Scientific Publications 2008
2008. "Large-Scale Parallel Calculations with Combined Coupled Cluster and Molecular Mechanics Formalism: Excitation Energies of Zinc-porphyrin in Aqueous Solution." Chemical Physics Letters 458(1-3):205-209. Abstract The vertical excitation energies of low-lying excited states of the zinc-porphyrin molecule in aqueous solution are characterized using a combination of coupled cluster and molecular mechanics descriptions. Coupled cluster description of excited states is based on equation-of-motion approach with singles and doubles (EOMCCSD) as well as its non-iterative extension for triply excited configurations. These results are compared with those obtained with time-dependent density functional theory (TD-DFT), which experiences severe problems with adequate description of low-lying states of chargetransfer character.
2008. "Atomlike, Hollow-Core–Bound Molecular Orbitals of C₆₀." Science 320(5874):359-362. doi:10.1126/science.1155866 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 atomic electron orbitals that underlie molecular bonding originate from the central Coulomb potential of the atomic core. We used scanning tunneling microscopy and density functional theory to explore the relation between the nearly spherical shape and unoccupied electronic structure of buckminsterfullerene (C60) molecules adsorbed on copper surfaces. Besides the known p* antibonding molecular orbitals of the carbon-atom framework, above 3.5 electron volts we found atomlike orbitals bound to the core of the hollow C60 cage. These “superatom” states hybridize like the s and p orbitals of hydrogen and alkali atoms into diatomic molecule-like dimers and free-electron bands of one-dimensional wires and two-dimensional quantum wells in C60 aggregates. We attribute the superatom states to the central potential binding an electron to its screening charge, a property expected for hollow-shell molecules derived from layered materials.
2008. "A Simple Method for the Prevention of Non-Specific Adsorption by Nanocrystals onto Surfaces." Journal of Nanoscience and Nanotechnology 8(11):5781-5786. doi:10.1166/jnn.2008.320 Abstract In this work we introduce an efficient method for averting non-specific adsorption of various nanoparticles to typical oxide-coated surfaces, such as glass, quartz, and sapphire through the attachment of a fluorinated self-assembled monolayer (SAM) that will minimize the interactions between stabilized nanoparticles and these surfaces. This surface treatment will be shown to be effective for a variety of nanoparticles in a range of solvent systems. As a result, loss of usually expensive nanomaterials to different surfaces can be prevented and the monitoring of nanomaterial processes can be readily performed.
2008. "Tuning and Quantifying the Dispersibility of Gold Nanocrystals in Liquid and Supercritical Solvents ." Journal of Physical Chemistry C 112(36):13947-13957. doi:10.1021/jp8038237 Abstract The application of nanomaterials relies on the ability to synthesize, purify, transport, and deposit them in a controllable fashion. The capacity to adjust the density, and thus the solvent strength, of a supercritical or near-critical fluid can be used to tune reaction and separation processes as well as to assemble nanomaterials in a controllable fashion. Herein we demonstrate and quantify density-tunable and reversible size-dependent dispersibility of octanethiol-stabilized gold nanocrystals with a size of 3.7 ± 2.2 nm in near-critical and supercritical solvents as a way to show the significant potential of these fluids for nanomaterials processing. This study introduced discrete variations on the pressure of nanocrystals dispersions in compressed ethane and propane at temperatures of 25, 45, and 65 °C until they reached a saturation region, at which point actual measurements of nanocrystal dispersibility were obtained using UV-Vis absorption spectroscopy. Transmission electron microscopy (TEM) was employed to correlate the dispersibility results with the actual size of the nanoparticles fractions at different densities. The results showed that stable dispersions of nanocrystals could be obtained at pressures as low as 50 atm in both solvents. Compressed ethane in its liquid or supercritical state was found to provide better dynamic tunability while propane provided higher dispersibility of these nanocrystals under the studied pressure-temperature conditions. Two theoretical models, the total interaction theory and Chrastil equation, are briefly presented as a means of interpreting the experimental observations. It was determined that dispersibility depends strongly on the nanocrystal size, solvent density and carbon chain length of the solvent. These results clearly show that selected supercritical fluids can be remarkably effective for the manipulation of nanoparticles.
2008. "Reactivity Descriptors for Direct Methanol Fuel Cell Anode Catalysts." Surface Science 602(21):3424-3431. doi:10.1016/j.susc.2008.08.011 Abstract We have investigated the anode reaction in direct methanol fuel cells using a database of adsorption free energies for 16 intermediates on 12 close-packed transition metal surfaces calculated with periodic, selfconsistent, density functional theory (DFT–GGA). This database, combined with a simple electrokinetic model of the methanol electrooxidation reaction, yields mechanistic insights that are consistent with previous experimental and theoretical studies on Pt, and extends these insights to a broad spectrum of other transition metals. In addition, by using linear scaling relations between the adsorption free energies of various intermediates in the reaction network, we find that the results determined with the full database of adsorption energies can be estimated by knowing only two key descriptors for each metal surface: the free energies of OH and CO on the surface. Two mechanisms for methanol oxidation to CO₂ are investigated: an indirect mechanism that goes through a CO intermediate and a direct mechanism where methanol is oxidized to CO₂ without the formation of a CO intermediate. For the direct mechanism, we find that, because of CO poisoning, only a small current will result on all non-group 11 transition metals; of these metals, Pt is predicted to be the most active. For methanol decomposition via the indirect mechanism, we find that the onset potential is limited either by the ability to activate methanol, by the ability to activate water, or by surface poisoning by CO* or OH*/O*. Among pure metals, there is no obvious candidate for a good anode catalyst, and in order to design a better catalyst, one has to look for bi-functional surfaces such as the well-studied PtRu alloy.
2008. "Characterization of CeO2-Supported Cu-Pd Bimetallic Catalyst for the Oxygen-Assisted Water-Gas Shift Reaction." Journal of Catalysis 260(2):358-370. doi:10.1016/j.jcat.2008.08.018 Abstract This study was focused to investigate the roles of Cu and Pd in CuPd/CeO2 bimetallic catalysts containing 20-30 wt% Cu and 0.5-1 wt% Pd used in the oxygen-assisted water-gas shift (OWGS) reaction employing a combined bulk and surface characterization techniques such as XRD, TPR, CO chemisorption, and in-situ XPS. The catalytic activity for CO conversion and the stability of catalyst during on-stream operation increased by the addition of Cu to Pd/CeO2 or Pd to Cu/CeO2 monometallic catalysts, especially when the OWGS reaction was performed under low temperatures, below 200oC. The bimetallic catalyst after leaching with nitric acid retained about 60% of its original activity. The TPR of monometallic Cu/CeO2 showed reduction of CuO supported on CeO2 in two distinct regions, around 150 and 250oC. The high temperature peak disappeared and reduction occurred in a single step around 150oC upon Pd addition. The Pd dispersion decreased from 38.5% for Pd/CeO2 to below 1% for CuPd/CeO2 bimetallic catalyst. In-situ XPS studies showed a shift in Cu 2p peaks toward lower binding energy (BE) with concommitant shift in the Pd 3d peaks toward higher BE. Addition of Pd decreased the surface Cu concentration while the concentration of Pd remained unaltered. All these observations indicated the formation of Cu-Pd surface alloy. The valence band XP spectra collected below 10 eV corroborated the core level XP spectra and indicated that Cu is mainly involved in the catalytic reaction. The improved catalytic activity and stability of CuPd/CeO2 bimetallic catalyst was attributed to the alloy formation.
2008. "Crystal Structure of the BARD1 Ankyrin Repeat Domain and ItsFunctional Consequences." Journal of Biological Chemistry 283(30):21179-21186. doi:10.1074/jbc.M802333200 Abstract BARD1 is the constitutive nuclear partner to the breast and ovarian cancer specific tumor suppressor BRCA1. Together, they form a heterodimeric complex responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control.
2008. "Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution." Journal of Chemical Theory and Computation 4(12):2141-2149. doi:10.1021/ct8002964 Abstract Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a -chitin nanoparticle, adopt the so-called 2-fold helix with and values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.
2008. "Electron Transfer at the Microbe-Mineral Interface: A Grand Challenge in Biogeochemistry." Geobiology 6(3):245-253. Abstract The interplay between microorganisms and minerals is a complex and dynamic process that has sculpted the geosphere for nearly the entire history of the Earth. The work of Dr. Terry Beveridge and colleagues provided some of the first insights into metal-microbe and mineral-microbe interactions and established a foundation for subsequent detailed investigations of interactions between microorganisms and minerals. Beveridge also envisioned that interdisciplinary approaches and teams would be required to explain how individual microbial cells interact with their immediate environment at nano- or sub-molecular scales and that through such approaches and using emerging technologies that the details of such interactions would be revealed at the molecular level. With this vision as incentive and inspiration, a multidisciplinary, collaborative team-based investigation was initiated to probe the process of electron transfer at the microbe-mineral interface. This grand challenge to this team was to address the hypothesis that multi-heme c-type cytochromes of dissimilatory metal reducing bacteria localized to the cell exterior function as the terminal reductases in electron transfer to Fe(III) and Mn(IV) oxides. This question has been the subject of extensive investigation for years yet the answer has remained elusive. The team involves an integrated group of experimental and computational capabilities at DOE’s Environmental Molecular Sciences Laboratory, a national scientific user facility, as the collaborative focal point. The approach involves a combination of in vitro and in vivo biologic and biogeochemical experiments and computational analyses that, when integrated, provide a conceptual model of the electron transfer process. The resulting conceptual model will be evaluated by integrating and comparing various experimental, i.e., in vitro and in vivo ET kinetics, and theoretical results. Collectively the grand challenge will provide a detailed view of how organisms engage with mineral surfaces to exchange energy and electron density as required for life function.