Scientific Publications 2008
2008. "Building Conceptual Models of Field-Scale Uranium Reactive Transport in a Dynamic Vadose Zone-Aquifer-River System." Water Resources Research 44:W12403. doi:10.1029/2007WR006617 Abstract Subsurface simulation is being used to build, test, and couple conceptual process models to better understand controls on a 0.4 km by 1.0 km uranium plume that has persisted above the drinking water standard in the groundwater of the Hanford 300 Area over the last 15 years. At this site, uranium-contaminated sediments in the vadose zone and aquifer are subject to significant variations in water levels and velocities driven by the diurnal, weekly, seasonal, and episodic Columbia River stage dynamics. Groundwater flow reversals typically occur twice a day with significant exchange of river water and groundwater in the near-river aquifer. Mixing of the dilute solution chemistry of the river with the groundwater complicates the uranium sorption behavior as the mobility of U(VI) has been shown experimentally to be a function of pH, carbonate, calcium, and uranium. Furthermore, uranium mass transfer between solid and aqueous phases has been observed to be rate-limited in the context of the high groundwater velocities resulting from the river stage fluctuations and the highly transmissive sediments (hydraulic conductivities ~1500 m/d). One- and two-dimensional vertical cross-sectional simulations of variably-saturated flow and reactive transport, based on laboratory-derived models of distributed rate mass transfer and equilibrium multicomponent surface complexation, are used to assess uranium transport at the dynamic vadose zone – aquifer interface as well as changes to uranium mobility due to incursions of river water into the aquifer.
2008. "Stardust in Antarctic Micrometeorites." Meteoritics and Planetary Science 43(8):1287-1298. Abstract We report the discovery of presolar silicate, oxide (hibonite) and (possibly) SiC grains from four Antarctic micrometeorites. The oxygen isotopic compositions of the eighteen presolar silicate (and one oxide) grains found are consistent with those observed previously in primitive meteorites and interplanetary dust particles, and indicate origins in oxygen-rich red giant or asymptotic giant branch stars. Four grains with anomalous C isotopic compositions were also detected. 12C/13C as well as Si ratios are similar to those of mainstream SiC grains; the N isotopic composition of one grain is also consistent with a mainstream SiC classification. Presolar silicate grains were found in three of the seven AMMs studied, and are heterogeneously distributed within these micrometeorites. Fourteen of the 18 presolar silicate grains and 3 of the 4 C-anomalous grains were found within one AMM, T98G8. The presence of magnesiowüstite, which forms mainly through the decomposition of carbonates, in AMMs without presolar silicates, and its absence in the presolar silicate-bearing micrometeorites, suggests that parent body processes (specifically aqueous alteration) may determine the presence or absence of presolar silicates in Antarctic micrometeorites.
2008. "Negative Electron Binding Energies Observed in a Triply Charged Anion: Photoelectron Spectroscopy of 1-Hydroxy-3, 6, 8-Pyrene-Trisulfonate ." Journal of Chemical Physics 128(9):Art. No. 091102. doi:10.1063/1.2889001 Abstract We report the observation of negative electron binding energies in a triply charged anion, 1-hydroxy-3,6,8-pyrene-trisulfonate (HPTS3–). Low-temperature photoelectron spectra were obtained for HPTS3– at several photon energies, revealing three detachment features below 0 electron binding energy. The HPTS3– trianion was measured to possess a negative electron binding of -0.66 eV. Despite the relatively high excess energy stored in HPTS3–, it was observed to be a long-lived anion due to its high repulsive Coulomb barrier (~3.3 eV), which prevents spontaneous electron emission. Theoretical calculations were carried out, which confirmed the negative electron binding energies observed. The calculations further showed that the highest occupied molecular orbital in HPTS3– is an anti-bonding orbital on the pyrene rings, followed by lone pair electrons in the peripheral –SO3– groups. Negative electron binding energy is a unique feature of multiply-charged anions due to the presence of the repulsive Coulomb barrier. Such metastable species may be good models to study electron-electron and vibronic interactions in complex molecules.
2008. "Photoelectron Spectroscopy of Anions at 118.2 nm: Observation of High Electron Binding Energies in Superhalogens MCI4- (M=Sc, Y, La)." Journal of Chemical Physics 128(20):Art. No. 201102. doi:10.1063/1.2938390 Abstract High energy photon is needed for photoelectron spectroscopy (PES) of anions with high electron binding energies, such as superhalogens and O-rich metal oxide clusters. The highest energy photon used for anion PES in the laboratory has been 157 nm (7.866 eV) from F2 eximer lasers. Here, we report an anion PES experiment using coherent vacuum ultraviolet radiation at 118.2 nm (10.488 eV) by tripling the third harmonic output (355 nm) of a Nd:YAG laser in a Xe/Ar cell. Our study focuses on a set of superhalogen species, MCl4 − (M=Sc, Y, La), which were expected to possess very high electron binding energies. While the 157 nm photon can only access the ground state detachment features for these species, more transitions to the excited states at binding energies higher than 8 eV are observed at 118.2 nm. The adiabatic detachment energies are shown to be, 6.84, 7.02, and 7.03 eV for ScCl4 −, YCl4 −, and LaCl4 − eV, respectively, whereas their corresponding vertical detachment energies are measured to be 7.14, 7.31, and 7.38 eV.
2008. "Isotope effects in methanol synthesis and the reactivity of copper formates on a Cu/SiO2 catalyst." Catalysis Letters 125(3-4):201-208. doi:10.1007/s10562-008-9592-4 Abstract Here we investigate isotope effects on the catalytic methanol synthesis reaction and the reactivity of copper-bound formate species in CO2-H2 atmospheres on Cu/SiO2 catalysts by simultaneous IR and MS measurements, both steady-state and transient. Studies of isotopic variants (H/D, 12C/13C) reveal that bidentate formate dominates the copper surface at steady state. The steady-state formate coverages of HCOO (in 6 bar 3:1 H2:CO2) and DCOO (in D2:CO2) are similar and the steady-state formate coverages in both systems decrease by ~80% from 350 K to 550 K. Over the temperature range 413K – 553K, the steady-state methanol synthesis rate shows a weak H/D isotope effect (1.05 ± 0.05) with somewhat higher activation energies in H2:CO2 (79 kJ/mole) than D2:CO2 (71 kJ/mole) over the range 473K-553K. The reverse water gas shift (RWGS) rates are higher than methanol synthesis and also shows a weak positive H/D isotope effect with higher activation energy for H2/CO2 than D2/CO2 (108 vs. and 102 kJ/mole). The reactivity of the resulting formate species in 6 bar H2, 6 bar D2 and 6 bar Ar is strongly dominated by decomposition back to CO2 and H2. H2 and D2 exposure compared to Ar do not enhance the formate decomposition rate. The decomposition profiles on the supported catalyst deviate from first order decay, indicating distributed surface reactivity. The average decomposition rates are similar to values previously reported on single crystals. The average activation energies for formate decomposition are 90 ± 17 kJ/mole for HCOO and 119 ± 11 kJ/mole for DCOO. By contrast to the catalytic reaction rates, the formate decomposition rate shows a strong H/D kinetic isotope effect (H/D ~ 8 at 413K), similar to previously observed values on Cu(110).
2008. "Experimental and Theoretical Studies of the Structures and Interactions of Vancomycin Antibiotics with Cell Wall Analogues." Journal of the American Chemical Society 130(39):13013-13022. doi:10.1021/ja802643g Abstract Surface-induced dissociation (SID) of the singly protonated complex of vancomycin antibiotic with cell wall peptide analogue (Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala) was studied using a 6 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) specially configured for SID experiments. The binding energy between the vancomycin and the peptide was obtained from the RRKM modeling of the time- and energy resolved fragmentation efficiency curves (TFECs) of the precursor ion and its fragments. Electronic structure calculations of the geometries, proton affinities and binding energies were performed for several model systems including vancomycin (V), vancomycin aglycon (VA), Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala, and non-covalent complexes of VA with N-acetyl-D-Ala-D-Ala and Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala at the B3LYP/6-31G(d) level of theory. Comparison between the experimental and computational results suggests that the most probable structure of the complex observed in our experiments corresponds to the neutral peptide bound to the vancomycin protonated at the secondary amino group of the N-methyl-leucine residue. The experimental binding energy of 30.9 ± 1.8 kcal/mol is in good agreement with the binding energy of 29.3 ± 2.5 kcal/mol calculated for the model system representing the preferred structure of the complex.
2008. "The Effect of the Secondary Structure on Dissociation of Peptide Radical Cations: Fragmentation of Angiotensin III and Its Analogues." Journal of Physical Chemistry B 112(39):12468-12478. doi:10.1021/jp805226x Abstract Fragmentation of protonated RVYIHPF and RVYIHPF-OMe and the corresponding radical cations was studied using time- and collision energy-resolved surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. Both the energetics and mechanisms of dissociation of even-electron and odd-electron angiotensin III ions are quite different. Protonated molecules are much more stable towards fragmentation than the corresponding radical cations. RRKM modeling of the experimental data suggests that this stability is largely attributed to differences in threshold energies for dissociation while activation entropies are very similar. Detailed analysis of the experimental data obtained for radical cations demonstrated the presence of two distinct structures separated by a high free-energy barrier. The two families of structures were ascribed to the canonical and zwitterionic forms of the radical cations produced in our experiments.
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. "Detection of Cd, Pb, and Cu in non-pretreated natural watersand urine with thiol functionalized mesoporous silica andNafion composite electrodes." Analytica Chimica Acta (620):55-63. doi:10.1016/j.aca.2008.05.029 Abstract Electrochemical sensors have great potential for environmental monitoring of toxic metal ions in waters due to their portability, field-deployability and excellent detection limits. However, electrochemical sensors employing mercury-free approaches are normally suffered from metal binding competition and fouling by organic substances and surfactants in natural waters, thus tedious sample pretreatments such as wet ashing are needed. In this work, we have developed mercury-free sensors by coating a composite of thiol self-assembled monolayers on mesoporous supports (SH-SAMMS) and Nafion on glassy carbon electrodes. With a combined benefit of SH-SAMMS as outstanding metal preconcentrator and Nafion as antifouling binder, the sensors could detect 2.5 ppb of Cd and 0.5 ppb of Pb in river water, Hanford groundwater, and seawater after 3 and 6 minutes of preconcentration and without sample pretreatment. They could also detect 2.5 ppb of Cd, Pb, and Cu simultaneously after 5 minutes of preconcentration. The electrodes have long life time and excellent single and inter-electrode reproducibility (%RSD of 5 after 8 consecutive measurements). Unlike SAMMS-carbon paste electrodes, the SAMMS-Nafion electrodes were not fouled in samples containing albumin. Successful detection of Cd in human urine was also demonstrated. Other factors including pH effect, diffusion resistance, and Tl interference on the metal detection at SAMMS-Nafion electrodes were studied. With the ability to reliably detect low metal concentration ranges without sample pretreatment and fouling, the SAMMS-Nafion composite sensors have the potential to become the next generation metal analyzers for environmental and bio- monitoring of toxic metals.
2008. "Direct detection of Pb in urine and Cd, Pb, Cu, and Ag in natural waters using electrochemical sensors immobilized with DMSA functionalized magnetic nanoparticles." The Analyst 133(3):348-355. doi:10.1039/b711199a Abstract Urine is universally recognized as one of the best non-invasive matrices for biomonitoring exposure to a broad range of xenobiotics including toxic metals. For direct, simple, and field-deployable monitoring of urinary Pb, electrochemical sensors employing superparamagnetic iron oxide (Fe3O4) nanoparticles with a surface functionalization of dimercaptosuccinic acid (DMSA) has been developed. The metal detection involves rapid collection of dispersed metal-bound nanoparticles from a sample solution at a magnetic or electromagnetic electrode, followed by the stripping voltammetry of the metal in acidic medium. The sensors were evaluated as a function of solution pH, the binding affinity of Pb to DMSA-Fe3O4, the ratio of nanoparticles per sample volume, preconcentration time, and Pb concentrations. The effect of binding competitions between the DMSA-Fe3O4 and urine constituents for Pb on the sensor responses was studied. After 90s of preconcentration in samples containing 25 vol.% of rat urine and 0.1 g/L of DMSA-Fe3O4, the sensor could detect background level of Pb (< 1 ppb) and yielded linear responses from 0 to 50 ppb of Pb, excellent reproducibility (%R.S.D of 5.3 for seven measurements of 30 ppb Pb), and Pb concentrations comparable to those measured by ICP-MS. The sensor could also simultaneously detect background levels (< 1 ppb) of Cd, Pb, Cu, and Ag in river and seawater.
2008. "Impact of nonaqueous phase liquid (NAPL) source zone architecture on mass removal mechanisms in strongly layered heterogeneous porous media during soil vapor extraction ." Journal of Contaminant Hydrology 100(1-2):58-71. doi:10.1016/j.jconhyd.2008.05.006 Abstract An existing multiphase flow simulator was modified in order to determine the effects of four mechanisms on NAPL mass removal in a strongly layered heterogeneous vadose zone during soil vapor extraction (SVE): a) NAPL flow, b) diffusion and dispersion from low permeability zones, c) slow desorption from sediment grains, and d) rate-limited dissolution of trapped NAPL. The impact of water and NAPL saturation distribution, NAPL type (i.e., free, residual, or trapped) distribution, and spatial heterogeneity of the permeability field on these mechanisms were evaluated. Two different initial source zone architectures (one with and one without trapped NAPL) were considered and these architectures were used to evaluate seven different SVE scenarios. For all runs, slow diffusion from low permeability zones that gas flow bypassed was a dominant factor for diminished SVE effectiveness at later times. This effect was more significant at high water saturation due to the decrease of gas-phase relative permeability. Transverse dispersion contributed to fast NAPL mass removal from the low permeability layer in both source zone architectures, but longitudinal dispersion did not affect overall mass removal time. Both slow desorption from sediment grains and rate-limited mass transfer from trapped NAPL only marginally affected removal times. However, mass transfer from trapped NAPL did affect mass removal at late time, as well as the NAPL distribution. NAPL flow from low to high permeability zones contributed to faster mass removal from the low permeability layer, and this effect increased when water infiltration was eliminated. These simulations indicate that if trapped NAPL exists in heterogeneous porous media, mass transfer can be improved by delivering gas directly to zones with trapped NAPL and by lowering the water content, which increases the gas relative permeability and changes trapped NAPL to free NAPL.
2008. "The Alpha Project: a model system for systems biology research." IET Systems Biology 2(5):222-233. doi:10.1049/iet-syb:20080127 Abstract One goal of systems biology is to understand how genome-encoded parts interact to produce quantitative phenotypes. The Alpha Project is a medium-scale, interdisciplinary systems biology effort that aims to achieve this goal by understanding fundamental quantitative behaviours of a prototypic signal transduction pathway, the yeast pheromone response system from Saccharomyces cerevisiae. The Alpha Project distinguishes itself from many other systems biology projects by studying a tightly bounded and well-characterised system that is easily modified by genetic means, and by focusing on deep understanding of a discrete number of important and accessible quantitative behaviours. During the project, the authors have developed tools to measure the appropriate data and develop models at appropriate levels of detail to study a number of these quantitative behaviours. The authors have also developed transportable experimental tools and conceptual frameworks for understanding other signalling systems. In particular, the authors have begun to interpret system behaviours and their underlying molecular mechanisms through the lens of information transmission, a principal function of signalling systems. The Alpha Project demonstrates that interdisciplinary studies that identify key quantitative behaviours and measure important quantities, in the context of well-articulated abstractions of system function and appropriate analytical frameworks, can lead to deeper biological understanding. The authors’ experience may provide a productive template for systems biology investigations of other cellular systems.
2008. "Nitrate Ion Photochemistry at Interfaces: A New Mechanism for Oxidation of alpha-Pinene." Physical Chemistry Chemical Physics. PCCP 10(21):3063-3071. doi:10.1039/b719495a Abstract The photooxidation of 0.6 - 0.9 ppm α-pinene in the presence of a deliquesced thin film of NaNO3, and for comparison increasing concentrations of NO2, was studied in a 100 L Teflon® chamber at relative humidities from 70 − 88% and temperatures from 296 − 304 K. The loss of α-pinene and the formation of gaseous products were followed with time using proton transfer mass spectrometry. The yields of gas phase products were smaller in the NaNO3 experiments than in NO2 experiments. In addition, pinonic acid, pinic acid, trans-sobrerol and other unidentified products were detected in the extracts of the wall washings only for the NaNO3 photolysis. These data indicate enhanced loss of α-pinene at the NaNO3 thin film during photolysis. Supporting the experimental results are molecular dynamics simulations which predict that α-pinene has an affinity for the surface of the deliquesced nitrate thin film, enhancing the opportunity for oxidation of the impinging organic gas during the nitrate photolysis. This new mechanism of oxidation of organics may be partially responsible for the correlation between nitrate and the organic component of particles observed in many field studies, and may also contribute to the missing source of SOA needed to reconcile model predictions and field measurements. In addition, photolysis of nitrate on surfaces in the boundary layer may lead to oxidation of co-adsorbed organics.
2008. "Photooxidation of Alpha-Pinene at High Relative Humidity in the Presence of Increasing Concentrations of NOx." Atmospheric Environment 42(20):5044-5060. doi:10.1016/j.atmosenv.2008.02.026 Abstract The photooxidation of ~1 ppm alpha-pinene in the presence of increasing concentrations of NO2 was studied in a Teflon chamber at relative humidities from 70 - 88% and temperatures from 296 - 304 K. The loss of alpha-pinene and formation of gas phase products were followed using proton transfer reaction mass spectrometry (PTR-MS). Gas phase reaction products measured by PTR-MS and their yields include formaldehyde (5 + 1%), formic acid (2.5 + 1.4%), methanol (0.6 + 0.3%), acetaldehyde (3.9 + 1.7%), acetic acid (10 + 2%), acetone (11.5 + 3.1%), pinonaldehyde (22 + 6%), and pinene oxide (0.9 + 0.1%). There was evidence of organic nitrates in the gas phase and small peaks were tentatively assigned to norpinonaldehyde, 4-oxopinonaldehyde, propanedial, 2,3-dioxobutanal and 3,5,6-trioxoheptanal or 3-hydroxymethyl-2,2-dimethylcyclobutylethanone. The formation and growth of new particles were followed using a scanning mobility particle sizer (SMPS), and their chemical composition was probed using single particle mass spectrometry (SPLAT II). SPLAT II analysis also provided measurements of the vacuum aerodynamic diameters of the newly formed secondary organic aerosol (SOA) particles and, in combination with the electrical mobility diameter, a particle density of 1.21 + 0.02 g cm-3 was calculated, 20% larger than often assumed in calculating SOA yields. SPLAT II showed that the suspended SOA consisted of a complex mixture of organic nitrates and organics, possibly including pinonic acid, pinic acid and trans-sobrerol. Three-wavelength light scattering measurements made using an integrating nephelometer were consistent with particles having a refractive index characteristic of organic compounds, but the data could not be well matched at all three wavelengths with a single refractive index. The effect of addition of cyclohexane or NO on particle formation showed that ozonolysis was the major mechanism of SOA formation in this system. However, unlike simple ozonolysis, organic nitrates are formed in both the gas and particle phases. Identifying and measuring specific organic nitrates in both the gas and particle phases in air may help to elucidate why SOA formation has been reported in field studies to be associated with polluted urban areas, yet the carbon in these particles is largely contemporary, i.e., non-fossil fuel carbon.
2008. "Conductivity of Oriented Samaria-Doped Ceria Thin Films Grown by Oxygen-plasma-assisted Molecular Beam Epitaxy." Electrochemical and Solid-State Letters 11(5):B76-B78. doi:10.1149/1.2890122 Abstract We have used oxygen-plasma-assisted molecular beam epitaxy (OPA-MBE) to grow highly oriented Ce1-xSmxO2-δ films on single crystal c-Al2O3. The samarium concentration, x, was varied in the range 1-33 atom%. It was observed that dominant (111) orientation in Ce1-xSmxO2-δ films can be maintained up to about 10 samarium atom% concentration. Films higher than 10 atom% Sm concentration started to show polycrystalline features. The highest conductivity of 0.04 S.cm-1, at 600 0C, was observed for films with ~ 5 atom% Sm concentration. A loss of orientation, triggering an enhanced grain boundary scattering, appears to be responsible for the decrease in conductivity at higher dopant concentrations.