Scientific Publications 2008
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B
2008. "Photoelectron Spectrum of Valence Anions of Uracil and First-principles Calculations of Excess Electron Binding Energies." Journal of Chemical Physics 129:054309. doi:10.1063/1.2965128 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree–Fock and second-order Møller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within ±1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of ≈−0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.
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.
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. "Ionization-induced effects in amorphous apatite at elevated temperatures." Journal of Materials Research 23(4):962-967. doi:10.1557/JMR.2008.0114 Abstract Electron-beam induced effects in pre-amorphized Sr2Nd8(SiO4)6O2 is investigated in situ using transmission electron microscopy with 200 keV electrons at temperatures ranging from 380 to 780 K. While epitaxial recrystallization is observed from amorphous/crystalline toward surface within the electron irradiated area with its rate increasing as temperature increases from 380 to 580 K, structural contrast features (i.e., O deficient amorphous materials) as well as recrystallization are observed even outside of the irradiation area at temperatures from 680 to 780 K. Ionization-induced processes and local non-stoichiometry induced by oxygen migration and desorption are possible mechanisms for the electron-beam induced recrystallization and for the formation of the structural contrast features, respectively.
2008. "Temperature dependence of electron-beam induced effects in amorphous apatite ." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 266(12-13):3037-3042. doi:10.1016/j.nimb.2008.03.160 Abstract Irradiation effects on pre-amorphized Sr2Nd8(SiO4)6O2 have been investigated under 200 and 300 keV electron-beam irradiation at 130 and 480 K using in situ transmission electron microscopy. At 480 K, recrystallization occurred from the amorphous/crystalline interface under both 200 and 300 keV e-beam irradiation. At 130 K, the 200 keV e-beam irradiation induced recrystallization only; however, 300 keV e-beam irradiation induced both recrystallization and an electron hammering effect in the amorphous material that resulted in radial expansion perpendicular to the incident electron-beam direction and shrinkage parallel to the electron-beam direction. Ionization-induced processes and knock-on displacement damage are suggested to be the mechanisms for the recrystallization and the electron hammering effect, respectively.
2008. "Characterization Challenges for Nanomaterials." Surface and Interface Analysis 40(3-4):529-537. doi:10.1002/sia.2726 Abstract Nanostructured materials are increasingly subject to nearly every type of chemical and physical analysis possible. Because of their small feature size there is a significant focus on tools with high spatial resolution. Because of their high surface area, it is also natural to characterize nanomaterials using tools designed to analyze surfaces. Regardless of the approach, nanostructured materials present a variety of obstacles to adequate, useful and needed analysis. This paper provides short overviews to some of the issues and complications including: particle stability, environmental effects, specimen handling, surface coating, contamination and time. Some specific examples are provided from a our work focused on ceria nanoparticles and iron metal-core/oxide-shell nanoparticles in which we use a combination of tools for routine analysis including XPS, TEM, and XRD and apply other methods as needed to obtain essential information.
2008. "A New Analysis of X-Ray Adsorption Branching Ratios: Use of Russell-Saunders Coupling ." Chemical Physics Letters 455(4-6):331-334. Abstract The intensities of X-Ray absorption peaks at core-level edges are considered in terms of Russell-Saunders multiplets. The contributions of different multiplets to the relativistic wavefunctions of the excited states are determined and the absorption intensity related to the contributions of the dipole allowed multiplets. This is a powerful method because the selection rules for multiplets are stronger than for relativistic J levels. It is also shown that differences in the radial extent of the spin-orbit split core spinors modify the intensity given by these symmetry arguments. Applications are considered for cases involving different degrees of Russell-Saunders or j-j coupling.
2008. "Effects of gamma-sterilization on the physico-chemical properties of naturalsediments." Chemical Geology 251(1-4):1-7. doi:10.1016/j.chemgeo.2008.01.003 Abstract A series of experiments were completed to determine the effects of soil sterilization on various soil chemical properties including U(VI) sorption, soil pH, natural organic matter (NOM), cation exchange capacity (CEC), and iron oxidation state. Soils under investigation were a saprolitic sequence of interbedded weathered shale and limestone collected from the Oak Ridge Reservation (ORR). Sediments were sterilized by either steam sterilization at 121oC or by γ-irradiation using a cobalt-60 source. Subsamples of sediments were pretreated with dithionate-citrate-bicarbonate (DCB) and/or H2O2 to remove reducible Fe(III) oxides and NOM. Results from aerobic U(VI) sorption experiments indicated that γ-sterilized sediments sorbed more U(VI) compared to non-sterile sediments. Results from sorption experiments completed using DCB and H2O2-treated samples indicated that the iron oxide and NOM fractions of the sediment accounted for the majority of U(VI) sorption and that γ-irradiation of these phases resulted in increased sorption of U(VI). Mössbauer spectra of γ-sterilized sedimentsdisplayed a decrease in the amount of ferric iron associated with goethite and a small increase in the amount of reduced iron in silicate minerals compared to spectra from non-sterile samples. Our results suggest that sterilization by γ-irradiation induced iron reduction that may have increased sorption of U(VI) on these sediments.
2008. "The Effect of Solvent on the Analysis of Secondary Organic Aerosol Using Electrospray Ionization Mass Spectrometry." Environmental Science & Technology 42(19):7341-7346. doi:10.1021/es801226w Abstract Solvent-analyte reactions in organic aerosol (OA) extracts prepared for analysis by electrospray ionization mass spectrometry (ESI-MS) were examined. Secondary organic aerosol (SOA) produced by ozonation of d-limonene as well as several test organic chemicals with functional groups typical for OA constituents were dissolved and stored in methanol, d3-methanol, acetonitrile, and d3-acetonitrile to investigate the extent and relative rates of reactions between analyte and solvent. High resolution ESI-MS showed that reactions of carbonyls with methanol produce significant amounts of hemiacetals and acetals on time scales ranging from several minutes to several days, with the reaction rates increasing in acidified solutions. Carboxylic acid groups were observed to react with methanol resulting in the formation of esters. In contrast, acetonitrile extracts showed no evidence of reactions with analyte molecules, suggesting that acetonitrile is the preferred solvent for SOA extraction. The use of solvent-analyte reactivity as an analytical chemistry tool for the improved characterization of functional groups in complex organic mixtures was also demonstrated. Direct comparison between ESI mass spectra of the same SOA samples extracted in reactive (methanol) versus non-reactive (acetonitrile) solvents was used to estimate the relative fractions of ketones (38%), aldehydes (6%), and carboxylic acids (55%) in d-limonene SOA.
2008. "Energy and Site Selectivity in O-Atom Photodesorption from Nanostructured MgO." Surface Science 602(11):1968-1973. doi:10.1016/j.susc.2008.03.046 Abstract Electronic excitation of wide gap ionic solids can induce desorption of neutral atoms with distinct hyperthermal and thermal kinetic energy distributions. Hyperthermal atomic desorption results from electronic surface excitation while thermal desorption is initiated primarily by bulk excitation. Calculations indicate that surface-localized transitions can be excited independently from bulk transitions using selected photon energies. The photon energy required to excite specific surface sites depends upon the site coordination with successively lower energies required to excite terrace, step, and corner sites. Here, we excite low-coordinated surface sites of nanostructured MgO samples using 4.7 eV UV laser pulses and observe dominant hyperthermal O-atom emission. We then selectively excite bulk sites of nanostructured MgO, using a 7.9 eV laser, and observe dominant thermal O-atom desorption. These results are analyzed in terms of laser desorption models developed previously for alkali halide crystals. We propose a multi-step mechanism for hyperthermal O-atom desorption, under surface selective excitation, based on hole trapping at 3C (corner) O-atom sites followed by exciton decomposition. The proposed “hole plus exciton” model has similarities to the surface exciton desorption model, established for alkali halides, but is more complex and requires more steps. Nonetheless, the principle of site-specific photoreaction, established for alkali halide crystals, is clearly extendable to a prototypical metal oxide.
2008. "PNNL streamlines energy-guzzling computers." DOE Pulse 272(October 6, 2008):2. Abstract In a room the size of a garage, two rows of six-foot-tall racks holding supercomputer hard drives sit back-to-back. Thin tubes and wires snake off the hard drives, slithering into the corners. Stepping between the rows, a rush of heat whips around you -- the air from fans blowing off processing heat. But walk farther in, between the next racks of hard drives, and the temperature drops noticeably. These drives are being cooled by a non-conducting liquid that runs right over the hardworking processors. The liquid carries the heat away in tubes, saving the air a few degrees. This is the Energy Smart Data Center at Pacific Northwest National Laboratory. The bigger, faster, and meatier supercomputers get, the more energy they consume. PNNL's Andres Marquez has developed this test bed to learn how to train the behemoths in energy efficiency. The work will help supercomputers perform better as well. Processors have to keep cool or suffer from "thermal throttling," says Marquez. "That's the performance threshold where the computer is too hot to run well. That threshold is an industry secret." The center at EMSL, DOE's national scientific user facility at PNNL, harbors several ways of experimenting with energy usage. For example, the room's air conditioning is isolated from the rest of EMSL -- pipes running beneath the floor carry temperature-controlled water through heat exchangers to cooling towers outside. "We can test whether it's more energy efficient to cool directly on the processing chips or out in the water tower," says Marquez. The hard drives feed energy and temperature data to a network server running specially designed software that controls and monitors the data center. To test the center’s limits, the team runs the processors flat out – not only on carefully controlled test programs in the Energy Smart computers, but also on real world software from other EMSL research, such as regional weather forecasting models. Marquez's group is also developing "power aware computing", where the computer programs themselves perform calculations more energy efficiently. Maybe once computers get smart about energy, they'll have tips for their users.
2008. "Growth and characterization of highly oriented gadolinia-doped ceria (111) thin films on zirconia (111)/sapphire (0001) substrates." Thin Solid Films 516(18):6088-6094. doi:10.1016/j.tsf.2007.11.007 Abstract Highly-oriented pure and gadolinia-doped ceria thin films have been grown on pure and ZrO2 (111)-buffered Al2O3 (0001) substrates using oxygen plasma-assisted molecular beam epitaxy (OPA-MBE) to understand the oxygen ionic transport processes in ceria based oxide thin films. Gadolinia-doped ceria films grown on pure Al2O3(0001) substrate show polycrystalline features due to structural deformations resulting from the large lattice mismatch between the Al2O3(0001) substrate and the films. However, the films, grown on a thin layer of ZrO2(111) buffered Al2O3 (0001) substrate, appears to be highly oriented. These films were characterized using high resolution transmission electron microscopy (HRTEM) and x-ray photoelectron spectroscopy (XPS) depth profiling. Oxygen ionic conductivity in gadolinia-doped ceria films was measured as a function of Gd concentration and these results were compared with the ion conductance data of the polycrystalline and single crystalline yttria-stabilized zirconia (YSZ).
2008. "Another Role of Proline: Stabilization Interactions in Proteins and ProteinComplexes Concerning Proline and Tryptophane." Physical Chemistry Chemical Physics. PCCP 10:6350-6359. doi:10.1039/b805087b Abstract Proline–tryptophan complexes derived from experimental structures are investigated by quantum chemical procedures known to properly describe the London dispersion energy. We study two geometrical arrangements: the “L-shaped”, stabilized by an H-bond, and the “stacked-like”, where the two residues are in parallel orientation without any H-bond. Interestingly, the interaction energies in both cases are comparable and very large (~7 kcal mol⁻¹). The strength of stabilization in the stacked arrangement is rather surprising considering the fact that only one partner has an aromatic character. The interaction energy decomposition using the SAPT method further demonstrates the very important role of dispersion energy in such arrangement. To elucidate the structural features responsible for this unexpectedly large stabilization we examined the role of the nitrogen heteroatom and the importance of the cyclicity of the proline residue. We show that the electrostatic interaction due to the presence of the dipole, caused by the nitrogen heteroatom, contributes largely to the strength of the interaction. Nevertheless, the cyclic arrangement of proline, which allows for the largest amount of dispersive contact with the aromatic partner, also has a notable-effect. Geometry optimizations carried out for the “stackedlike” complexes show that the arrangements derived from protein structure are close to their gas phase optimum geometry, suggesting that the environment has only a minor effect on the geometry of the interaction. We conclude that the strength of proline non-covalent interactions, combined with this residue’s rigidity, might be the explanation for its prominent role in protein stabilization and recognition processes.
2008. "On the protonation of oxo- and hydroxo- groups of the goethite (a-FeOOH) surface: A FTIR spectroscopic investigation of surface O-H stretching vibrations." Geochimica et Cosmochimica Acta 72(14):3338-3357 . doi:10.1016/j.gca.2008.04.022 Abstract The O-H stretching region of goethite particles evaporated at different levels of acidity was investigated by Attenuated Total Reflectance (ATR) Fourier Transform InfraRed (FTIR) spectroscopy. A 2D IR correlation analysis of the spectra was used to identify correlations between different sets of discrete surface OH stretches. Four groups were identified: Group I (3648 and 3578 cm-1), Group II (3668, 3660 and 3490 cm-1), Group III (3698 and 3541 cm-1) and Group IV (3628 cm-1). Groups II and III were respectively assigned to singly- (-OH) and doubly- (-OH) coordinated hydroxyls of mostly the {110} plane of goethite. Groups I and IV assigned to a minor sub-set of singly- (-OH) and doubly- (-OH) coordinated hydroxyls. Their structural origins, for example whether they arise from defects of are distinct hydroxyls of the {021} plane, remains to be determined. These band assignments were supported by estimates of the surface protonation level of goethite as well as the relative and absolute O-H stretching frequency calculations of all crystallographically-available surface sites of the goethite surface using the results of previous theoretical studies. A reexamination of Temperature Programmed Desorption (TPD) FTIR data of one goethite sample evaporated from alkaline conditions [Boily et al., Geochim. Cosmochim Acta, 70, 3613-3624] also provided further constraints to this band assignment and helped formulate a possible route for surface dehydroxylation reactions. This model suggests that important cooperative effects between hydrogen-bonded surface hydroxyls play a crucial role on the variations of the position and intensity of discrete O-H stretching bands as a function of protonation level and temperature.
2008. "Evaluation of Characterization Techniques for Iron Pipe Corrosion Products and Iron Oxide Thin Films." Journal of Environmental Engineering (ASCE) 134(10):835-844. Abstract A common problem faced by drinking water studies is that of properly characterizing the corrosion products (CP) in iron pipescor synthetic Fe (hydr)oxides used to simulate the iron pipe used in municipal drinking-water systems. The present work compares the relative applicability of a suite of imaging and analytical techniques for the characterization of CPs and synthetic Fe oxide thin films and provide an overview of the type of data that each instrument can provide as well as their limitations to help researchers and consultants choose the best technique for a given task. Crushed CP from a water distribution system and synthetic Fe oxide thin films formed on glass surfaces were chosen as test samples for this evaluation. The CP and synthetic Fe oxide thin films were analyzed by atomic force microscopy (AFM), scanning electron microscopy (SEM), energy-dispersive spectroscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray powder diffractometry (XRD), grazing incident diffractometry (GID), transmission electron microscopy (TEM), selected area electron diffraction, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared, Mössbauer spectroscopy, Brunauer-Emmett-Teller N2 adsorption and Fe concentration was determined by the ferrozine method. XRD and GID were found to be the most suitable techniques for identification of the mineralogical composition of CP and synthetic Fe oxide thin films, respectively. AFM and a combined ToF-SIMS-AFM approach proved excellent for roughness and depth profiling analysis of synthetic Fe oxide thin films, respectively. Corrosion products were difficult to study by AFM due to their surface roughness, while synthetic Fe oxide thin films resisted most spectroscopic methods due to their limited thickness (118 nm). XPS analysis is not recommended for mixtures of Fe (hydr)oxides due to their spectral similarities. SEM and TEM provided great detail on mineralogical morphology.
2008. "Nuclear-spin relaxation of ²º⁷Pb in ferroelectric powders." Physical Review. A. 77(2):Art. No. 022102. doi:10.1103/PhysRevA.77.022102 Abstract The ²º⁷Pb nuclear system (nuclear spin I = 1/2; magnetic Moment μ ≈0.58 μN; isotopic abundance ≈ 22%) in ferroelectric solids has been proposed for a search for a Schiff moment associated with simultaneous violation of parity (P) and time-reversal invariance (T) in fundamental interactions [1] (see also a discussion of the sensitivity of such search in Ref. [2]). The idea is that, due to the Schiff moment, a ferroelectric sample would acquire a P,T-odd magnetic polarization along the direction of its electric polarization. In conclusion, we have presented the first experimental study of relaxation properties of ²º⁷Pb in PT and PZT below room temperature. We find that above T≈ 50 K, longitudinal relaxation rate follows the T² dependence characteristic of the two-phonon Raman process. On the other hand, as the temperature is decreased below T≈ 50 K, the longitudinal relaxation rates drop slower than ∝T2 (as opposed to ∝T7 expected for the Raman process), and the relaxation is probably due to a direct process associated with paramagnetic impurities and nuclear-spin diffusion. While the longitudinal relaxation times T₁ vary between several seconds and over an hour in the temperature range between 290 and 10 K, the transverse relaxation time T₂ is found to be ≈1.5 ms for all temperatures and all powder samples studied. D: we never discuss the origin of T₂ relaxation. Maybe we should. 1.5 ms is only a bit shorter from what would be expected from nuclear spin-spin interactions. Any comments? At some point Sasha asked Oleg to calculate T₂ exactly for PT and PZT, but I forgot what was the result. If such calculation exists, it would be great to compare with the expt. result. The obtained results provide an important input in the design of the experiments to search for P,T-violating effects in solid ferroelectrics
2008. "H2O and Cation Structure and Dynamics in Expandable Clays: 2H and 39K NMR Investigations of Hectorite." Journal of Physical Chemistry C 112(16):6430-6438. doi:10.1021/jp7119087 Abstract The dynamic behavior of H2O and ionic species in two- and three-dimensional confinement plays a variety of important roles in processes such as ion transport and adsorption, water storage in hostile environments, dissolution/precipitation reactions in aqueous environments, and the swelling of smectite clays (low charge 2:1 type phyllosilicates with expandable interlayers). Historically, the structure and dynamics of ions and water in confined spaces and at solid-fluid interfaces have been difficult to characterize on the molecular scale, but the continued evolution of molecular modeling, neutron scattering, and nuclear magnetic resonance (NMR) spectroscopy has permitted ever more detailed theoretical and experimental investigations, particularly regarding the special case of H2O in the two-dimensional, nanometer-scale interlayer space of phyllosilicates.
2008. "Functionalized Silicone Nanospheres: Synthesis, Transition Metal Immobilization, and Catalytic Applications." Chemistry of Materials 21(1):174-185. doi:10.1021/cm8018154 Abstract Silicone nanospheres containing a variety of functional groups (pyridines, phosphines, thiols, amines, etc.) have been prepared by emulsion copolymerization of methyltrimethoxysilane, MeSi(OMe)3, and the functionalized monomer of interest, RSi(OMe)3. This procedure provides a reproducible synthesis of spherical particles in the 12-28 nm size regime as determined by transmission electronSilicone nanospheres containing a variety of functional groups (pyridines, phosphines, thiols, amines, etc.) have been prepared by emulsion copolymerization of methyltrimethoxysilane, MeSi(OMe)₃, and the functionalized monomer of interest, RSi(OMe)₃. This procedure provides a reproducible synthesis of spherical particles in the 12-28 nm size regime as determined by transmission electron microscopy (TEM). The presence of the functional groups is supported by a combination of spectroscopic methods including DRUV-vis, DRIFTS, and NMR spectroscopy. Comonomer dispersity within the nanospheres was probed using elemental mapping techniques, and these support a homogeneous distribution of functional groups within the particles. Palladium(0) immobilization on phosphine-substituted nanospheres also results in a random distribution of the transition metal throughout the particles. Nanospheres containing multiple acid/base functionalities were also prepared, and these demonstrate functional group cooperativity based on enhanced conversions in the base-catalyzed Henry reaction, relative to nanosphere catalysts containing only basic groups. The diversity of functional groups that may be incorporated into the spheres suggests that these materials hold considerable promise as ligand supports and catalysts.Graphene nanoribbons (GNRs) have been suggested as a promising material for its use as nanoelectromechanical reasonators for highly sensitive force, mass, and charge detection. Therefore the accurate determination of the size-dependent elastic properties of GNRs is desirable for the design of graphene-based nanoelectromechanical devices. In this study we determine the size-dependent Young’s modulus and carbon-carbon binding energy in a homologous series of GNRs, C4n2+6n+2H6n+4 (n=2–12), with the use of all electron first principles computations. An unexpected linearity between the binding energy and Young’s modulus is observed, making possible the prediction of the size-dependent Young’s modulus of GNRs through a single point energy calculation of the GNR ground state. A quantitative-structure-property relationship is derived, which correlates Young’s modulus to the total energy and the number of carbon atoms within the ribbon. In the limit of extended graphene sheets we determine the value of Young’s modulus to be 1.09 TPa, in excellent agreement with experimental estimates derived for graphite and suspended grapheme sheets. microscopy (TEM). The presence of the functional groups is supported by a combination of spectroscopic methods including DRUV-vis, DRIFTS, and NMR spectroscopy. Comonomer dispersity within the nanospheres was probed using elemental mapping techniques, and these support a homogeneous distribution of functional groups within the particles. Palladium(0) immobilization on phosphine-substituted nanospheres also results in a random distribution of the transition metal throughout the particles. Nanospheres containing multiple acid/base functionalities were also prepared, and these demonstrate functional group cooperativity based on enhanced conversions in the base-catalyzed Henry reaction, relative to nanosphere catalysts containing only basic groups. The diversity of functional groups that may be incorporated into the spheres suggests that these materials hold considerable promise as ligand supports and catalysts.
2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295. Abstract The elucidation of critical functional pathways employed by pathogens and hosts during an infectious cycle is both challenging and central to our understanding of infectious diseases. In recent years, mass spectrometry-based proteomics has been used as a powerful tool to identify key pathogenesis-related proteins and pathways. Despite the analytical power of mass spectrometry-based technologies, samples must be appropriately prepared to characterize the functions of interest (e.g. host-response to a pathogen or a pathogen-response to a host). The preparation of these protein samples requires multiple decisions about what aspect of infection is being studied, and it may require the isolation of either host and/or pathogen cellular material.
2008. "Structural Studies of the SET Domain from RIZ1 Tumor Suppressor." Biochemical and Biophysical Research Communications 366(3):807-813. doi:10.1016/j.bbrc.2007.12.034 Abstract Histone lysine methyltransferases (HKMTs) are involved in regulation of chromatin structure, and, as such, are important for longterm gene activation and repression that is associated with cell memory and establishment of cell-type specific transcriptional programs. Most HKMTs contain a SET domain, which is responsible for their catalytic activity. RIZ1 is a transcription regulator and tumor suppressor that catalyzes methylation of lysine 9 of histone H3 and contains a rather distinct SET domain. Similar SET domains, sometimes refererred to as PR (PRDI-BF1 and RIZ1 homology) domains, are also found in other proteins including Blimp-1/PRDI-BF1, MDS1-EVI1 and Meisetz. We determined the solution structure of the PR domain from RIZ1 and characterized its interaction with S-adenosyl homocysteine (SAH) and a peptide from histone H3. Despite low sequence identity with canonical SET domains, the PR domain displays a typical SET fold including a pseudo-knot at the C-terminus. The N-flanking sequence of RIZ1 PR domain adopts a novel conformation and interacts closely with the SET fold. The C-flanking sequence contains an α-helix that exhibits higher mobility than the SET fold and points away from the protein face that harbors active site in other SET domains. Residues that interact with the methylation cofactor in SET domains are not conserved in RIZ1 or other PR domains, and the SET fold of RIZ1 does not bind SAH. However, the PR domain of RIZ1 interacts specifically with a synthetic peptide comprising residues 1-20 of histone H3.
2008. "MASS-REMOVAL AND MASS-FLUX-REDUCTION BEHAVIOR FOR IDEALIZED SOURCE ZONES WITH HYDRAULICALLY POORLY-ACCESSIBLE IMMISCIBLE LIQUID." Chemosphere 71(8):1511-1521. Abstract A series of flow-cell experiments was conducted to investigate aqueous dissolution and mass-removal behavior for systems wherein immiscible liquid was non-uniformly distributed in physically heterogeneous source zones. The study focused specifically on characterizing the relationship between mass flux reduction and mass removal for systems for which immiscible liquid is poorly accessible to flowing water. Two idealized scenarios were examined, one wherein immiscible liquid at residual saturation exists within a lower-permeability unit residing in a higher-permeability matrix, and one wherein immiscible liquid at higher saturation (a pool) exists within a higher-permeability unit adjacent to a lower-permeability unit. The results showed that significant reductions in mass flux occurred at relatively moderate mass-removal fractions for all systems. Conversely, minimalmass flux reduction occurred until a relatively large fraction of mass (>80%) was removed for the control experiment, which was designed to exhibit ideal mass removal. In general, mass flux reduction was observed to follow an approximately one-to-one relationship with mass removal. Two methods for estimating mass-flux-reduction/mass-removal behavior, one based on system-indicator parameters (ganglia-to-pool ratio) and the other a simple mass-removal function, were used to evaluate the measured data. The results of this study illustrate the impact of poorly accessible immiscible liquid on mass-removal and mass-flux processes, and the difficulties posed for estimating mass-flux-reduction/mass-removal behavior.
2008. "Two-Electron Three-Centered Bond in Side-On (η2) Uranyl(V) Superoxo Complexes." Journal of Physical Chemistry A 112(26):5777-5780. doi:10.1021/jp804202q Abstract Mononuclear dioxygen-metal compounds, such as FeO2 complexes with Schiff base and porphyrin ligands, play an essential role in chemistry ranging from oxyhemoglobin to cytochrome P-450 and cytochrome oxidase. It is well known that the superoxo complexes involved in these systems have end-on (η1) coordination geometries with O–O bond lengths of ~1.30 Å, Fe–O–O bond angles of ~135o, and vibrational frequencies of ~1150 cm-1,1 which reflects a formal change of the oxidation state from Mn+ to Mn+1. In addition, there are side-on (η2) peroxospecies, such as [Fe(porphyrin)(O2)]–, in which the O–O bond lengths is ~1.46 Å and vibrational frequencies of ~820 cm-1.1 These reflect a formal change of the oxidation state from Mn+ to Mn+2.
2008. "1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein. ." Biomolecular NMR Assignments 2(1):89-91. Abstract Amelogenin is the predominant matrix protein in developing dental enamel. Making extensive use of residue-specific 15N-labeled amino acids samples, the majority of the main and side chain resonances for murine amelogenin were assigned in 2% aqueous acetic acid at pH 3.0. This research was performed at Pacific Northwest National Laboratory, operated by Battelle for the US-DOE. A large part of this research was performed at the W.R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by U.S. Department of Energy’s Office of Biological and Environmental Research (BER) program located at Pacific Northwest National Laboratory (PNNL).
2008. "A Solution NMR Investigation into the Early Events of Amelogenin Nanosphere Self-Assembly Initiated with Sodium Chloride or Calcium Chloride." Biochemistry 47(50):13215-13222. doi:10.1021/bi8018288 Abstract Using solution-state NMR spectroscopy, new insights into the early intermolecular interactions stabilizing amelogenin supramolecular assembly and the potential role of calcium ions have been discovered. Two-dimensional 1H-15N spectra were recorded for 15N-labeled amelogenin as a function of increasing Ca2+ concentration starting from monomeric conditions. Evidence for protein-protein interactions were observed between residues E18 and E40 in the N-terminus. At higher Ca2+ concentrations there was concurrent involvement of residues in both the N- (Y12-Q56) and the C-terminus (Q144-T171). Neither specific residues nor their stepwise interaction have previously been identified in the initial stages of nanosphere assembly.
2008. "Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family." Biomolecular NMR Assignments 2:25-28. Abstract The recently sequenced genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 (contig 83.1_1_243_746) contains the sequence for an hypothetical protein that falls into the DUF683 family. As observed for the other 54 DUF683 proteins currently listed in the GenBank database, this 78-residue (9.0 kDa) protein in Cyanothece is also found in a nitrogen fixation gene cluster suggesting that it is involved in the process. To date no structural information exists for any of the proteins in the DUF683 family. In an effort to elucidate the biochemical role DUF683 may play in nitrogen fixation and to obtain structural information for a member of the DUF683 protein family, a construct containing DUF683 from Cyanothece 51142 was generated, expressed, purified, and the solution properties characterized. A total rotational correlation time (tc) of 17.1 ns was estimated by nuclear magnetic resonance (NMR) spectroscopy suggesting a molecular weight of ~ 40 kDa, an observation dictating that DUF683 is a tetramer in solution. Using triple-labeled (2H, 13C, 15N) and residue-specific 15N-labeled amino acids (L, K, V, and E/Q) samples, most of the backbone and side chain resonances for DUF683 were assigned. The 13C alpha chemical shifts and NOESY NMR data indicate that the protein is helical from K18-E75.
2008. "Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel Nudix hydrolase with a preference for cytosine (deoxy) ribonucleoside 5'-di- and triphosphates." Biochemistry 47(25):6571-82. Abstract The Deinococcus radiodurans Nudix hydrolase DR0079 was assayed for activity towards a wide variety of substrates and observed to have a marked specificity for cytosine ribonucleoside 5’-diphosphate (CDP) and cytosine ribonucleoside 5’-triphosphate (CTP) with a slight preference for CDP. The next most specific substrates, with a relative activity of <50%, were the corresponding deoxyribose nucleosides, dCDP and dCTP. Enzyme hydrolase activity at the site of the phosphodiester bond was corroborated using 31P NMR spectroscopy to follow the phosphorus resonances for two substrates, CDP and IDP, and the hydrolysis products, NMP and Pi. Optimum activity for CDP was determined to be at pH 9.0 – 9.5. The optimal divalent cation for CDP hydrolysis at this pH was Mg2+ followed by Mn2+ (~47%) and Co2+(~27%). The biochemical data is discussed with reference to the crystal structure for the D. radiodurans DR0079 that was determined in the apo-metal form at 1.9 Å resolution. The protein in the crystal structure contains nine β-strands, three α-helices, and two 3-10 helices that are organized into three subdomains; an N-terminal β-sheet, a central Nudix core, and a C-terminal helixturn- helix motif. As observed for all known structures of Nudix hydrolases, the α-helix of the ‘Nudix box’ is one of two helices that sandwich a ‘four-strand’ mixed β-sheet. Using 15N-labelled DR0079, NMR chemical shift mapping experiments were performed with the paramagnetic divalent cation Co2+ and the non-hydrolyzable substrate thymidine- 5’-O-(α,β-methylenediphosphate (TMP-CP). The results of the chemical shift perturbation experiments were mapped onto the crystal structure of DR0079 and a model for substrate binding proposed.
2008. "Insights into the structural variation between pentapeptide repeat proteins - Crystal structure of Rfr23 from Cyanothece 51142." Journal of Structural Biology 162(1):184-192. Abstract Cyanothece sp. PCC 51142 contains 35 pentapeptide repeat proteins (PRPs), proteins that contain a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. Published crystal structures of PRPs show that the tandem pentapeptide repeats adopt a type of right-handed quadrilateral β-helix called an Rfr-fold. To characterize how structural features of Rfr-folds vary with different amino acid sequences, the crystal structure of Cyanothece Rfr23 (174 residues) was determined at 2.1 Å resolution. The structure is dominated by an Rfr-fold capped at the N-terminus with a nine-residue α-helix (M26* - E34). The Rfr-fold of Rfr23 contains four structural features previously unobserved in Rfr-folds. First, Rfr23 is composed entirely of type II β-turns. Second, the pentapeptide repeats are not all tandem in the primary amino acid sequence. Rfr23 contains a 24-residue loop protruding outside one corner of the first complete N-terminal coil of the Rfr-fold (L56 – P79) for which little electron density is observed (24-residue loop). Third, a disulfide bond exists at the corner of one β-turn in the first coil (disulfide bracket). Size exclusion chromatography and NMR and CD spectroscopy indicate that the reduction of the disulfide bracket with the addition of DTT destroys the entire Rfr-fold. Fourth, a single-residue loop in the C-terminal coil perturbs the last coil slightly about one corner of the Rfr-fold (single-residue loop).
2008. "Characterization of uraninite nanoparticles produced by Shewanella oneidensis MR-1 ." Geochimica et Cosmochimica Acta 72(20):4901-4915. doi:10.1016/j.gca.2008.07.016 Abstract The reduction of uranium(VI) by Shewanella oneidensis MR-1 was studied to examine the effects of bioreduction kinetics and background electrolyte on the physical properties and reactivity to re-oxidation of the biogenic uraninite, UO2(s). Bioreduction experiments were conducted with uranyl acetate as the electron acceptor and sodium lactate as the electron donor under resting cell conditions in a 30 mM NaHCO3 buffer, and in a PIPES-buffered artificial groundwater (PBAGW). MR-1 was cultured in batch mode in a defined minimal medium with a specified air-to-medium volume ratio such that electron acceptor (O2) limiting conditions were reached just when cells were harvested for subsequent experiments. The rate of U(VI) bioreduction was manipulated by varying the cell density and the incubation temperature (1.0 _ 108 cell ml_1 at 20 _C or 2.0 _ 108 cell ml_1 at 37 _C) to generate U(IV) solids at ‘‘fast” and ‘‘slow” rates in the two different buffers. The presence of Ca in PBAGW buffer altered U(VI) speciation and solubility, and significantly decreased U(VI) bioreduction kinetics. High resolution transmission electron microscopy was used to measure uraninite particle size distributions produced under the four different conditions. The most common primary particle size was 2.9–3.0 nm regardless of U(VI) bioreduction rate or background electrolyte. Extended X-ray absorption fine-structure spectroscopy was also used to estimate uraninite particle size and was consistent with TEM results. The reactivity of the biogenic uraninite products with dissolved oxygen was tested, and neither U(VI) bioreduction rate nor background electrolyte had any statistical effect on oxidation rates. With MR-1, uraninite particle size was not controlled by the bioreduction rate of U(VI) or the background electrolyte. These results for MR-1, where U(VI) bioreduction rate had no discernible effect on uraninite particle size or oxidation rate, contrast with our recent research with Shewanella putrefaciens CN32, where U(VI) bioreduction rate strongly influenced both uraninite particle size and oxidation rate. These two studies with Shewanella species can be viewed as consistent if one assumes that particle size controls oxidation rates, so the similar uraninite particle sizes produced by MR-1 regardless of U(VI) bioreduction rate would result in similar oxidation rates. Factors that might explain why U(VI) bioreduction rate was an important control on uraninite particle size for CN32 but not for MR-1 are discussed.
2008. "Hydrodesulfurization Properties of Cobalt–nickel Phosphide Catalysts:Ni-rich Materials are Highly Active." Journal of Catalysis 260(2):262-269. doi:10.1016/j.jcat.2008.10.001 Abstract The HDS properties of a series of CoxNi2−xPy/SiO2 catalysts have been investigated as a function of the Co/Ni molar ratio (for a fixed P/Me molar ratio) and of the P/Me molar ratio (for a fixed Co/Ni molar ratio). An oxidic precursor composition of Co0.08Ni1.92P2.00 on the silica support yielded the bimetallic phosphide phase having the highest HDS activity, 34% higher than that of an optimized nickel phosphide catalyst prepared from an oxidic precursor having a composition of Ni2.00P1.60. X-ray photoelectron spectroscopy revealed Ni-rich CoxNi2−xPy/SiO2 catalysts to have surface enrichment of P (relative to Ni2.00P1.60/SiO2 and Co2.00P1.00/SiO2 catalysts) and to incorporate remarkably low amounts of S during HDS testing. The high activity of these CoxNi2−xPy/SiO2 catalysts is attributed to surface enrichment of P relative to nickel phosphide, which results in improved resistance to S incorporation under HDS conditions. Consistent with these findings and the solid-state chemistry evidence that suggests that Ni atoms in Ni-rich CoxNi2−xPy/SiO2 catalysts occupy disproportionately more pyramidal M(2) sites than tetrahedral M(1) sites, we conclude that the high site densities of these catalysts are due to Ni atoms in surface M(2) sites, which results in P-enriched surfaces that are resistant to site blockage due to S incorporation.
2008. "One-Electron-Transfer Reactions of Polychlorinated Ethylenes: Concerted and Stepwise Cleavages." Journal of Physical Chemistry A 112(16):3712-3721. Abstract Reaction barriers were calculated by using ab initio electronic structure methods for the reductive dechlorination of the polychlorinated ethylenes: C2CL4, C2Cl4, C2HCl3, trans-1,2-C2H2Cl2, cis-1,2-C2H2Cl2, 1,1-C2H2Cl2, and C2HCl3. Concerted and stepwise cleavages of R-Cl bonds were considered. Stepwise cleavages yielded lower activation barriers than concerted cleavages for the reduction of C2Cl4, C2HCl3, and trans-1,2-C2H2Cl2 via strong reducing agents. However, for typical ranges of reducing strength concerted cleavages were found to be favored. Both gas-phase and aqueous-phase calculations predicted C2Cl4 to have the lowest reaction barrier. Additionally, the reduction of C2HCl3 was predicted to have a significant amount of selectivity of cis-1,2-C2HCl2 over the corresponding reactions leading to the trans-1,2-C2HCl2, and 1,1-C2HCl2 radicals. These results illustrate how ab initio electronic structure methods, by providing experimentally inaccessible thermodynamics properties and activation energies, are able to sort out possible reactions mechanisms of reactions that have broad relevance in environmental chemistry.
