Scientific Publications 2009
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2009. "Growth and characterization of barium oxide nanoclusters on YSZ(111)." Journal of Physical Chemistry C 113(32):14324-14328. doi:10.1021/jp9020068 Abstract Barium oxide (BaO) was grown on YSZ(111) substrate by oxygen-plasma-assisted molecular beam epitaxy (OPA-MBE). In-situ reflection high-energy electron diffraction, ex-situ x-ray diffraction, atomic force microscopy and x-ray photoelectron spectroscopy have confirmed that the BaO grows as clusters on YSZ(111). During and following the growth under UHV conditions, BaO remains in single phase. When exposed to ambient conditions, the clusters transformed to BaCO3 and/or Ba(OH)2 H2O. However, in a few attempts of BaO growth, XRD results show a fairly single phase cubic BaO with a lattice constant of 0.5418(1) nm. XPS results show that exposing BaO clusters to ambient conditions results in the formation BaCO3 on the surface and partly Ba(OH)2 throughout in the bulk. Based on the observations, it is concluded that the BaO nanoclusters grown on YSZ(111) are highly reactive in ambient conditions. The variation in the reactivity of BaO between different attempts of the growth is attributed to the cluster size.
2009. "Promotion of Hydrogen Release from Ammonia Borane with Mechanically Activated Hexagonal Boron Nitride." Journal of Physical Chemistry C 113(3):1098-1103. doi:10.1021/jp8087385 Abstract We present the activation of hydrogen release from AB by the presence of mechanically activated h–BN. Hydrogen is released at lower temperatures and the dehydrogenation is less exothermic than neat AB. This approach provides all the benefits of a light-weight scaffold without additional foreign contamination that might complicate AB recycling. Several beneficial effects that pertain to the hydrogen desorption properties of the mixtures of AB:nano-BN are notable, such as the decrease of hydrogen desorption temperature, the decrease in NH3 formation as well as the decrease of the exothermicity of hydrogen desorption with increasing the nano-BN concentration. The lower exothermicity of H2 release from AB in the mesoporous silica and the nano-BN may be due physical and chemical interactions between the PAB oligomers and the interface of the silica scaffold or BN support. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2009. "Surface and Interfacial Properties of Nonaqueous-Phase Liquid Mixtures Released to the Subsurface at the Hanford Site ." Vadose Zone Journal 8(2):344-351. Abstract Surface and interfacial tensions that arise at the interface between different phases are key parameters affecting Nonaqueous Phase Liquid (NAPL) movement and redistribution in the vadose zone after spill events. In this study, the impact of major additive components on surface and interfacial tensions for organic mixtures and wastewater was investigated. Organic mixture and wastewater compositions are based upon carbon tetrachloride (CT) mixtures released at the Hanford site, where CT was discharged simultaneously with dibutyl butyl phosphonate (DBBP), tributyl phosphate (TBP), dibutyl phosphate (DBP), and a machining lard oil (LO). A considerable amount of wastewater consisting primarily of nitrates and metal salts was also discharged. The tension values measured in this study revealed that the addition of these additive components caused a significant lowering of the interfacial tension with water or wastewater and the surface tension of the wastewater phase in equilibrium with the organic mixtures, compared to pure CT, but had minimal effect on the surface tension of the NAPL itself. These results lead to large differences in spreading coefficients for several mixtures, where the additives caused both a higher (more spreading) initial spreading coefficient and a lower (less spreading) equilibrium spreading coefficient. This indicates that if these mixtures migrate into uncontaminated areas, they will tend to spread quickly, but form a higher residual NAPL saturation after equilibrium, as compared to pure CT. Over time, CT likely volatilizes more rapidly than other components in the originally disposed mixtures and the lard oil and phosphates would become more concentrated in the remaining NAPL, resulting in a lower interfacial tension for the mixture. Spreading coefficients are expected to increase and perhaps change the equilibrated organic mixtures from nonspreading to spreading in water-wetting porous media. These results show that the behavior of organic chemical mixtures should be accounted for in numerical flow and transport models.
2009. "Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem." Journal of Chemical Theory and Computation 5(3):491-499. doi:10.1021/ct8002892 Abstract Relativistic spin-orbit density functional theory (DFT) methods have been implemented in the molecular Gaussian DFT and pseudopotential plane-wave DFT modules of the NWChem electronic-structure program. The Gaussian basis set implementation is based upon the zeroth-order regular approximation (ZORA) while the planewave implementation uses spin-orbit pseudopotentials that are directly generated from the atomic Dirac-Kohn-Sham wavefunctions or atomic ZORA-Kohn-Sham wavefunctions. Compared to solving the full Dirac equation these methods are computationally efficient, but robust enough for a realistic description of relativistic effects such as spin-orbit splitting, molecular orbital hybridization, and core effects. Both methods have been applied to a variety of small molecules, including I$_{\text{2}}$, IF, HI, Br$_{\text{2}}$, Bi$_{\text{2}}$, AuH, and Au$_{\text{2}}$, using various exchange-correlation functionals. Our results are in good agreement with experiment and previously reported calculations.
2009. "Surface Segregation Energies in Low-Index Open Surfaces of Bimetallic Transition Metal Alloys." Surface Science 603(1):91-96. doi:10.1016/j.susc.2008.10.029 Abstract We present a database of 24 x 24 segregation energies of single transition metal impurities in low-index surfaces of transition metal hosts, calculated using the localized self-consistent Green’s function (LSGF) method, in combination with the atomic sphere approximation including a multipole correction to the electrostatic potential and energy. The surface energies of {100} facets for fcc and bcc transition metals, and the more stable of the two {10Ī0} facets of hcp transition metals are also calculated and compared with available theoretical results. Insights derived should be useful for determining the nature of active sites in a variety of catalytic reactions employing bimetallic catalysts.
2009. "Cleavage of [4Fe--4S]-Type Clusters: Breaking the Symmetry." Journal of Physical Chemistry A 113(19):5710–5717. doi:10.1021/jp900402y Abstract The cleavage of [4Fe--4S]-type clusters is thought to be important in proteins such as Fe--S scaffold proteins and nitrogenase. However, most [4Fe--4S]2⁺ clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe2.5⁺+--Fe2.5⁺ pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe--4S] core into two [2Fe--2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe3⁺--Fe2⁺ pairs. Cleavage first through the weak Fe2⁺--S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe₄S₄L₄]2⁻ (L = SCH3, Cl, H) and heteroligand [Fe₄S₄ (SCH3)2L2]2⁻ (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe--4S] cluster in their biological function might have spin-localized [4Fe--4S] clusters.
2009. "Cleavage of [4Fe-4S]-Type Clusters: Breaking the Symmetry." Journal of Physical Chemistry A 113(19):5710-5717. doi:10.1021/jp900402y Abstract The cleavage of [4Fes4S]-type clusters is thought to be important in proteins such as FesS scaffold proteins and nitrogenase. However, most [4Fes4S]2+ clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe2.5+sFe2.5+ pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fes4S] core into two [2Fes2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe3+sFe2+ pairs. Cleavage first through the weak Fe2+sS bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe4S4L4]2- (L ) SCH3, Cl, H) and heteroligand [Fe4S4(SCH3)2L2]2- (L ) Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fes4S] cluster in their biological function might have spin-localized [4Fes4S] clusters.
2009. "Insight into Environmental Effects on Bonding and Redox Properties of [4Fe-4S] Clusters in Proteins." Journal of the American Chemical Society 131(16):5724-5725. doi:10.1021/ja900406j Abstract The large differences in redox potentials between the HiPIPs and ferredoxins are generally attributed to hydrogen bonds and electrostatic effects from the protein and solvent. Recent ligand K-edge X-ray absorption studies by Solomon and co-workers show that the Fe−S covalencies of [4Fe−4S] clusters in the two proteins differ considerably apparently because of hydrogen bonds from water, indicating electronic effects may be important. However, combined density function theory (DFT) and photoelectron spectroscopy studies by our group and Wang and co-workers indicate that hydrogen bonds tune the potential of [4Fe−4S] clusters by mainly electrostatics. The DFT studies here rationalize both results, namely that the observed change in the Fe−S covalency is due to differences in ligand conformation between the two proteins rather than hydrogen bonds. Moreover, the ligand conformation affects the calculated potentials by 100 mV and, thus, is a heretofore unconsidered means of tuning the potential.
2009. "Probing Ligand Effects on the Redox Energies of [4Fe-4S] Clusters UsingBroken-Symmetry Density Functional Theory." Journal of Physical Chemistry A 113(19):5671–5676. doi:10.1021/jp809446q Abstract A central issue in understanding redox properties of iron-sulfur proteins is determining the factors that tune the reduction potentials of the Fe-S clusters. Recently, Solomon and coworkers have shown that the Fe-S bond covalency of protein analogs measured by %L, the percent ligand character of the Fe 3d orbitals, from ligand K-edge X-ray absorption spectroscopy (XAS) correlates with the electrochemical redox potentials. Also, Wang and coworkers have measured electron detachment energies for iron-sulfur clusters without environmental perturbations by gas-phase photoelectron spectroscopy (PES). Here the correlations of the ligand character with redox energy and %L character are examined in [Fe₄S₄L₄]2⁻ clusters with different ligands by broken symmetry density functional theory (BS-DFT) calculations using the B3LYP functional together with PES and XAS experimental results. These gas-phase studies assess ligand effects independently of environmental perturbations and thus provide essential information for computational studies of iron-sulfur proteins. The B3LYP oxidation energies agree well with PES data, and the %L character obtained from natural bond orbital analysis correlates with XAS values, although it systematically underestimates them because of basis set effects. The results show that stronger electron-donating terminal ligands increase %Lt, the percent ligand character from terminal ligands, but decrease %Sb, the percent ligand character from the bridging sulfurs. Because the oxidized orbital has significant Fe-Lt antibonding character, the oxidation energy correlates well with %Lt. However, because the reduced orbital has varying contributions of both Fe-Lt and Fe-Sb antibonding character, the reduction energy does not correlate with either %Lt or %Sb. Overall, BSDFT calculations together with XAS and PES experiments can unravel the complex underlying factors in the redox energy and chemical bonding of the [4Fe-4S] clusters in iron-sulfur proteins.
