Kevin M. Rosso's Publications

2009

Bickmore BR, KM Rosso, ID Brown, and SN Kerisit. 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.
Gibbs GV, AF Wallace, DF Cox, RT Downs, NL Ross, and KM Rosso. 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
Gibbs GV, AF Wallace, DF Cox, PM Dove, RT Downs, NL Ross, and KM Rosso. 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.
Kerisit SN, KM Rosso, BD Cannon, F Gao, and YL Xie. 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.
Murugesan V, SN Kerisit, CM Wang, Z Nie, KM Rosso, Z Yang, GL Graff, J Liu, and JZ Hu. 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.
Shi L, D Richardson, Z Wang, SN Kerisit, KM Rosso, JM Zachara, and JK Fredrickson. 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.
Wigginton NS, KM Rosso, AG Stack, and MF Hochella. 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.
Zarzycki PP, and KM Rosso. 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.

2008

Badireddy AR, S Chellam, S Yanina, PL Gassman, and KM Rosso. 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.
Badireddy AR, BR Korpol, S Chellam, PL Gassman, MH Engelhard, AS Lea, and KM Rosso. 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.

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