Scientific Publications 2006
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2006. "n-alkanes on Pt(111) and on C(0001)/Pt(111): Chain Length Dependence of Kinetic Desorption Parameters." Journal of Chemical Physics 125(23):Art. No. 234308. doi:10.1063/1.2400235 Abstract We have measured the desorption of seven small n-alkanes (CNH2N+2, N = 1-4, 6, 8, 10) from the Pt(111) and C(0001) surfaces by temperature programmed desorption. We compare these results to our recent study of the desorption kinetics of these molecules on MgO(100) [J. Chem. Phys. 122, 164708 (2005)]. There we showed an increase in the desorption pre-exponential factor by several orders of magnitude with increasing n-alkane chain length and a linear desorption energy scaling with a small y-intercept value. We suggest that the significant increase in desorption prefactor with chain length is not particular to the MgO(100) surface, but is a general effect for desorption of the small n-alkanes. This argument is supported by statistical mechanical arguments for the increase in the entropy gain of the molecules upon desorption. In this work, we demonstrate that this hypothesis holds true on both a metal surface and a graphite surface. We observe an increase in prefactor by five orders of magnitude over the range of n-alkane chain lengths studied here. On each surface, the desorption energies of the n-alkanes are found to increase linearly with the molecule chain length and have a small y-intercept value. Prior results of other groups have yielded a linear desorption energy scaling with chain length that has unphysically large y-intercept values. We demonstrate that by allowing the prefactor to increase according to our model, a reanalysis of their data resolves this y-intercept problem to some degree.
2006. "Two-Hole Localization Mechanism for Electron Bond Rupture of Surface Atoms by Laser-Induced Valence Excitation of Semiconductors." Physical Review. B, Condensed Matter and Materials Physics 74(3):Art. No. 035337. doi:10.1103/PhysRevB.74.035337 Abstract We examine the mechanism of electronic bond rupture on semiconductor surfaces induced by laser-generated three-dimensional non-equilibrium valence excitation associated with strong carrier diffusion. For such excited systems, the density of sub-surface valence holes that contribute to two-hole localization on the surface is characterized by quasi Fermi level and effective temperature. The rate of two-hole localization, formulated for equilibrated two-dimensional electronic systems by Sumi [Surf. Sci, 248, 382 (1991)], is re-formulated, and a simple analytical expression is yielded for moderate excitation densities. The resulting theoretical model has been successfully applied in the analysis of recent laser-induced atomic desorption experiments on InP and Si surfaces
2006. "Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH." Physical Chemistry Chemical Physics. PCCP 8(40):4678-4684. doi:10.1039/b609743j Abstract Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.
2006. "Structural Studies of Apo Nosl, an Accessory Protein of the Nitrous OxideReductase System: Insights from Structural Homology with MerB, a MercuryResistance Protein." Biochemistry 45(40):12240-12252. doi:10.1021/bi061089 Abstract The formation of the unique catalytic tetranuclear copper cluster (CuZ) of nitrous oxide reductase, N2OR, requires the coexpression of a multiprotein assembly apparatus encoded by the nosDFYL operon. NosL, one of the proteins encoded by this transcript, is a 20 kDa lipoprotein of the periplasm that has been shown to bind copper(I), although its function has yet to be detemined. Cu(I) EXAFS data collected on the holo protein demonstrated that features of the copper binding site are consistent with a role for this protein as a metallochaperone, a class of metal ion transporters involved in metal resistance, homeostasis, and metallocluster biosynthesis. To test this hypothesis and to gain insight into other potential functional roles for this protein in the N2OR system, the three-dimensional solution structure of apo NosL has been solved by solution NMR methods. The structure of apo NosL consists of two relatively independent homologous domains that adopt an unusual topology.
2006. "First Principles Reaction Modeling of the Electrochemical Interface:Consideration and Calculation of a Tunable Surface Potential from Atomic and Electronic Structure." Physical Review. B, Condensed Matter 73(16):165402 1-16. doi:10.1103/PhysRevB.73.165402 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. A method for calculating and subsequently tuning the electrochemical potential of a half cell using periodic plane-wave density functional theory and a homogenous counter-charge is presented and evaluated by comparison to simulations which explicitly model the countercharge by a plane of ions. The method involves the establishment of two reference potentials, one related to the potential of the free electron in vacuo, and the other related to the potential of H₂O species far from the electrode. The surface potential can be specifically adjusted by the explicit introduction of excess or deficit surface charges in the simulation cell and the application of periodic boundary conditions. We demonstrate the absence of field emission from the electrode over the range of realistic electrochemical potentials covered and confirm that the method can explicitly determine reaction energies and adsorption geometries as a function of electrochemical potential. This latter point is most useful as it asserts the viability of this method to model electrochemical and electrocatalytical systems of academic as well as applied interest. We present two case studies. The first examines the changes in the structure of water at the metal interface as a function of potential over Cu(111). At cathodic potential, we observe the repulsion of H₂O from the interface and the rotation of the water dipole toward the interface. The second study follows the initial pathways for the electrocatalytical activation of methanol over Pt(111) and the corresponding potential dependent reaction energetics for these paths. The results demonstrate that changes in the electrochemical potential can significantly alter the reaction energetics as well as the overall reaction selectivity. While the case studies presented herein described equilibrium geometries (i.e., the ideal forms at zero kelvin), the method is also suitable for application to ensembles of thermally activated systems.
2006. "Applications of High Energy Ion Beam Techniques in Environmental Science: Investigation Associated with Glass and Ceramic Waste Forms." Journal of Electron Spectroscopy and Related Phenomena 150(2-3):195-207. doi:10.1016/j.elspec.2005.06.010 Abstract High energy ion beam capabilities including Rutherford backscattering spectrometry (RBS) and nuclear reaction analysis (NRA) have been very effectively used in environmental science to investigate the ion exchange mechanisms in glass waste forms and the effects of irradiation in glass and ceramic waste forms in the past. In this study, RBS and NRA along with SIMNRA simulations were used to monitor the Na depletion and D and 18O uptake in alumina silicate glasses, respectively, after the glass coupons were exposed to aqueous solution. These results show that the formation of a reaction layer and an establishment of a region where diffusion limited ion exchange occur in these glasses during exposure to silica-saturated solutions. Different regions including reaction and diffusion regions were identified on the basis of the depth distributions of these elements. In the case of ceramics, damage accumulation was studied as a function of ion dose at different irradiation temperatures. A sigmoidal dependence of relative disorder on the ion dose was observed. The defect dechanneling factors were calculated for two irradiated regions in SrTiO₃ using the critical angles determined from the angular yield curves. The dependence of defect dechanneling parameter on the incident energy was investigated and it was observed that the generated defects are mostly interstitial atoms and amorphous clusters. Thermal recovery experiments were performed to study the damage recovery processes up to a maximum temperature of 870 K.
2006. "Control of Formation and Cellular Detachment from Shewanella oneidensis MR-1 Biofilms by Cyclic di-GMP." Journal of Bacteriology 188(7):2681-2691. doi:10.1128/JB.188.7.2681-2691.2006 Abstract Stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. Biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. Using Shewanella oneidensis MR-1, an environmentally versatile, Fe(III) and Mn(IV)) mineral -reducing microorganism, we identified mxdABCD as a new set of genes essential for formation of a three-dimensional biofilm. Molecular analysis revealed that mxdA encodes a cyclic bis(3',5')guanylic acid (cyclic di-GMP)-forming enzyme with an unusual GGDEF motif, i.e., NVDEF, which is essential for its function. mxdB encodes a putative membrane-associated glycosyl transferase. Both genes are essential for matrix attachment. The attachment- deficient phenotype of a Delta mxdA mutant was rescued by ectopic expression of VCA0956, encoding another diguanylate cyclase. Interestingly, a rapid cellular detachment from the biofilm occurred upon induction of yhjH, a gene encoding an enzyme that has been shown to have phosphodiesterase activity. In this way, it was possible to bypass the previously identified sudden depletion of molecular oxygen as an environmental trigger to induce biofilm dissolution. We propose a model for c-di-GMP as a key intracellular regulator for controlling biofilm stability by shifting the state of a biofilm cell between attachment and detachment in a concentration -dependent manner.
2006. "Development of a Field Design for In Situ Gaseous Treatment of Sediment Based on Laboratory Column Test Data." Journal of Environmental Engineering (ASCE) 132(12):1626-1632. Abstract A testing methodology is presented that supports the development of a field design for in situ gaseous treatment of sediments with diluted hydrogen sulfide. This approach involves the collection of column breakthrough test results at various flow rates, allowing a relationship to be developed between pore velocity of the carrier gas and velocity of the hydrogen sulfide reaction front that permits sizing to the field scale. A regression fit of a set of laboratory column breakthrough test data collected in this study is utilized to illustrate the development of a field design based on a 2D radial flow analytical model. Information regarding treatment time and hydrogen sulfide consumption characteristics associated with in situ gaseous treatment can then be obtained from this model and used as a basis for estimation of treatment schedule and costs. The regression relationship can also be utilized in numerical models in more complex geometries to support the field design of in situ gaseous treatment operations.
2006. "Nitrogen Release from a NOx Storage and Reduction Catalyst." Catalysis Today 114(1):94-101. doi:10.1016/j.cattod.2006.02.005 Abstract In a NOx storage and reduction (NSR) catalyst the release and reduction of NOx occurs over a very short period. The speed of the NOx release and reduction creates difficulties in analyzing the chemistry using normal analytical techniques, which are typically better suited to slower, steady state studies. We have investigated the time dependence of NO, NO2, NH3, N2O and N2 released by an NSR catalyst using a combination of FTIR and gas chromatographic techniques. Nitrogen was detected with the GC by using He rather than N2 as the background gas. The FTIR was used not only to monitor NO, NO2, NH3 and N2O, but also to establish cycle-to-cycle reproducibility. Under these conditions we used the GC to sample the effluent at multiple times over many lean-rich cycles. To the extent that the chemistry was truly periodic and reproducible, we obtained the time dependence of the release of nitrogen after the lean-to-rich transition. Similar information was obtained for O2, H2 and N2O. Combining the FTIR and GC data we obtained good cycle averaged nitrogen balances, indicating that all the major products were accounted for.
