precipitation, sorption/desorption, or catalytic activity involving the sulfide surface at an interface with a fluid phase.
2006. "Reactivity of Sulfide Mineral Surfaces." Chapter 10 in Sulfide Mineralogy and Geochemistry, Reviews in Mineralogy & Geochemistry, vol. 61, ed. Jodi J. Rosso, pp. 557-607. The Mineralogical Society of America, Chantilly, VA. Abstract In the preceding chapter, the fundamental nature of sulfide mineral surfaces has been discussed, and the understanding we have of the ways in which the surface differs from a simple truncation of the bulk crystal structure reviewed. This naturally leads on to considering our understanding of sulfide surface chemistry, in the sense of how sulfide surfaces interact and react, particularly with gases and liquids. As noted elsewhere in this volume, research on sulfide mineral surfaces and surface reactivity is a relatively recent concern of mineralogists and geochemists, partly prompted by the availability of new imaging and spectroscopic methods, powerful computers and new computer algorithms. There has been a significantly longer history of sulfide mineral surface research associated with technologists working with, or within, the mining industry. Here, electrochemical methods, sometimes combined with analytical and spectroscopic techniques, have been used to probe surface chemistry. The motivation for this work has been to gain a better understanding of the controls of leaching reactions used to dissolve out metals from ores, or to understand the chemistry of the froth flotation systems used in concentrating the valuable (usually sulfide) minerals prior to metal extraction. The need for improved metal extraction technologies is still a major motivation for research on sulfide surfaces, but in the last couple of decades, new concerns have become important drivers for such work. In particular, much greater awareness of the negative environmental impact of acid and toxic metal-bearing waters derived from breakdown of sulfide minerals at former mining operations has prompted research on oxidation reactions, and on sorption of metals at sulfide surfaces. At the interface between fundamental geochemistry and industrial chemistry, the role of sulfide substrates in catalysis, and in the self-assembly and functionalization of organic molecules, has become an area of significant interest. Such work ranges in its application from the development of new industrial processes, to fundamental questions of the possible role of sulfide surfaces in catalyzing the formation of the complex organic molecules leading to the emergence of life on Earth. In this chapter, we aim to provide an overview of current understanding of sulfide surface chemistry. The size of this research fi eld is already such that it is impossible to discuss all of the published work, but key examples are considered and readers directed to the main literature sources. The chapter begins with some examples of reaction with gaseous species (O2, H2O, H2S, CH3OH) as these are the most accessible in terms of understanding reactivity at the molecular scale. The very important oxidation and related electron transfer reactions, in both air and aqueous solution, are then considered before considering examples of catalysis and functionalization/self-assembly and interaction with organic molecules. In the final section, sorption of metal ions onto sulfide mineral surfaces is discussed before a few words concerning the future outlook for research in this entire area.
2006. "Is there hope for multi-site complexation modeling?" Chapter 9 in Surface Complexation Modeling, pp. 269-283. Elsevier, Amsterdam, Netherlands. Abstract It has been shown here that the standard formulation of the MUSIC model does not deliver the molecular-scale insight into oxide surface reactions that it promises. The model does not properly divide long-range electrostatic and short-range contributions to acid-base reaction energies, and it does not treat solvation in a physically realistic manner. However, even if the current MUSIC model does not succeed in its ambitions, its ambitions are still reasonable. It was a pioneering attempt in that Hiemstra and coworkers recognized that intrinsic equilibrium constants, where the effects of long-range electrostatic effects have been removed, must be theoretically constrained prior to model fitting if there is to be any hope of obtaining molecular-scale insights from SCMs. We have also shown, on the other hand, that it may be premature to dismiss all valence-based models of acidity. Not only can some such models accurately predict intrinsic acidity constants, but they can also now be linked to the results of molecular dynamics simulations of solvated systems. Significant challenges remain for those interested in creating SCMs that are accurate at the molecular scale. It will only be after all model parameters can be predicted from theory, and the models validated against titration data that we will be able to begin to have some confidence that we really are adequately describing the chemical systems in question.
2006. "Defect Distribution and Dissolution Morphologies on Low-Index Surfaces of alpha-Quartz ." Geochimica et Cosmochimica Acta 70(5):1113-1127. doi:10.1016/j.gca.2005.11.019 Abstract The dissolution of prismatic and rhombohedral quartz surfaces by KOH/H2O solutions was investigated by atomic force microscopy. Rates of dissolution of different classes of surface features (e.g., steps, voids, dislocation etch pits) were measured. The prismatic surface etched almost two orders of magnitude faster than the rhombohedral surface, mostly due to the difference in the number and the rate of dissolution of extended defects, such as dislocations. Because of the presence of imperfect twin boundaries, defect densities on the prismatic surface were estimated at 50 – 100 µm2, whereas the rhombohedral surface possessed only ~0.5 – 1.0 µm2, mostly in the form of crystal voids. Crystal voids etched almost one order of magnitude faster on the prismatic surface than on the rhombohedral surface due to differences in the number and the density of steps formed by voids on the different surfaces. In the absence of extended defects, both surfaces underwent step-wise dissolution at similar rates. Average rates of step retreat were comparable on both surfaces (~3 – 5 nm/h on the prismatic surface and ~5 – 10 nm/h on the rhombohedral surface). Prolonged dissolution left the prismatic surface reshaped to a hill-and-valley morphology, whereas the rhombohedral surface dissolved to form coalescing arrays of oval-shaped etch pits.
2006. "Kinetics of Triscarbonato Uranyl Reduction by Aqueous Ferrous Iron: A Theoretical Study." Journal of Physical Chemistry A 110(31):9691-9701. doi:10.1021/jp062325t S1089-5639(06)02325-5 Abstract Uranium is a pollutant whose mobility is tied to its oxidation state. While U(VI) in the form of the uranyl cation is capable of being reduced by a range of natural reductants, complexation by carbonate greatly reduces its reduction potential as well as imposing increased electron transfer (ET) distances. Very little is known about the elementary processes involved in uranium reduction from U(VI) to U(V) to U(IV) in general. In this study, we examine the theoretical kinetics of ET from ferrous iron to triscarbonato uranyl in aqueous solution. A combination of molecular dynamics (MD) simulations and density functional theory (DFT) electronic structure calculations are employed to compute the ET parameters that enter into Marcus’ model, including the thermodynamic driving force, reorganization energies, and electronic coupling matrix elements. MD simulations predict that two ferrous iron atoms will bind in an inner-sphere fashion to the three-membered carbonate ring of tricarbonato uranium, forming the charge-neutral Fe2UO2(CO3)3(H2O)8 complex. Through a sequential proton-coupled electron transfer mechanism, the first ET step converting U(VI) to U(V) is predicted by DFT to occur at a rate on the order of 1 s^-1. The second ET step converting U(V) to U(IV) is predicted to be significantly endergonic. Therefore, U(V) is a stabilized end-product in this ET system.
2006. "Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation." Journal of Physical Chemistry B 110(31):15582-15588. doi:10.1021/jp057068r Abstract A method for calculating the electron-transfer matrix element VRP using density functional theory Kohn-Sham orbitals is presented and applied to heme dimers of varying relative orientation. The electronic coupling decays with increased iron separation according to VRP ) V0RP exp(-βr/2) with a distance dependence parameter β ≈ 2 Å-1 for hemes with parallel porphyrins and either 1.1 or 4.0 Å-1 when the porphyrin planes are perpendicular, depending on the alignment of the iron dл orbital. These findings are used to interpret the observed orientation of the hemes in tetraheme redox proteins such as Flavocytochrome c3 fumarate reductase (Ifc3, PDB code 1QJD) of Shewanella frigidimarina, another flavocytochrome from the same bacterium (Fcc3, 1E39) and a small tetraheme cytochrome of Shewanella oneidensis strain MR1 (1M1P). Our results show that shifting and rotating the hemes controls the adiabaticity of the three electron hopping steps.
2006. "Electron Transfer in Environmental Systems: A Frontier for Theoretical Chemistry ." Theoretical Chemistry Accounts 116(1-3):124-136. doi:10.1007/s00214-005-0016-x Abstract Advances in understanding the kinetic behavior of certain environmental electron transfer (ET) systems are presented. Emphasis is placed on the homogeneous ET chemistry of transition metals, particularly the FeII/III system, in various relevant forms. In the context of modern ET theory, we examine the utility of computational chemistry methods for the calculation of ET quantities such as the reorganization energy and electronic coupling matrix element. We discuss successful application of the methods to topics of homogeneous oxidation of dissolved metal ions by molecular oxygen in aqueous solution, as well as the prediction of electron mobility in solid phase iron oxide crystals. The examples illustrate the significant potential for many more advances in understanding environmental ET systems through the combination of ET theory and computational chemistry.
2006. "Computer Simulation of Electron Transfer at Hematite Surfaces." Geochimica et Cosmochimica Acta 70(8):1888-1903. doi:10.1016/j.gca.2005.12.021 Abstract Molecular dynamics simulations in combination with ab initio calculations were carried out to determine the rate of electron transfer in bulk hematite (α-Fe2O3) and at two low-index surfaces, namely the (012) and (001) surfaces. The electron transfer reactions considered here involve the II/III valence interchange between nearest-neighbor iron atoms. Two electron transfer directions were investigated namely the basal plane and c direction charge transfers. Electron transfer rates obtained in bulk hematite were in good agreement with ab initio electronic structure calculations thus validating the potential model. The surfaces were considered both in vacuum and in contact with an equilibrated aqueous solution. The reorganization energy is found to increase significantly at the first surface layer and this value is little affected by the presence of water. In addition, in the case of the (012) surface, the electronic coupling matrix element for the topmost basal plane transfer was calculated at the Hartree-Fock level and was found to be weak compared to the corresponding charge transfer in the bulk. Therefore, most surfaces show a decrease in the rate of charge transfer at the surface. However, where iron atoms involved in the charge transfer reaction are directly coordinated to water molecules, water lowers the free energy of activation to a great extent and provides a large driving force for electrons to diffuse toward the bulk thus opposing the intrinsic surface effect. The surfaces considered in this work show different charge transfer properties. Hematite has been shown to exhibit anisotropic conductivity and thus different surfaces will show different intra- and inter-layer rates depending on their orientation. Moreover, the calculations of charge transfers at the hydroxyl- and iron-terminated (001) surfaces revealed that surface termination has a significant effect on the charge transfer parameters in the vicinity of the surface. Finally, our findings indicate that undercoordinated terminal iron atoms could act as electron traps at the surface.
2006. "Electrically Conductive Bacterial Nanowires Produced by Shewanella Oneidensis Strain MR-1 and Other Microorganisms ." Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363. Abstract Shewanella oneidensis MR-1 produced electrically conductive pilus-like appendages called bacterial nanowires in direct response to electron-acceptor limitation. Mutants deficient in genes for c-type decaheme cytochromes MtrC and OmcA, and those that lacked a functional Type II secretion pathway displayed nanowires that were poorly conductive. These mutants were also deficient in their ability to reduce hydrous ferric oxide and in their ability to generate current in a microbial fuel cell. Nanowires produced by the oxygenic phototrophic cyanobacterium Synechocystis PCC6803 and the thermophilic, fermentative bacterium Pelotomaculum thermopropionicum reveal that electrically conductive appendages are not exclusive to dissimilatory metal-reducing bacteria and may, in fact, represent a common bacterial strategy for efficient electron transfer and energy distribution.
2006. "Si-O Bonded Interactions in Silicate Crystals and Molecules: A Comparison." Journal of Physical Chemistry A 110(46):12678 (6 pages). Abstract Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, ρ(r), calculated for silicates like quartz and molecules like disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in crystals are short-ranged and molecular-like. Using the G(rc)/ρ(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc) = G(rc) + V(rc), and the oordination number of the Si atom decrease, and as the value of the electron density at the bond critical point, ρ(rc) and the Laplacian, ∇2ρ(rc), increase. The G(rc)/ρ(rc) and H(rc)/ρ(rc) ratios categorize the bond as observed for other second row atom M-O bonds into nonequivalent classes with the covalent character of each of the M-O bonds increasing with the H(rc)/ρ(rc) ratio. Some workers consider the Si-O bond to be highly ionic and others considered it to be either intermediate or substantially covalent. The character of the bond is examined in terms of the large net atomic basin charges conferred on the Si atoms comprising disiloxane, stishovite, quartz and forsterite, the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is intermediate in character between Al-O and P-O bonded interations rather than being ionic or covalent.
2006. "Classification of metal-oxide bonded interactions based on local potential- and kinetic-energy densities." Journal of Chemical Physics 124(8):Art. No. 084704. doi:10.1063/1.2161425 Abstract A classification of the HF bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio |V(rc)|/G(rc) where |V(rc)| is the magnitude of the local potential energy density and G(rc) is the local kinetic density evaluated at the bond critical points, rc. A calculation of the ratio for the MO bonded interactions comprising a relatively large number of molecules and earth materials, together with the constraints imposed by the values of Ñ2ρ(rc) and the local electronic energy density H(rc) = G(rc) + V(rc) in the HF study, yielded the same classification for the oxides as found for the fluorides. This is true despite the different trends of the bond critical point and local energy properties with the bond length displayed by the HF and MO bonded interactions. LiO, NaO and MgO bonded interactions classify as closed shell ionic bonds, BeO, AlO, SiO, BO and PO bonded interactions classify as bonds of intermediate character and NO bonded interactions classify as shared covalent bonds. CO and SO bonded interactions classify as both intermediate and covalent bonded interactions. The CO triple bonded interaction classifies as a bond of intermediate character and the CO single bonded interaction classifies as a covalent bond whereas their H(rc) value indicates that they are both covalent bonds. The |V(rc)|/G(rc) ratios for the BeO, AlO and SiO bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between |V(rc)|/G(rc) and the character of the bonded interaction is consistent with trends expected from electronegativity considerations. The connection between the net charges and the experimental SiO bond length evaluated for the Si and O atoms comprising two orthosilicates are examined in terms of the |V(rc)|/G(rc) values.
2006. "Bond Length and Local Energy Density Property Connections for Non-transition- Metal-Oxide-Bonded Interactions." Journal of Physical Chemistry A 110(44):12259-12266. doi:10.1021/jp062992m Abstract For a variety of molecules and Earth materials, the theoretical local kinetic energy density, G(rc), increases and the local potential energy density, V(rc), decreases as the MO bond lengths (M = first and second row metal atoms) decrease and electron density, ρ(rc), is localized at the bond critical points, rc. Despite claims that the ratio, G(rc)/ρ(rc), classifies bonded interactions as shared covalent when less than unity and closed shell ionic when greater than unity, the ratio was found to increase from 0.5 to 2.5 a.u. as the local electronic energy density H(rc) = G(rc) + V(rc) decreases and becomes progressively more negative. In any event, the ratio is indicated to be a measure of the character for a given M-O bond, the greater the ratio, the larger the value of ρ(rc), the smaller the coordination number of the M atom and the more covalent the bond. H(rc)/ρ(rc) vs. G(rc)/ρ(rc) scatter diagrams categorize the M-O bond data into domains with the H(rc)/ρ(rc) ratio tending to increase as the electronegativity of the M atoms increase. Estimated values of G(rc) and V(rc), using an expression based on gradient corrected electron gas theory, are in good agreement with theoretical values, particularly for bonded interactions involving second row M atoms. The agreement is poorer for the more covalent C-O and N-O bonds.
2006. "Ferromagnetism in Oxide Semiconductors ." Materials Today 9(11):28-35. Abstract In order to become a practical technology, semiconductor spintronics requires the discovery and utilization of ferromagnetic semiconductors which exhibit spin polarization in the majority carrier band at and above room temperature. Intrinsic remanent magnetization would allow spin polarized currents to be propagated in such materials without the need for a continuous magnetic field. However, the discovery and understanding of such materials is proving to be a grand challenge in solid-state science. Indeed, one of the 125 critical unanswered scientific questions recently posed in Science magazine asks, “Is it possible to create magnetic semiconductors that work at room temperature?”
2006. "Bond-valence methods for pKa prediction. II. Bond-valence, electrostatic, molecular geometry, and solvation effects ." Geochimica et Cosmochimica Acta 70(16):4057-4071. doi:10.1016/j.gca.2006.06.006 Abstract In a previous contribution, we outlined a method for predicting (hydr)oxy-acid and oxide surface acidity constants based on three main factors: bond valence, Me–O bond ionicity, and molecular shape. Here electrostatics calculations and ab initio molecular dynamics simulations are used to qualitatively show that Me–O bond ionicity controls the extent to which the electrostatic work of proton removal departs from ideality, bond valence controls the extent of solvation of individual functional groups, and bond valence and molecular shape controls local dielectric response. These results are consistent with our model of acidity, but completely at odds with other methods of predicting acidity constants for use in multisite complexation models. In particular, our ab initio molecular dynamics simulations of solvated monomers clearly indicate that hydrogen bonding between (hydr)oxo-groups and water molecules adjusts to obey the valence sum rule, rather than maintaining a fixed valence based on the coordination of the oxygen atom as predicted by the standard MUSIC model.
2005. "Effects of Compositional Defects on Small Polaron Hopping in Micas." Journal of Chemical Physics 122(24):244709 (9 pages). Abstract Hartree-Fock calculations and electron transfer (ET) theory were used to model the effects of compositional defects on ET in the brucite-like octahedral sheet of mica. ET was modeled as a FeII/III valence interchange reaction across shared octahedral edges of the M2-M2 iron sublattice. The model entails the hopping of localized electrons and small polaron behavior. Hartree-Fock calculations indicate that substitution of F for structural OH bridges increases the reorganization energy l, decreases the electronic coupling matrix element VAB, and thereby substantially decreases the hopping rate. The l increase arises from modification of the metal‑ligand bond force constants, and the VAB decrease arises from reduction of superexchange interaction through anion bridges. Deprotonation of an OH bridge, consistent with a possible mechanism of maintaining charge neutrality during net oxidation, yields a net increase in the ET rate. Although substitution of Al or Mg for Fe in M1 sites distorts the structure of adjacent Fe-occupied M2 sites, the distortion has little net impact on ET rates through these M2 sites. Hence the main effect of Al or Mg substitution for Fe, should it occur in the M2 sublattice, is to block ET pathways. Collectively, these findings pave the way for larger-scale oxidation/reduction models to be constructed for realistic, compositionally diverse micas
2005. "Cell Adhesion of Shewanella Oneidensis to Iron Oxide Minerals: Effect of Different Single Crystal Faces." Geochemical Transactions 6(4):77-84. Abstract The results of experiments designed to test the hypothesis that near-surface molecular structure of iron oxide minerals influences adhesion of dissimilatory iron reducing bacteria are presented. These experiments involved the measurement, using atomic force microscopy, of interaction forces generated between Shewanella oneidensis MR-1 cells and single crystal growth faces of iron oxide minerals. Significantly different adhesive force was measured between cells and the (001) face of hematite, and the (100) and (111) faces of magnetite. A role for electrostatic interactions is apparent. The trend in relative forces of adhesion generated at the mineral surfaces is in agreement with predicted ferric site densities published previously. These results suggest that near-surface structure does indeed influence initial cell attachment to iron oxide surfaces; whether this is mediated via specific cell surface-mineral surface interactions or by more general interfacial phenomena remains untested.
2005. "Charge Transfer in FeO: A combined Molecular-Dynamics and Ab Initio Study." Journal of Chemical Physics 123:224712-224722. doi:10.1063/1.2137319 Abstract Molecular dynamics simulations and ab initio electronic structure calculations were carried out to determine the rate of charge transfer in stoichiometric wüstite (FeO). The charge transfer of interest occurs by II/III valence interchange between nearest-neighbor Fe atoms, with the Fe(III) constituting a ‘hole’ electronic defect. There are two possible nearest-neighbor charge transfers in the FeO lattice, which occur between edge-sharing or corner-sharing FeO6 octahedra. Molecular dynamics simulations predict charge transfer rates of 3.7x1011 and 1.9x109 s-1 for the edge and corner transfers, respectively, in good agreement with those calculated using an ab initio cluster approach (1.6x1011 and 8.0x108 s-1, respectively). The calculated rates are also similar to those along basal and c-axis directions in hematite (α-Fe2O3) determined previously. Therefore, as is the case for hematite, wüstite is predicted to show anisotropic electrical conductivity. Our findings indicate that a rigid ion model does not give acceptable results, thus showing the need to account for the change in polarizability of the system upon charge transfer. Our model achieves this by using a simple mechanical shell model. By calculating the electronic coupling matrix elements for many transition state configurations obtained from the molecular dynamics simulations, we found evidence that the position of the bridging oxygen atoms can greatly affect the amount electronic coupling between the donor and acceptor states. Finally, we address the effect of oxygen vacancies on the charge transfer. It was found that an oxygen vacancy not only creates a driving force for holes to transport away from the vacancy (or equivalently for electrons to diffuse toward the vacancy) but also lowers the free energy barriers for charge transfer. In addition, the reorganization energy significantly differed from the non-defective case in a small radius around the defect.
2005. "Theoretical Characterization of Charge Transport in Chromia (α-Cr2O3)." Journal of Chemical Physics 123(7):074710 (1-11). Abstract Transport of conduction electrons and holes through the lattice of α-Cr2O3 (chromia) is modeled as a valence alternation of chromium cations using ab initio electronic structure calculations and electron transfer theory. In the context of the small polaron model, a cluster approach was used to compute quantities controlling the mobility of localized electrons and holes, i.e. the reorganization energy and the electronic coupling matrix element that enter Marcus’ theory. The calculation of the electronic coupling followed the Generalized Mulliken-Hush approach and the quasi-diabatic method using the complete active space self-consistent field (CASSCF) method. Our findings indicate that hole mobility is more than three orders of magnitude larger than electron mobility in both (001) and [001] lattice directions. The difference arises mainly from the larger internal reorganization energy calculated for electron transport relative to hole transport processes while electronic couplings have similar magnitudes. The much larger hole mobility vs electron mobility in α-Cr2O3 is in contrast to similar hole and electron mobility in hematite α-Fe2O3 previously calculated. Our calculations also indicate that the electronic coupling for all charge transfer processes of interest is smaller than for the corresponding processes in hematite. This variation is attributed to weaker interaction between the metal 3d states and the O(2p) states in chromia than in hematite, leading to smaller overlap between the charge transfer donor and acceptor wavefunctions and smaller super-exchange coupling in chromia. Nevertheless, the weaker coupling in chromia is still sufficiently large to suggest that charge transport processes in chromia are adiabatic in nature. The electronic coupling is found to depend on both the superexchange interaction through the bridging oxygen atoms and the d-shell electron spin coupling within the Cr-Cr donor-acceptor pair, while the reorganization energy is essentially independent of the electron spin coupling.
2005. "Charge Transport in Metal Oxides: A Theoretical Study of Hematite α-Fe2O3 ." Journal of Chemical Physics 122(14):144305. Abstract Transport of conduction electrons and holes through the lattice of Fe2O3 (hematite) is modeled as a valence alternation of iron cations using ab initio electronic structure calculations and electron transfer theory. Experimental studies have shown that the conductivity along the (001) basal plane is four orders of magnitude larger than the conductivity along the [001] direction. In the context of the small polaron model, a cluster approach was used to compute quantities controlling the mobility of localized electrons and holes, i.e. the reorganization energy and the electronic coupling matrix element that enter Marcus’ theory. The calculation of the electronic coupling followed the Generalized Mulliken-Hush approach using the complete active space self-consistent field (CASSCF) method. Our findings demonstrate an approximately three orders of magnitude anisotropy in both electron and hole mobility between directions perpendicular and parallel to the c-axis, in good accord with experimental data. The anisotropy arises from the slowness of both electron and hole mobility across basal oxygen planes relative to that within iron bi-layers between basal oxygen planes. Interestingly, for elementary reaction steps along either of the directions considered, there is only approximately one order of magnitude difference in mobility between electrons and holes, in contrast to accepted classical arguments. Our findings indicate that the most important quantity underlying mobility differences is the electronic coupling, albeit the reorganization energy contributes as well. The large values computed for the electronic coupling suggest that charge transport reactions in hematite are adiabatic in nature. The electronic coupling is found to depend on both the superexchange interaction through the bridging oxygen atoms and the d-shell electron spin coupling within the FeFe donor-acceptor pair, while the reorganization energy is essentially independent of the electron spin coupling.
2005. "Experimental and Theoretical Bond Critical Point Properties for Model Electron Density Distributions for Earth Materials ." Physics and Chemistry of Minerals 32(2):114-125. Abstract Generalized X-ray scattering factor model experimental electron density distributions and bond critical point, bcp, properties generated in recent studies for the earth materials stishovite, forsterite, fayalite and cuprite with high energy single crystal synchrotron X-ray diffraction data and those generated with high resolution diffraction data for coesite and senarmonite were found to be adequate and in relatively good agreement, ~5% on average, with those calculated with quantum chemical methods with relatively robust basis sets. High resolution low energy single crystal diffraction data, recorded for the molecular sieve AlPO4-15, were also found to yield model electron density distribution values at the bcp points for the AlO and PO bonded interactions that are in relatively good to moderately good agreement with the theoretical values, but the Laplacian values of the distribution at the points for the two bonded interactions were found to be in relatively poor agreement. In several cases, experimental bcp properties, generated with conventional low energy X-ray diffraction data for several rock forming minerals, were found overall to be in poorer agreement with the theoretical properties. The overall agreement between theoretical bcp properties generated with computational quantum methods and experimental properties generated with synchrotron high energy radiation not only provides a basis for using computational strategies for studying and modeling structures and their electron density distributions, but it also provides a basis for improving our understanding of the crystal chemistry and bonded interactions for earth materials. Theoretical bond critical point properties generated with computational quantum methods are believed to rival the accuracy of those determined experimentally. As such the calculations provide a powerful and efficient method for evaluating electron density distributions and the bonded interactions for a wide range of earth materials.
2005. "Electron Density Distributions Calculated For The Ni-Sulfides Millerite, Vaesite and Heazlewoodite and Nickel Metal: A case for The Importance Of NiNi Bond Paths For Electron Transport." Journal of Physical Chemistry B 109(46):21788-21795. Abstract Bond paths and the bond critical point properties (the electron density, ρ, and the Hessian of ρ at the bond critical point) have been calculated for the bonded interactions comprising the Ni–sulfide minerals millerite, vaesite and heazlewoodite and Ni metal. The experimental NiS bond lengths decrease linearly as the magnitudes of the properties at the bond critical point, bcp, increase in value. NiNi bond paths exist between the Ni atoms in heazlewoodite and millerite for NiNi separations that match the shortest NiNi separation in Ni metal, an indicator that the Ni atoms are bonded. NiNi bond paths also exist between the Ni atoms in bulk Ni metal. The bcp properties of the NiNi bonded interactions in Ni metal are virtually the same as those in the two Ni sulfides. NiNi bond paths are absent in vaesite where the NiNi separations are 60% longer than those in Ni metal. The bcp properties for the NiNi bonded interactions scatter along protractions of the NiS bond length–bcp property trends, suggesting that the two bonded interactions have similar characteristics. The NiNi bond paths radiate throughout Ni metal and the metallic heazlewoodite structures as continuous networks of interconnected NiNi bond paths whereas the NiNi paths in millerite, a highly covalent d,p metal, are restricted to isolated Ni3 rings of NiNi bond paths interconnected by S atoms. Electron transport in Ni metal and heazlewoodite is pictured as occurring along the bond paths, which behave as networks of atomic size wires that radiate in a contiguous circuit throughout the two structures. Unlike heazlewoodite, the electron transport in millerite is pictured as involving a cooperative hopping of the d–orbital electrons from the Ni3 rings comprising Ni3S9 clusters to Ni3 rings in adjacent clusters via the p–orbitals on the interconnecting S atoms. Vaesite, an insulator at low temperatures and a doped semiconductor at higher temperatures, lacks NiNi bond paths. The net charges conferred on the Ni and S atoms are about a quarter that of their nominal formal valences for the atoms in millerite and vaesite with the net charge on Ni increasing with increasing NiS bond length. The reduced net charge on the Ni atom in heazlewoodite is related to its NiNi metal bonded interactions and the contiguity of the NiNi bond paths.
2005. "A Mapping of the Electron Localization Function for Earth Materials ." Physics and Chemistry of Minerals 32(3):208-221. doi:10.1007/s00269-005-0463-x Abstract The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering it more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies are reviewed for finding potential H docking sites in the silica polymorphs and related materials. As observed in an earlier study, the ELF is capable of generating bond and lone pair domains that are similar in number and arrangement to those provided by Laplacian and deformation electron density distributions. The formation of the bond and lone pair domains in the silica polymorphs and the progressive decrease in the SiO length as the value of the electron density at the bond critical point increases indicates that the SiO bonded interaction has a substantial component of covalent character.
2004. "Reaction of Hydroquinone with Hematite II: Calculated Electron Transfer Rates and Comparison to the Reductive Dissolution Rate." Journal of Colloid and Interface Science 274(2):442-450. Abstract Reaction of hydroquinone with hematite II: Calculated electron transfer rates and comparison to the reductive dissolution rate
2004. "Molecular Dynamics Investigation of Ferrous-Ferric Electron Transfer in a Hydrolyzing Aqueous Solution: Calculation of the pH Dependence of the Diabatic Transfer Barrier and the Potential of Mean Force." Journal of Chemical Physics 120(16):7607-7615. Abstract We present a molecular model for ferrous–ferric electron transfer in an aqueous solution that accounts for electronic polarizability and exhibits spontaneous cation hydrolysis. An extended Lagrangian technique is introduced for carrying out calculations of electron-transfer barriers in polarizable systems. The model predicts that the diabatic barrier to electron transfer increases with increasing pH, due to stabilization of the Fe31 by fluctuations in the number of hydroxide ions in its first coordination sphere, in much the same way as the barrier would increase with increasing dielectric constant in the Marcus theory. We have also calculated the effect of pH on the potential of mean force between two hydrolyzing ions in aqueous solution. As expected, increasing pH reduces the potential of mean force between the ferrous and ferric ions in the model system. The magnitudes of the predicted increase in diabatic transfer barrier and the predicted decrease in the potential of mean force nearly cancel each other at the canonical transfer distance of 0.55 nm. Even though hydrolysis is allowed in our calculations, the distribution of reorganization energies has only one maximum and is Gaussian to an excellent approximation, giving a harmonic free energy surface in the reorganization energy F(DE) with a single minimum. There is thus a surprising amount of overlap in electron-transfer reorganization energies for Fe21– Fe(H2O)6 31, Fe21– Fe(OH)(H2O)521, and Fe21– Fe(OH)2(H2O)1 couples, indicating that fluctuations in hydrolysis state can be viewed on a continuum with other solvent contributions to the reorganization energy. There appears to be little justification for thinking of the transfer rate as arising from the contributions of different hydrolysis states. Electronic structure calculations indicate that Fe(H2O)6 21– Fe(OH)n(H2O)62n (32n)1 complexes interacting through H3O2 2 bridges do not have large electronic couplings.
2004. "Self-Exchange Electron Transfer Kinetics and Reduction Potentials for Anthraquinone Disulfonate." Journal of Physical Chemistry A 108(16):3292-3303. Abstract Self-exchange electron transfer kinetics and reduction potentials for anthraquinone disulfonate
2004. "Reorganization Energy Associated with Small Polaron Mobility in Iron Oxide." Journal of Chemical Physics 120(15):7050-7054. Abstract The reorganization energy is an important quantity controlling electron transfer rates. The internal contribution arising from the energy to reorganize donor/acceptor bonds can be evaluated by the ‘direct’ and ‘4-point’ methods. We examine how spatial separation leading to the non-interacting character of the donor and acceptor affects the reorganization energy. We show that the direct method captures contributions from interaction of the donor and acceptor while the 4-point method does not, and the two methods converge at large separation. Comparing reorganization energies determined by the two methods yields a measure of the degree of interaction between the initial and final states. The analysis is illustrated in the characterization of small polarons in iron oxides.
2004. "Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions." Journal of Physical Chemistry A 108(24):5242-5248. Abstract Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions
2004. "An Improved MUSIC Model for Gibbsite Surfaces." Geochimica et Cosmochimica Acta 68(11):A123, (Supplement S). Abstract Here we use gibbsite as a model system with which to test a recently published, bond-valence method for predicting intrinsic pKa values for surface functional groups on oxides. At issue is whether the method is adequate when valence parameters for the functional groups are derived from ab initio structure optimization of surfaces terminated by vacuum. If not, ab initio molecular dynamics (AIMD) simulations of solvated surfaces (which are much more computationally expensive) will have to be used. To do this, we had to evaluate extant gibbsite potentiometric titration data that where some estimate of edge and basal surface area was available. Applying BET and recently developed atomic force microscopy methods, we found that most of these data sets were flawed, in that their surface area estimates were probably wrong. Similarly, there may have been problems with many of the titration procedures. However, one data set was adequate on both counts, and we applied our method of surface pKa int prediction to fitting a MUSIC model to this data with considerable success—several features of the titration data were predicted well. However, the model fit was certainly not perfect, and we experienced some difficulties optimizing highly charged, vacuum-terminated surfaces. Therefore, we conclude that we probably need to do AIMD simulations of solvated surfaces to adequately predict intrinsic pKa values for surface functional groups.
2004. "A Connection Between Empirical Bond Strength and the Localization of the Electron Density at the Bond Critical Points of the SiO Bonds in Silicates ." Journal of Physical Chemistry A 108:7643-7645. Abstract The empirical bond strength of the SiO bond correlates with the value of the electron density at the bond critical point calculated for a large number of silicates and observed for the silica polymorphs stishovite and coesite. The greater the bond strength, the greater the localization of the electron density at the critical point, the shorter the bond, and the greater the covalent character of the bonded interaction. Bond strength and resonance bond number are considered to represent similar properties of the electronic structure of the bond.
2004. "Adatom Fe(III) on the hematite surface: Observation of a key reactive surface species." Geochemical Transactions 5(2):33-40. Abstract Nonperiodic adatom Fe(III) on the hematite surface: Direct observation of a key reactive surface species
2004. "Bond-Valence Methods for pK(a) Prediction: Critical Re-Analysis and a New Approach." Geochimica et Cosmochimica Acta 68(9):2025-2042. Abstract Bond-valence methods for pKa prediction: Critical re-analysis and a new approach
2003. "Ab initio investigation of the structures of NaOH hydrates and their Na+ and OH- coordination polyhedra." American Mineralogist 88(2-3):436-449. Abstract Ab initio investigation of the structures of NaOH hydrates and their Na+ and OH- coordination polyhedra
2003. "Proximity Effects on Semiconducting Mineral Surfaces II: Distance Dependence of Indirect Interactions." Geochimica et Cosmochimica Acta 67(5):941-953. Abstract Proximity Effects on Semiconducting Mineral Surfaces II: Distance Dependence of Indirect Interactions
2003. "Nonlocal Bacterial Electron Transfer to Hematite Surfaces." Geochimica et Cosmochimica Acta 67(5):1081-1087. Abstract Non-Local Bacterial Electron Transfer to Hematite Surfaces
2003. "Charge transport in micas: The kinetics of FeII/III electron transfer in the octahedral sheet." Journal of Chemical Physics 119(17):9207-9218. Abstract The two principal FeII/III electron exchange reactions underlying charge transport in the octahedral sheet of ideal end-member annite were modeled using a combination of ab initio calculations and Marcus electron transfer theory. A small polaron model was applied which yielded electron hopping activation energies that agree well with the limited available experimental data. A small ab initio cluster model successfully reproduced several important structural, energetic, and magnetic characteristics of the M1 and M2 Fe sites in the annite octahedral sheet. The cluster enabled calculation of the internal reorganization energy and electronic coupling matrix elements for the M2-M2 and M1-M2 electron transfer reactions. The M2-M2 electron transfer is symmetric with a predicted forward/reverse electron hopping rate of 106 s-1. The M1-M2 electron transfers are asymmetric due to the higher ionization potential by 0.46 eV of FeII in the M1 site. The electronic coupling matrix elements for these reactions are predicted to be small and of similar magnitude, suggesting the possibility that the coupling is essentially direction independent amongst hopping directions in the octahedral sheet. M1 Fe sites are predicted to be efficient electron traps and charge transport should occur by nearest-neighbor electron hops along the M2 Fe sublattice.
2003. "An Ab Initio Model of Electron Transport in Hematite (a-Fe2O3) Basal Planes." Journal of Chemical Physics 118(14):6455-6466. Abstract Transport of conduction electrons through basal planes of the hematite lattice was modeled as a valence alternation of iron cations using ab initio molecular orbital calculations and electron transfer theory. A cluster approach was successfully implemented to compute electron transfer rate-controlling quantities such as the reorganization energy and electronic coupling matrix element. Localization of a conduction electron at an iron lattice site is accompanied by large iron?oxygen bond length increases that give rise to a large inner-sphere component of the reorganization energy. The interaction between the reactant and product electronic states in the crossing?point configuration is substantial and leads to an adiabatic electron transfer system. Electron transfer is predicted to possess a small positive activation energy that turns out to be in excellent agreement with values deduced from conductivity measurements. Measured electron mobility can be explained in terms of nearest neighbor electron hops without significant contribution from iron atoms further away. Comparison of the predicted maximum polaron binding energy with the predicted half bandwidth indicates compliance with the small polaron condition. Therefore the localized electron treatment is appropriate to describe electron transport in this system.
2003. "Potential Docking Sites and Positions of Hydrogen in High-Pressure Silicates." American Mineralogist 88:1452-1459. Abstract Potential Docking Sites and Positions of Hydrogen in High-Pressure Silicates
2003. "Surface Structure Effects on Direct Reduction of Iron Oxides by Shewanella Oneidensis." Geochimica et Cosmochimica Acta 67(23):4489-4503. Abstract Surface Structure Effects on Direct Reduction of Iron Oxides by Shewanella Oneidensis
2003. "A physical basis for Pauling's definition of bond strength ." Physics and Chemistry of Minerals 30(5):317-320. Abstract The average strength, s, of the bonded interactions comprising a cation containing oxide anion coordination polyhedron and the value of the electron density, „(rc), at the bond-critical points are inversely correlated with bond length. in each case, the observed bond lengths, r, were modeled with power-law expressions defined in terms of s/r and „(rc)/r, respectively, where r is the periodic table row number of the cation involved in the bonded interaction. on the basis of the close connection between bond strength and the value of the electron density at the bond-critical point, we conclude that bond strength is a direct measure of bond type; the greater its value, the greater the localization of electron density in the binding region and the greater the shared-electron covalent character of the bonded interaction.
2003. "Characterization of the Structure and the Surface Reactivity of a Marcasite Thin Film." Geochimica et Cosmochimica Acta 67(5):807-812. Abstract Characterization of the structure and the surface reactivity of a marcasite thin film for surface science studies
2003. "The Structure of Hematite (001) Surfaces in Aqueous Media: Scanning Tunneling Microscopy and Resonant Tunneling Calculations of Co-Existing O and Fe Terminations." Geochimica et Cosmochimica Acta 67(5):985-1000. Abstract The Structure of Hematite (001) Surfaces in Aqueous Media: Scanning Tunneling Microscopy and Resonant Tunneling Calculations of Co-Existing O and Fe Terminations
2003. "Ab Initio Determination of Edge Surface Structures for Dioctahedral 2 : 1 Phyllosilicates: Implications for Acid-Base Reactivity ." Clays and Clay Minerals 51(4):359-371. Abstract The atomic structure of dioctahedral 2:1 phyllosilicate edge surfaces was calculated using pseudopotential planewave density functional theory. Bulk structures of pyrophyllite and ferripyrophyllite were optimized using periodic boundary conditions, after which crystal chemical methods were used to obtain initial terminations for ideal (110)- and (010)-type edge surfaces. The edge surfaces were protonated using various schemes to neutralize the surface charge, and total minimized energies were compared to identify which schemes are the most energetically favorable. The calculations show that significant surface relaxation should occur on the (110)-type faces, as well as in response to different protonation schemes on both surface types. This result is consistent with atomic force microscopy observations of phyllosilicate dissolution behavior. Bond-valence methods incorporating bond lengths from calculated structures can be used to predict intrinsic acidity constants for surface functional groups on (110)- and (010)-type edge surfaces. However, the occurrence of surface relaxation poses problems for applying current bond-valence methods. An alternative method is proposed that considers bond relaxation, and accounts for the energetics of various protonation schemes on phyllosilicate edges.
2003. "Metal Island Growth and Dynamics on Molybdenite Surfaces." Geochimica et Cosmochimica Acta 67(5):923-934. Abstract Metal Island Growth and Dynamics on Molybdenite Surfaces
2003. "Advances in Oxide and Sulfide Mineral Surface Chemistry." Geochimica et Cosmochimica Acta 67(5):797. Abstract Advances in Oxide and Sulfide Mineral Surface Chemistry
2002. "Trivalent Ion Hydrolysis Reactions II: Analysis of Electron Density Distributions in Metal-Oxygen Bonds." Journal of Physical Chemistry A 106(35):8133-8138. Abstract Trivalent Ion Hydrolysis Reactions II: Analysis of Electron Density Distributions in Metal-Oxygen Bonds
2002. "Outer-Sphere Electron Transfer Kinetics of Metal Ion Oxidation by Molecular Oxygen." Geochimica et Cosmochimica Acta 66(24):4223-4233. Abstract Outer-Sphere Electron Transfer Kinetics of Metal Ion Oxidation by Molecular Oxygen
2002. "Nanogeoscience: From the Movement of Electrons to Lithosphere Plates." Eos 83(6):1. Abstract Nanogeoscience: From the Movement of Electrons to Lithosphere Plates
2002. "A Comparison of Procrystal and Ab Initio Model Representations of the Electron-density Distributions of Minerals." Physics and Chemistry of Minerals 29(5):369-385. Abstract Abstract The procrystal calculation of the electron densityis a veryrapid procedure that offers a quick way to analyze various bonding properties of a crystal. This studyexplores the extent to which the positions, number, and properties of bond-critical points determined from the procrystal representations of the electron densityfor minerals are similar to those of first-princi- ples ab initio model distributions. The purpose of the studyis to determine the limits imposed upon interpretation of the procrystal electron density. Procrystal calculations of the electron densityfor more than 300 MO bonds in crystals were compared with those previously calculated using CRYSTAL98 and TOPOND software. For everybond-critical point found in the ab initio calculations, an equivalent one was also found in the procrystal model, with similar magnitudes of electron density, and at similar positions along the bonds. The curvatures of the electron densities obtained from the ab initio and the procrystal distributions are highly correlated. It is concluded that the procrystal distributions are capable of providing good estimates of the bonded radii of the atoms and the properties of the electron-density distributions at the bond-critical points. Because the procrystal model is so fast to compute, it is especially useful in addressing the question as to whether a pair of
2001. "The Structure and Reactivity of Semiconducting Mineral Surfaces: Convergence of Molecular Modeling and Experiment." Chapter 7 in Molecular Modeling Theory and Applications in the Geosciences, Reviews in Mineralogy & Geochemistry , vol. 42, ed. Randy T. Cygan and James D. Kubicki, pp. 199-271. Mineralogical Society of America, Washington, DC. Abstract The Structure and Reactivity of Semiconducting Mineral Surfaces: Convergence of Molecular Modeling and Experiment
2001. "A computational quantum chemical study of the bonded interactions in earth materials and structurally and chemically related molecules." Chapter 10 in Molecular Modeling Theory: Applications in Geosciences. Reviews in Mineralogy and Geochemistry, vol. 42, ed. Randall T. Cygan and James D. Kubicki, pp. 345-382. Mineralogical Society of America, Washington DC. Abstract A computational quantum chemical study of the bonded interactions in earth materials and structurally and chemically related molecules
2001. "The Structures and Energies of AlOOH and FeOOH Polymorphs from Plane Wave Pseudopotential Calculations." American Mineralogist 86:312-317. Abstract The Structures and Energies of AlOOH and FeOOH Polymorphs from Plane Wave Pseudopotential Calculations
2001. "The Cs/K Exchange in Muscovite Interlayers: An Ab Initio Treatment." Clays and Clay Minerals 49(6):500-513. Abstract The Cs/K Exchange in Muscovite Interlayers: An Ab Initio Treatment
2001. "The Proximity Effect on Semiconducting Mineral Surfaces: A new aspect of Mineral Surface Reactivity and Surface Complexation Theory?" Geochimica et Cosmochimica Acta 65(16):2641-2649. Abstract The observation and description of surface proximity effects, whereby the chemical reaction of one surface site influences the electronic structure and reactivity of neighboring or nearby sites, is presented in this study for semiconducting minerals pyrite (FeS2) and galena (PbS) using ab initio molecular orbital calculations as well as scanning tunneling microscopy and spectroscopy. Surface complexation theory, an important model for attachment/detachment reactions at mineral-water interfaces, will eventually need to be modified to include the influence of proximity effects.
2001. "Step Edges on Galena (100): Probing the Basis for Defect Driven Surface Reactivity at the Atomic Scale." American Mineralogist 86:862-870. Abstract Step Edges on Galena (100): Probing the Basis for Defect Driven Surface Reactivity at the Atomic Scale
2000. "Surface Defects and Self-Diffusion on Pyrite {100}: an Ultra-High Vacuum Scanning Tunneling Microscopy and Theoretical Modeling Study." American Mineralogist 85:1428-1436. Abstract A variety of defects on {100} cleavage surfaces of pyrite (FeS2) are observed directly using ultra high vacuum scanning tunneling microscopy. Step edges are aligned along <10> and <11> surface directions. Atomic scale images indicate that the atomic structure, with a respect to the Fe lattice, and local density of occupied states is unchanged at a step edge, including kink and corner sites. The inferred presence of monosulfides at step edges, based on X-ray photoelectron spectra on similar surfaces elsewhere, does not lead to occupied states higher in energy that dz2 dangling bond states at Fe sites. A sequence of consecutive images at the atomic scale captured evidence of dynamic structural changes at defects on this surface at room temperature. Step edges are seen to be generally stable over the course of the STM observations, whereas vacancies, their surrounding sites, and corner step edge sites are not. Theoretical maps of the attachment energy for an Fe adatom over a {100} surface cell indicate the presence of low energy diffusion channels along the topology of the closest S atoms in the uppermost atomic S monolayer. Calculation of the activation energy barriers for the self-diffusion of an Fe adatom over a {100} terrace predict low 0.1 eV diffusion barriers along channels and 0.24 eV across channels. Subsequently, calculated Fe adatom mobilities over the time scale of the STM observations are very high, ranging from 105-106 ? over the course of one minute, calculated for room temperature and depending on the diffusion direction. The structural changes documented in the STM images are explained as resulting from the natural process of surface self-diffusion.
2000. "Ab Initio Calculation of Homogeneous Outer Sphere Electron Transfer Rates: Application to M(OH2)(6)(3+/2+) Redox Couples." Journal of Physical Chemistry A 104(29):6718-6725. Abstract Abstract - Ab initio density functional theory calculations are applied to the prediction of homogeneous outer sphere electron transfer rates for a series of transition metal hexaquo ions in a background electrolyte. Reorganization energies, frequency factors, and the effective electron transfer distances are calculated for use in Marcus' theory. Theoretical inner sphere contributions to the reorganization energies correlate very well with total reorganization energies estimated from experimental self-exchange rates. Important energy contributions arising from Jahn-Teller distortions are accurately included in the inner sphere term. Effective electron transfer distances are found to be only slightly longer than the sum of the average calculated M-O distances. Calculated adiabatic self-exchange rates agree well with observed self-exchange rates. The driving force for bimolecular electron transfers, calculated from total energy differences, is found to compare well with estimations using experimental reduction potentials to within 4 kJ/mol. The choice of basis set is found to be very important in these calculations and, for this system, the 6-311+G basis set outperforms DZVP. The methods presented provide a convenient means to produce usefully accurate parameters for Marcus theory to predict outer sphere electron transfer rates.
2000. "Model Structures and Electron Density Distributions of the Silica Polymorph Coesite at Pressure: An assesment of OO bonded interactions." Journal of Physical Chemistry B 104(45):10534-10542. Abstract The crystal structure and the bond critical point (bcp) properties of the electron density distribution of coesite were modeled at pressures up to ~17 GPa, using first principles calculations. The nonequivalent SiO bond lengths and the SiOSi and OsiO angles of the model structures agree with those observed to within a few percent. With compression, the SiO bond lengths and the variable SiOSi angles both decrease. Also, the value of the electron density, p(rc), the curvatures and the Laplacian of the electron density distribution at the bond critical points each increase slightly. As found in a recent modeling of the low quartz structure, the distribution is nearly static and changes relatively little with compression. The bcp properties of the model structure agree with those observed for coesite at ambient conditions to within 5 and 15%, on average, and several of the properties correlate with the observed SiO bond lengths. Secondary bond critical points were found between the oxide anions of adjacent silicate tetrahedra. The value of the electron density at these points increases with decreasing separation between the anions. The behavior of bcp properties of the points is similar t that exhibited by the primary critical points between Si and O. In contrast, the value of the electron density at the points is about one order of magnitude less. In several cases, the points disappear with increasing pressure. Despite their closer contacts, no critical points were found between the anions that comprise the individual silicate tetrahedra nor are they likely to be found. The presence of the secondary points in procrystal representations of the electron density distributions suggests that the formation of the points is more an artifact of the spherical electron density distribution of the core electrons than one of the valence electrons.
1999. "Trivalent Ion Hydrolysis Reactions: A Linear Free-Energy Relationship Based on Density Functional Electronic Structure Calculations." Journal of the American Chemical Society 121(13):3234-3235. Abstract Metal ion hydrolysis is fundamental in aqueous chemistry because of the influence of coordinating hydroxide ions on reaction rates; examples include enhanced labilization of coordinating water molecules in hydrolyzed complexes1 and stabilization of oxidized products in electron-transfer reactions involving hydrolyzed reductants.2 Moreover, the role of metal hydrolysis reactions in defining a baseline for establishing trends in metalligand binding has motivated efforts toward comprehensive integration of Mz+ xOHy stability constants.3-5
1999. "The interaction of pyrite {100} surfaces with O2 and H2O: Fundamental oxidation mechanisms." American Mineralogist 84(10):1549-1561. Abstract The interaction of pyrite {100} surfaces with O2 and H2O: Fundamental oxidation mechanisms
1999. "SiO bonded interactions in coesite: A comparison of crystalline, molecular and experimental electron density distributions." Physics and Chemistry of Minerals 26(3):264-272. Abstract SiO bonded interactions in coesite: A comparison of crystalline, molecular and experimental electron density distributions
1999. "Atomically resolved electronic structure of pyrite {100} surfaces: An experimental and theoretical investigation with implication for reactivity." American Mineralogist 84(10):1535-1548. Abstract Atomically resolved electronic structure of pyrite {100} surfaces: An experimental and theoretical investigation with implication for reactivity
1999. "A UHV STM/STS and ab initio investigation of covellite {001} surfaces." Surface Science 423(2-3):364-374. Abstract A UHV STM/STS and ab initio investigation of covellite {001} surfaces
1999. "Model Structure and Properties of the Electron Density Distribution for Low Quartz at Pressure: A Study of the SiO Bond." Journal of Molecular Structure - Theochem 486:13-25. Abstract The crystal structure, the electron density distribution and the topological properties of the distribution for low quartz were modeled at pressure, using first principles calculations. The geometry optimized nonequivalent SiO bond lengths and the SiOSi angles of the model structures match those observed at pressure to within a few percent. As the bond lengths and angles decrease with compression, the electron density distribution at the bond critical points, p(rc), along the bonds increases slightly whereas the bonded radii of both Si and O decrease with the radius of the oxide anion compressing about twice as fast as that of the Si cation. The magnitudes of the new charges on both Si and O obtained in a virial partitioning of the electron density distribution also decrease slightly. The significance of secondary bond critical points and bond paths displayed between the oxide anions of adjacent silicate tetrahedra at pressures of 2.5 GPa and greater is discussed. The nature of these interactions is not clear, particularly since they are also exhibited by procrystal representations of the electron density distributions. As the p(rc) values observed for the SiO bonds in silicate minerals with four-coordinate Si are substantially greater than those reported for bonded interactions close to the closed shell ionic limit but less than those close to the shared covalent limit, the bond is indicated to be more intermediate in character than either ionic or covalent, despite claims to the contrary. Negative values of the Laplacian, ?2p(rc), for MO bonds of first-and second-row M-atoms are not always typical of predominantly covalent bonds.