Scientific Publications 2009
2009. "Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein." Proceedings of the National Academy of Sciences of the United States of America 106(29):11931-11936. doi:10.1073/pnas.0900629106 Abstract The interaction of the HIV-1 transactivator protein Tat with its transactivation response (TAR) RNA is an essential step in viral replication and therefore an attractive target for developing antivirals with new mechanisms of action. Numerous compounds that bind to the 3-nt bulge responsible for binding Tat have been identified in the past, but none of these molecules had sufficient potency to warrant pharmaceutical development. We have discovered conformationally-constrained cyclic peptide mimetics of Tat that are specific nM inhibitors of the Tat-TAR interaction by using a structure-based approach. The lead peptides are nearly as active as the antiviral drug nevirapine against a variety of clinical isolates in human lymphocytes. The NMR structure of a peptide–RNA complex reveals that these molecules interfere with the recruitment to TAR of both Tat and the essential cellular cofactor transcription elongation factor-b (P-TEFb) by binding simultaneously at the RNA bulge and apical loop, forming an unusually deep pocket. This structure illustrates additional principles in RNA recognition: RNA-binding molecules can achieve specificity by interacting simultaneously with multiple secondary structure elements and by inducing the formation of deep binding pockets in their targets. It also provides insight into the P-TEFb binding site and a rational basis for optimizing the promising antiviral activity observed for these cyclic peptides.
2009. "Magnesium Silicate Dissolution Investigated by 29Si MAS, 1H-29Si CP MAS, 25Mg QCPMG, and 1H-25Mg CP QCPMG NMR." Physical Chemistry Chemical Physics. PCCP 11(32):7013-7021. doi:10.1039/b907494e Abstract Olivine has been the subject of frequent investigation in the earth sciences because of its simple structure and rapid dissolution kinetics. Several studies have observed a preferential release of magnesium with respect to silica during weathering under acidic conditions, which has been correlated to the formation of a silicon rich leached layer. While leached layer formation has been inferred through the changing solution chemistry, a thorough spectroscopic investigation of olivine reacted under acidic conditions has not been conducted. In particular, the fate of magnesium in the system is not understood and spectroscopic interrogations through nuclear magnetic resonance can elucidate the changing magnesium coordination and bonding environment. In this study, we combine analysis of the changing solution chemistry with advanced spectroscopic techniques (29Si MAS, 1H-29Si CP MAS, 25Mg QCPMG, and 1H-25Mg 2 CP QCPMG NMR) to probe leached layer formation and possible secondary phase precipitation during the dissolution of forsterite at 150 oC.
2009. "Emission and Chemistry of Organic Carbon in the Gas and Aerosol Phase at a Sub-Urban Site Near Mexico City in March 2006 During the MILAGRO Study." Atmospheric Chemistry and Physics 9(10):3425-3442. Abstract Volatile organic compounds (VOCs) and carbonaceous aerosol were measured at a sub-urban site near Mexico City in March of 2006 during the MILAGRO study (Megacity Initiative: Local and Global Research Objectives). Diurnal variations of hydrocarbons, elemental carbon (EC) and hydrocarbon-like organic aerosol (HOA) were dominated by a high peak in the early morning when local emissions accumulated in a shallow boundary layer, and a minimum in the afternoon when the emissions were diluted in a significantly expanded boundary layer and, in case of the reactive gases, removed by OH. In comparison, diurnal variations of species with secondary sources such as the aldehydes, ketones, oxygenated organic aerosol (OOA) and water-soluble organic carbon (WSOC) stayed relatively high in the afternoon indicating strong photochemical formation. Emission ratios of many hydrocarbon species relative to CO were higher in Mexico City than in the U.S., but we found similar emission ratios for most oxygenated VOCs and organic aerosol. Secondary formation of acetone may be more efficient in Mexico City than in the U.S., due to higher emissions of alkane precursors from the use of liquefied petroleum gas. Secondary formation of organic aerosol was similar between Mexico City and the U.S. Combining the data for all measured gas and aerosol species, we describe the budget of total observed organic carbon (TOOC), and find that the enhancement ratio of TOOC relative to CO is conserved between the early morning and mid afternoon despite large compositional changes. Finally, the influence of biomass burning is investigated using the measurements of acetonitrile, which was found to correlate with levoglucosan in the particle phase. Diurnal variations of acetonitrile indicate a contribution from local burning sources. Scatter plots of acetonitrile versus CO suggest that the contribution of biomass burning to the enhancement of most gas and aerosol species was not dominant and perhaps not dissimilar from observations in the U.S.
2009. " Ti 3p electrons: core or valence?" Chemical Physics Letters 471(1-3):75-79. Abstract The debate over where Ti 3p electrons should be placed (in the core or valence) has been addressed using pseudopotential-based density functional theory. This work has focused on the TiO2 rutile phase using two different Ti pseudopotentials with 4 or 10 valence electrons, depending on how the Ti 3p electrons are treated. The electronic structure of bulk TiO2 are very similar for the two potentials, and both potentials show similar bulk properties (lattice parameters, bulk modulus). Adsorption of several different types of molecules on a (110) surface gives similar results for organic and inorganic molecules, while adsorption of metal atoms leads to noticeable differences in adsorption energies (26% difference between the two pseudopotentials). This discrepancy is attributed to a larger change in the electronic state of Ti upon metal adsorption, compared to organic or inorganic molecule adsorption. The results also show that the two pseudopotential methods describe oxygen vacancies slightly differently, with a difference in vacancy formation energy being 0.32 eV. Ti in other oxidation states was modeled and both pseudopotentials work reasonably well. This study shows that the 3p electrons can often be treated as core states, but care must be taken to verify that this does not affect the simulation accuracy. Funding was provided by the Department of Energy, Office of Basic Energy Sciences. Computational resources were provided by the Molecular Science Computing Facility located at the Environmental Molecular Science Laboratory in Richland, WA and the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory. All work was performed at Pacific Northwest National Laboratory (PNNL). Battelle operates PNNL for the U.S. Department of Energy.
2009. "Adsorption and diffusion of a single Pt atom on gamma-Al2O3 surfaces." Surface Science 603(17):2793-2807. Abstract Motivated to better understand the interactions between Pt and -Al2O3 support, the adsorption and diffusion of a single Pt atom on gamma-Al2O3 was studied using density functional theory. Two different surface models with atoms of various coordination (3 – 5) were used, one derived from a defected spinel structure, and another derived from the dehydration of boehmite (AlOOH). Adsorption energies are similar for the two surfaces, about -2 eV for the most stable sites, and involve Pt binding to surface O atoms. An unusually strong trapping geometry whereby Pt moves into the surface was identified over the boehmite-derived surface. In all cases the surface transfers ~0.2 to 0.3 e- to the Pt atom. The bonding is explained as being a combination of charge transfer between the surface and Pt atom, polarization of the metal atom, and some weak covalent bonding. The similarity of the two surfaces is attributed to the similar local environments of the surface atoms, as corroborated by geometry analysis, density of states, and Bader charge analysis. Calculated activation barriers (0.3-0.5 eV) for the defected spinel surface indicate fast diffusion and a kinetic Monte Carlo model incorporated these barriers to determine exact diffusion rates and behavior. The kinetic Monte Carlo results indicate that at low temperatures (< 500 K) the Pt atom can become trapped at certain surface regions, which could explain why the sintering process is hindered at low temperature. Finally we modeled the adsorption of Pt on hydrated surfaces and found adsorption to be weaker due to steric repulsion and/or decreased electron-donating ability of the surface. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2009. "Intrinsic Hole Migration Rates in TiO2 from Density Functional Theory." Journal of Physical Chemistry C 113(1):346-358. Abstract Migration and formation of hole polarons in bulk rutile and anatase TiO2 were modeled using density functional theory. We previously applied a similar method to model electron polarons and extended the approach to hole polarons. Holes were formed by removal of an O(2p) valence electron, and their quantum mechanical characterization (reorganization energy and electronic coupling) was performed with the DFT+U method, a method that corrects for the self-interaction errors and facilitates charge localization, combined with cluster calculations. We found that activation energies for hole hopping are about twice as large as those for electron hopping, in agreement with experiment. Activation energies typically vary in the range of 0.5 and 0.6 eV. We found that most of the hole hopping processes are adiabatic in rutile but non-adiabatic in anatase. Lattice distortions around hole polarons are also about twice as large as distortions around electron polarons. Our results show that holes are thermodynamically more stable in the rutile phase, while electrons are more stable in the anatase phase. A hole trapping site with hemi-bond structure (hole charge shared between two non-bonded oxygen sites) was identified in anatase as the result of the electronic coupling between the initial and final states being so large that the trapping structure corresponds to a hole delocalized between two oxygen atoms. We also modeled the formation of hole and electron polarons at the (110) surface. The activation energy for hole transfer on the surface is about 0.07 eV larger than in the bulk, while the activation energy for electron transfer on the surface is about 0.11 eV larger than in the bulk. These results form the basis for further development of models to describe polaron transport in TiO2 structures such as surfaces, interfaces, or non-perfect crystals. Funding was provided by the Department of Energy, Office of Basic Energy Sciences. Computational resources were provided by the Molecular Science Computing Facility located at the Environmental Molecular Science Laboratory in Richland, WA. All work was performed at Pacific Northwest National Laboratory (PNNL). Battelle operates PNNL for the U.S. Department of Energy.
2009. "Localized Electronic States from Surface Hydroxyls and Polarons in TiO2(110)." Journal of Physical Chemistry C 113(33):14583-14586 . Abstract Hydroxyls on a TiO2 surface and photo-induced e- polarons give rise to excess charges, the electronic structure of which is critical to the fundamental understanding of their role in the reactivity of surface absorbates and other photochemical processes. In this paper we studied the electronic structure of one excess electron in bare surfaces and surfaces with a single hydroxyl, in particular for the rutile (110) surface. The DFT+U electronic structure is one of a small polaron with its spin density and associated lattice distortion localized around a single site. Calculations indicate that the most stable Ti site in both bare and hydroxylated surfaces resides in the first sub-surface layer under the Ti5c row. The energy differences between several Ti sites are within 0.2 eV indicating that the Boltzmann population of these sites is significant at room temperature and that the excess electron will appear as fractionally occupying several sites. Based on earlier calculations the activation barrier for electron hopping from site to site is small, less than 0.1 eV, The stability ordering of the different Ti sites are very similar for the bare and hydroxylated surface, suggesting that the hydroxyl only weakly perturbs the surface electronic structure. This work was supported by the U.S. Department of Energy's Office of Basic Energy Sciences' Chemical Scienses program. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2009. "Defect Interactions and Ionic Transport in Scandia Stabilized Zirconia." Physical Chemistry Chemical Physics. PCCP 11(26):5506-5511. Abstract Atomistic simulation has been used to study ionic transport in scandia-stabilized zirconia, as well as scandia and yttria-co-doped zirconia, as a function of temperature and composition. The oxygen diffusion coefficient shows a peak at a composition of 6 mole % Sc2O3. Oxygen vacancies prefer to be second nearest neighbours to yttrium ions, but have little preference between first and second neighbour positions with respect to scandium ions. The Sc-O bond length is about 2.17 Å compared to 2.28 Å for the Y-O bond. Oxygen migration between cation tetrahedra is impeded less effectively by Sc-Sc edges than by Y-Y edges. A neutral cluster of two scandium ions with an oxygen vacancy in the common first neighbour position has a binding energy of -0.56 eV. The formation of such clusters may contribute to conductivity degradation of stabilized zirconia at elevated temperature.
2009. "Energetic recoils in UO2 simulated using five different potentials." Journal of Chemical Physics 130(17):Art. No. 174502. doi:10.1063/1.3125967 Abstract This report presents the results of classical molecular dynamics simulations of the diffuse pre-melting transition, melting, and defect production by 1 keV U recoils in UO2 using five different rigid-ion potentials. The experimentally-observed pre-melting transition occurred for all five cases. For all the potentials studied, dynamic defect annealing is highly effective and is accompanied by replacement events on the anion sublattice. The primary damage state after ~15 ps consists of isolated Frenkel pairs and interstitial and vacancy clusters of various sizes. The average displacement energy varies from ~28 to ~83 eV and the number of Frenkel pairs is different by a factor of three depending on the choice of potential. The size and spatial distribution of vacancy and interstitial clusters is drastically different for the potentials studied. The results provide statistics of defect production. They point to a pressing need to determine defect formation, migration and binding energies in UO2 from first principles and to develop reliable potentials based on this data for simulating microstructural evolution in nuclear fuel under operating conditions.
2009. "Radiation damage evolution in ceramics." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 267(18):3017-3021. doi:10.1016/j.nimb.2009.06.020 Abstract A review is presented of recent results on radiation damage production, defect accumulation and dynamic annealing in a number of ceramics, such as silicon carbide, zircon and zirconia. Under energetic particle irradiation, ceramics can undergo amorphization by the accumulation of point defects and defect clusters (silicon carbide) or direct impact amorphization (zircon). Ceramics that resist radiation-induced amorphization have mechanisms to dissipate the primary knock-on atom energy, such as replacement collision sequences that leave the lattice undisturbed and low-energy cation site exchange. The presence of engineered mobile defects, such as structural vacancies in stabilized zirconia, can dynamically anneal radiation damage. Thus, defect engineering is a promising strategy to design radiation tolerance for applications such as nuclear waste disposal.
2009. "Characterization and Application of Superlig 620 Solid Phase Extraction Resin for Automated Process Monitoring of 90Sr." Journal of Radioanalytical and Nuclear Chemistry 282(2):623-628. Abstract Characterization of SuperLig® 620 solid phase extraction resin was performed in order to develop an automated on-line process monitor for 90Sr. The main focus was on strontium separation from barium, with the goal of developing an automated separation process for 90Sr in high-level wastes. High-level waste contains significant 137Cs activity, of which 137mBa is of great concern as an interference to the quantification of strontium. In addition barium, yttrium and plutonium were studied as potential interferences to strontium uptake and detection. A number of complexants were studied in a series of batch Kd experiments, as SuperLig® 620 was not previously known to elute strontium in typical mineral acids. The optimal separation was found using a 2M nitric acid load solution with a strontium elution step of ~0.49M ammonium citrate and a barium elution step of ~1.8M ammonium citrate. 90Sr quantification of Hanford high-level tank waste was performed on a sequential injection analysis microfluidics system coupled to a flow-cell detector. The results of the on-line procedure are compared to standard radiochemical techniques in this paper.
2009. "High-Pressure Effects on the Electronic Structure of Anthracene Single Crystals: Role of Nonhydrostaticity." Journal of Physical Chemistry A 113(8):1489-1496. Abstract Optical spectroscopy methods were used to examine the effect of nonhydrostaticity on the electronic structure of anthracene single crystals compressed statically to 9 GPa. Two pressure-transmitting media, nitrogen (hydrostatic) and water (nonhydrostatic above ~ 5.5 GPa), were utilized. It was found that nonhydrostatic compression generates several new features both in the absorption and fluorescence spectra: (i) formation of new absorption and fluorescence bands, (ii) deviations in pressure shift of fluorescence peaks, (iii) extensive broadening of vibrational peaks, and (iv) irreversible changes in the spectra shape upon pressure unloading. Furthermore, the time-resolved fluorescence decay curves measured at the wavelength corresponding to the new fluorescence band show clear initial increase. These new features are accompanied by inhomogeneous color changes and macroscopic lines on the (001) plane of the crystal. All of the changes are discussed and correlated with microscopic transformations in the crystal. It is demonstrated that nonhydrostatic compression in anthracene crystal introduces inelastic changes in the form of dislocations along  and [1 10 ] directions. These dislocations lead to the development of dimeric structures and, consequently, to various changes in the electronic response of the compressed anthracene crystal.
2009. "Cation dopant distributions in nanostructures of transition-metal doped ZnO:Monte Carlo simulations." Physical Review. B, Condensed Matter and Materials Physics 79(7):Art. No. 075324. Abstract The path from trace doping to solid solution formation involves an intermediate regime in which the doping level is a few to several atomic percent. In this regime, dopant-dopant interactions, which are driven by the spatial arrangement of dopants, are critical factors in determining the resulting properties. Conventional wisdom counts on simple probabilistic methods for predicting dopant distributions. Here, we use Monte Carlo simulations to show that widely used, straightforward statistical models, such as that of Behringer1, are accurate only in the limit of infinitesimally small surface–to-volume ratio. For epitaxial films and nanoparticles, where much of the current interest resides, dopant distributions depend strongly on the surface-to-volume ratio. We present empirical expressions that accurately predict dopant bonding configurations as a function of film or particle size, shape and dopant concentration for doped ZnO, a material of particular interest in semiconductor spintronics.
2009. "Correlated substitution in paramagnetic Mn2+-doped ZnO epitaxial films." Physical Review. B, Condensed Matter and Materials Physics 79(15):Article number:155203. Abstract Epitaxial films of Mn-doped ZnO were deposited by pulsed laser deposition on -Al2O3(0001) utilizing targets created from Mn-doped ZnO nanoparticles. Using x-ray absorption spectroscopy and x-ray magnetic circular dichroism, Mn(II) was found to substitute for Zn in the würtzite ZnO lattice with only a paramagnetic dichroic component from the Mn, and no magnetic component from either the O or Zn. The dichroism reveals that, while substitutional, the Mn distribution in the ZnO lattice is not stochastic. Rather, Mn has a tendency to segregate upon substitution into regions of higher local concentration.
2009. "Imaging Consecutive Steps of O2 Reaction with Hydroxylated TiO2(110): Identification of HO2 and Terminal OH Intermediates." Journal of Physical Chemistry C 113(2):666-671. doi: 10.1021/jp807030n Abstract The hydroperoxyl (HO2) species is believed to be a key intermediate in many heterogeneous photochemical processes, but generally metastable and thus hard to prove. We report here that for the first time, we directly imaged stable, adsorbed HO2 species during O2 reaction with a partially hydroxylated TiO2(110). We also found terminal hydroxyl groups, another critical but never directly observed intermediates. By imaging species and tracking site-specific reactions with high-resolution scanning tunneling microscopy, and determining the energies and configurations with density functional theory calculations, we provide molecular-level insight into the underlying reaction mechanisms. These results are expected to have far reaching implications for various catalytic systems involving the interconversion of O2 and H2O.
2009. "Two Pathways for Water Interaction with Oxygen Adatoms on TiO2(110)." Physical Review Letters 102(9):Art. No. 096102. doi:10.1103/PhysRevLett.102.096102 Abstract Scanning tunneling microscopy and density functional theory studies show that oxygen adatoms (Oa), produced during O2 exposure of reduced TiO2(110) surfaces, alter the water dissociation/recombination chemistry through two distinctive pathways. Depending on whether H2O and Oa are on the same or adjacent Ti4+ rows, Oa facilitates H2O dissociation and proton transfer to form a terminal hydroxyl pair, positioned along- or across-Ti row, respectively. The latter process has not been reported previously, and it starts from “pseudo-dissociated” state of water. In both pathways, the subsequent reverse proton transfer results in H2O recombination and statistical oxygen atom scrambling, as manifested by an apparent along- or across-row motion of Oa’s.