Scientific Publications 2007
2007. "Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide." Applied Physics Letters 90(22):Art. No. 221915. doi:10.1063/1.2743751 Abstract The thermal stability of an antisite pair in 3C-SiC is studied using ab initio molecular dynamics within the framework of density functional theory. The lifetime of the antisite pair configuration is calculated for temperatures between 1800 and 2250 K, and the effective activation energy for antisite pair recombination is determined to be 2.52 eV. The recombination energy path and static energy barrier are also calculated using the nudged elastic band method, along with the dimer method to accurately locate the transition states. The consistency of the results suggests that the antisite pair cannot be correlated with the DI photoluminescence center, as proposed by previously theoretical interpretations. An extended exchange mechanism is found for the antisite pair recombination, and this may be a dominant mechanism for antisite pair recombination and diffusion of impurities in compound semiconductors.
2007. "Atomistic Simulations of Epitaxial Recrystallization in 4H-SiC along the  Direction." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 255(1):136-140. doi:10.1016/j.nimb.2006.11.016 Abstract Molecular dynamics (MD) methods have been employed to study the epitaxail recrystallization and amorphous-to-crystalline (a-c) transition in 4H-SiC, with simulation times of up to a few hundred ns and at temperatures of 1500 and 2000 K. Three nano-sized amorphous layers with the normal of a-c interfaces along the [-12-10 ], [-1010] and  directions, respectively, were created within a crystalline cell to investigate the anisotropies of recrystallization processes. The recovery of bond defects at the interfaces is an important process driving the initial epitaxial recrystallization of the amorphous layers. The amorphous layers with the a-c interface normal along the [-12-10] direction can be completely recrystallized at the temperatures of 1500 and 2000 K, and along the  direction at 2000 K. However, the recrystallized region is defected with dislocations and stacking faults. The temperatures required for complete recrystallization are in good agreement with those observed in experiments. On the other hand, the recrystallization processes for the a-c interface normal along [-1010] direction are hindered by the nucleation of polycrystalline phases. These secondary ordered phases have been identified as 4H- and 3C-SiC with different crystallographic orientations to the original 4H-SiC. The bond mismatches at the interfaces between different microcrystals result in the formation of a number of stacking faults. The temperature is an important parameter to control the nucleation of the secondary ordered phase, whereas the size of amorphous region has a significant effect on their growth. These results are in good agreement with the previous experimental observations.
2007. "Theoretical Electron Density Distributions for Fe- and Cu-Sulfide Earth Materials: A Connection between Bond Length, Bond Critical Point Properties, Local Energy Densities, and Bonded Interactions." Journal of Physical Chemistry B 111(8):1923-1931. doi:10.1021/jp065086i Abstract Bond critical point and local energy density properties together with net atomic charges were calculated for theoretical electron density distributions, F(r), generated for a variety of Fe and Cu metal-sulfide materials with high- and low-spin Fe atoms in octahedral coordination and high-spin Fe atoms in tetrahedral coordination. The electron density, F(rc), the Laplacian, 32F(rc), the local kinetic energy, G(rc), and the oxidation state of Fe increase as the local potential energy density, V(rc), the Fe-S bond lengths, and the coordination numbers of the Fe atoms decrease. The properties of the bonded interactions for the octahedrally coordinated low-spin Fe atoms for pyrite and marcasite are distinct from those for high-spin Fe atoms for troilite, smythite, and greigite. The Fe-S bond lengths are shorter and the values of F(rc) and 32F(rc) are larger for pyrite and marcasite, indicating that the accumulation and local concentration of F(r) in the internuclear region are greater than those involving the longer, high-spin Fe-S bonded interactions. The net atomic charges and the bonded radii calculated for the Fe and S atoms in pyrite and marcasite are also smaller than those for sulfides with high-spin octahedrally coordinated Fe atoms. Collectively, the Fe-S interactions are indicated to be intermediate in character with the low-spin Fe-S interactions having greater shared character than the highspin interactions. The bond lengths observed for chalcopyrite together with the calculated bond critical point properties are consistent with the formula Cu+Fe3+S2. The bond length is shorter and the F(rc) value is larger for the FeS4 tetrahedron displayed by metastable greigite than those displayed by chalcopyrite and cubanite, consistent with a proposal that the Fe atom in greigite is tetravalent. S-S bond paths exist between each of the surface S atoms of adjacent slabs of FeS6 octahedra comprising the layer sulfide smythite, suggesting that the neutral Fe3S4 slabs are linked together and stabilized by the pathways of electron density comprising S-S bonded interactions. Such interactions not only exist between the S atoms for adjacent S8 rings in native sulfur, but their bond critical point properties are similar to those displayed by the metal sulfides.
2007. "Acid/base equilibria in clusters and their role in proton exchange membranes: Computational insight." Physical Chemistry Chemical Physics. PCCP 9(43):5752-5760. doi:10.1039/b709752b Abstract We describe molecular orbital theory and ab initio molecular dynamics studies of acid/base equilibria of clusters AH:(H2O)n ⇔ A-:H+(H2O)n in low hydration regime (n=1-4), where AH is a model of perfluorinated sulfonic acids, RSO3H, encountered in polymeric electrolyte membranes of fuel cells. Free energy calculations on the neutral and ion pair structures for n=3 indicate that the two configurations are close in energy and are accessible in the fluctuation dynamics of proton transport. For n=1,2 the only relevant configuration is the neutral form. This was verified through ab initio metadynamics simulations. These findings suggest that bases are directly involved in the proton transport at low hydration levels. In addition, the gas phase proton affinity of the model sulfonic acid RSO3H was found to be comparable to the proton affinity of water. Thus, protonated acids can also play a role in proton transport under low hydration conditions and under high concentration of protons. This work was supported by the Division of Chemical Science, Office of Basic Energy Sciences, US Department of Energy (DOE under Contract DE-AC05-76RL)1830. Computations were performed on computers of the Molecular Interactions and Transformations (MI&T) group and MSCF facility of EMSL, sponsored by US DOE and OBER located at PNNL. This work was benefited from resource of the National Energy Research Scientific Computing Centre, supported by the Office of Science of the US DOE, under Contract No. DE-AC03-76SF00098.
2007. "Adsorption of iso-/n-butane on an Anatase Thin Film: A Molecular Beam Scattering and TDS Study." Catalysis Letters 116(1-2):9-14. doi:10.1007/s10562-007-9121-x Abstract Binding energies and adsorption probabilities have been determined for n/iso-butane adsorption on an anatase thin film grown on SrTiO3(001) by means of thermal desorption spectroscopy (TDS) and molecular beam scattering. The sample has been characterized by x-ray diffraction (XRD) and Auger electrons spectroscopy (AES).
2007. "CO oxidation on ruthenium: The nature of the active catalytic surface." Surface Science 601:L124 - L126. doi:10.1016/j.susc.2007.08.003 Abstract CO oxidation over ruthenium has been extensively studied over the last several decades from ultrahigh (UHV) vacuum to ambient pressures. While Ru is an inferior catalyst for this reaction compared to Pt, Rh, and Pd under ultrahigh vacuum conditions, it is comparable to these metals at or near atmospheric reaction conditions. Recent studies have suggested that the transformation from an inactive to an active catalyst can be attributed to a structural transformation of Ru to RuO2 and that an epitaxial film of RuO2(110) on Ru(0001) is the active catalytic surface under stoichiometric CO/O2 reaction condition at or approaching one atmosphere. Furthermore recent experimental and theoretical studies have suggested that under such elevated reactant pressures, a strongly bound CO (120 kJ/mol) on RuO2 reacts with O atoms from the oxide surface to form the CO2 product. However, that the active surface on Ru(0001) is a multilayer RuO2(110) oxide and that the CO reactant is strongly bound is inconsistent with early elevated pressure studies of CO oxidation on Ru showing: (i) the formation of a single surface oxide layer under elevated pressure reactant conditions; (ii) a weakly bound CO (<40 kJ/mol) is the reactant under elevated pressure reactant conditions; and (iii) the formation of RuO2 deactivates Ru as a catalyst. This article reviews CO oxidation over Ru for the last several decades emphasizing those aspects that rationalize the connection between the vacuum and high pressure results.
2007. "Reply to comment on "CO oxidation on ruthenium: the nature of the active catalytic surface" by H. Over, M. Muhler, and A.P. Seitsone." Surface Science 601(23):5663–5665. doi:10.1016/j.susc.2007.09.042 Abstract We first state that the premise of our Letter  was to state emphatically that the early studies of Peden and Goodman (PG)  can be entirely explained by and are only consistent with the active surface being a monolayer oxygen-covered Ru(0001) surface. Contrary to the authors’ contention in their Comment, the reaction conditions addressed in the experiments of PG  spanned the temperature range 375 to 600 K, a pressure range of O2 and CO pressures from 0.5 to 500 Torr, and CO/O2 ratios from 60 to .03. The authors state in their introduction that “the oxidation of Ru metal takes place to RuO2 only for temperatures higher than 500 K. Here we do not wish to address the oxidation of Ru in all morphologies, but rather the specific reaction conditions required for RuO2 to form on Ru(0001), the catalyst used in the experiments of PG and the subject of our previous Letter . Indeed, as pointed out in our Letter , Over and coworkers in a very definitive piece of work  showed that the critical conditions required for the formation of RuO2 on Ru(0001) were far outside those used in the experiments of PG with respect to temperature and oxygen chemical potential. Based on our earlier studies  and the work of Over and coworkers  we concluded in our Letter that RuO2 could not have formed to any appreciable extent in the PG experiments.
2007. "Mixed-Valent Fe Films ('Schwimmeisen') on the Surface of Reduced Ephemeral Pools." Clays and Clay Minerals 55(6):635-643. doi:10.1346/CCMN.2007.0550610 Abstract Floating, mixed-valent Fe films have been observed worldwide in wetlands, ferrous iron rich seeps, and in seasonally reduced soils, but are usually misidentified as oil or biofilms. Little characterization or explanation to their formation has taken place. Along the Oregon coast such films were found on ephemeral pools where Fe(II) rich groundwater (~ 100 μM Fe) discharged at the base of Pleistocene sand dunes. Fe(II) oxidized to Fe(III) at the air-water interface to form ~ 100 to 300nm thick films. Analyses indicated that the films contained both Fe(III) and Fe(II) in a ratio of 3:1. Si was the other main cation, OH was the main anion and some C was identified as well. The film morphology was flat, under optical and electron microscopy with some attached floccules having a stringlike morphology. Energy filtered electron diffraction patterns (EFED) showed three diffraction rings at 4.5, 2.6, and 1.4 Å in some places and 2 rings (2.6 and 1.4 Å) in others. Upon further oxidation the films became 2-line ferrihydrite. We are proposing the name „Schwimmeisen“ for the floating, mixed-valent Fe film.
2007. "On the Role of Subsurface Oxygen and Ethylenedioxy in Ethylene Epoxidation on Silver." Journal of Physical Chemistry C 111(22):7992-7999. doi:10.1021/jp070490i 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 thermochemical stability of various three-component phases containing oxygen, ethylene, and Ag(111) was determined as a function of oxygen and ethylene chemical potential using periodic, self-consistent density functional theory calculations. Ethylenedioxy is stable over a wide range of conditions, although its formation may be kinetically hindered in some cases. Ethylene and ethylene-containing oxametallacycles are also found to be stable over a reasonably large range of chemical potentials, particularly if ethylenedioxy formation is neglected. Furthermore, subsurface oxygen (Osb) is seen to be present in the three-component systems at a variety of conditions; minimum energy path calculations performed at a coverage of 1/2 ML Osb suggest that this species may actually increase the reaction barrier for ring closure leading to ethylene oxide elimination from Ag(111).
2007. "Mid-Infrared Vibrational Spectra of Discrete Acetone-Ligated Cerium Hydroxide Cations." Physical Chemistry Chemical Physics. PCCP 9(5):596-606. Abstract Cerium (III) hydroxy reactive sites are responsible for several important heterogeneous catalysis processes, and understanding the reaction chemistry of substrate molecules like CO, H2O, and CH3OH as they occur in heterogeneous media is a challenging task. We report here the first infrared spectra of model gas-phase cerium complexes and use the results as a benchmark to assist evaluation of the accuracy of ab initio calculations. Complexes containing [CeOH]2+ ligated by three- and four-acetone molecules were generated by electrospray ionization and characterized using wavelength-selective infrared multiple photon dissociation (IRMPD). The C=O stretching frequency for the [CeOH(acetone)4]2+ species appeared at 1650 cm-1 and was red-shifted by 90 cm-1 compared to unligated acetone. The magnitude of this shift for the carbonyl frequency was even greater for the [CeOH(acetone)3]2+ complex: the IRMPD peak consisted of two dissociation channels, an initial elimination of acetone at 1635 cm-1, and elimination of acetone accompanied by a serial charge separation producing [CeO(acetone)]+ at 1599 cm-1, with the overall frequency centered at 1616 cm-1. The increasing red shift observed as the number of acetone ligands decreases from four to three is consistent with transfer of more electron density per ligand in the less coordinated complexes. The lower frequency measured for the elimination/charge separation process is likely due to anharmonicity resulting from population of higher vibrational states. The C-C stretching frequency in the complexes is also influenced by coordination to the metal: it is blue-shifted compared to bare acetone, indicating a slight strengthening of the C-C bond in the complex, with the intensity of the absorption decreasing with decreasing ligation. Density functional theory (DFT) calculations using three different functionals (LDA, B3LYP, and PBE0) are used to predict the infrared spectra of the complexes. Calculated frequencies for the carbonyl stretch are within 40 cm-1 of the IRMPD of the three-acetone complex measured using the single acetone loss, and within 60 cm-1 of the measurement for the four-acetone complexes. The B3LYP and LDA functionals provided the best agreement with the measured spectra. The C-C stretching frequencies calculated using B3LYP are higher in energy than the measured values by ~ 30 cm-1, and reproduce the observed trend which shows that the C-C stretching frequency decreases with increasing ligation. Agreement between C-C frequency and calculation was not as good using the LDA functional, but still within 70 cm-1. The results provide an evaluation of changes in the acceptor properties of the metal center as ligands are added, and of the utility of DFT for modeling f-block coordination complexes.
2007. "Different Protonation Equilibria of4-Methylimidazole and Acetic Acid." Chemphyschem 8(17):2445-2451. doi:10.1002/cphc.200700442 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. Dynamic protonation equilibria in water of one 4-methylimidazole molecule as well as for pairs and groups consisting of 4- methylimidazole, acetic acid and bridging water molecules are studied using Q-HOP molecular dynamics simulation. We find a qualitatively different protonation behavior of 4-methylimidazole compared to that of acetic acid. On one hand, deprotonated, neutral 4-methylimidazole cannot as easily attract a freely diffusing extra proton from solution. Once the proton is bound, however, it remains tightly bound on a time scale of tens of nanoseconds. In a linear chain composed of acetic acid, a separating water molecule and 4-methylimidazole, an excess proton is equally shared between 4-methylimidazole and water. When a water molecule is linearly placed between two acetic acid molecules, the excess proton is always found on the central water. On the other hand, an excess proton in a 4-methylimidazole-water- 4-methylimidazole chain is always localized on one of the two 4- methylimidazoles. These findings are of interest to the discussion of proton transfer along chains of amino acids and water molecules in biomolecules.
2007. "Dynamic Protonation Equilibrium of Solvated Acetic Acid ." Angewandte Chemie International Edition 46(16):2939-2943. Abstract For the first time, the dynamic protonation equilibrium between an amino acid side chain analogue and bulk water as well as the diffusion properties of the excess proton were successfully reproduced through unbiased computer simulations. During a 50 ns Q-HOP MD simulation, two different regimes of proton transfer were observed. Extended phases of frequent proton swapping between acetic acid and nearby water were separated by phases where the proton freely diffuses in the simulation box until it is captured again by acetic acid. The pKa of acetic acid was calculated around 3.0 based on the relative population of protonated and deprotonated states and the diffusion coefficient of excess proton was computed from the average mean squared displacement in the simulation. Both calculated values agree well with the experimental measurements.
2007. "Au34-: A Fluxional Core-Shell Cluster." Journal of Physical Chemistry C 111(23):8228-8232. doi:10.1021/jp071960b Abstract Among the large Aun – clusters for n > 20, the photoelectron spectra of Au34 – exhibit the largest energy gap (0.94 eV) with well-resolved spectral features, making it a good candidate for structural consideration in conjunction with theoretical studies. Extensive structural searches at several levels of theory revealed that the low-lying isomers of Au34 – can be characterized as fluxional core-shell type structures with 4 or 3 inner atoms and 30 or 31 outer atoms, i.e., Au4@Au30 – and Au3@Au31 –, respectively. Detailed comparisons between theoretical and photoelectron results suggest that the most probable ground state structures of Au34 – are of the Au4@Au30 – type. The 30 outer atoms seem to be disordered or fluxional, giving rise to a number of low-lying isomers with very close energies and simulated photoelectron spectra. The fluxional nature of the outer layer in large gold clusters or nanoparticles may have important implications for their remarkable catalytic activities.
2007. "Accurate Thermochemical Properties for Energetic Materials Applications. II. Heats of Formation of Imidazolium-, 1,2,4-Triazolium-, and Tetrazolium-Based Energetic Salts fromIsodesmic and Lattice Energy Calculations." Journal of Physical Chemistry B 111(18):4788-4800. doi:10.1021/jp066420d 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 computational approach to the prediction of the heats of formation (∆Hf°’s) of solid-state energetic salts from electronic structure and volume-based thermodynamics (VBT) calculations is described. The method uses as its starting point reliable ∆Hf°’s for energetic precursor molecules and ions. The ∆Hf°’s of more complex energetics species such as substituted imidazole, 1,2,4-triazole, and tetrazole molecules and ions containing amino, azido, and nitro (including methyl) substituents are calculated using an isodesmic approach at the MP2/complete basis set level. On the basis of comparisons to experimental data for neutral analogues, this isodesmic approach is accurate to <3 kcal/mol for the predicted cation and anion ∆Hf°’s. The ∆Hf°’s of the energetic salts in the solid state are derived from lattice energy (UL) calculations using a VBT approach. Improved values for the ∝ and β parameters of 19.9 (kcal nm)/mol and 37.6 kcal/mol for the UL equation were obtained on the basis of comparisons to experimental UL’s for a series of 23 salts containing ammonium, alkylammonium, and hydrazinium cations. The total volumes are adjusted to account for differences between predicted and experimental total volumes due to different shapes of the ions (flat vs spherical). The predicted ∆Hf°’s of the energetic salts are estimated to have error bars of 6-7 kcal/mol, on the basis of comparisons to established experimental ∆Hf°’s of a subset of the salts studied. Energetic salts with the highest positive ∆Hf°’s are predicted for azido-containing cations, coupled with heterocyclic anions containing nitro substituents. The substitution of functional groups on carbon versus nitrogen atoms of the heterocyclic cations has interesting stabilization and destabilization effects, respectively.
2007. "Interactions of 1-Methylimidazole with UO₂(CH₃CO₂)₂ andUO₂(NO₃)₂: Structural, Spectroscopic, and TheoreticalEvidence for Imidazole Binding to the Uranyl Ion." Journal of the American Chemical Society 129(3):526-536. doi:10.1021/ja064592i 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 first definitive high-resolution single-crystal X-ray structure for the coordination of the 1-methylimidazole (Meimid) ligand to UO₂(Ac)₂ (Ac =CH₃CO₂) is reported. The crystal structure evidence is confirmed by IR, Raman, and UV-vis spectroscopic data. Direct participation of the nitrogen atom of the Meimid ligand in binding to the uranium center is confirmed. Structural analysis at the DFT (B3LYP) level of theory showed a conformational difference of the Meimid ligand in the free gas-phase complex versus the solid state due to small energetic differences and crystal packing effects. Energetic analysis at the MP2 level in the gas phase supported stronger Meimid binding over H₂2O binding to both UO₂(Ac)₂ and UO₂(NO₃)₂. In addition, self-consistent reaction field COSMO calculations were used to assess the aqueous phase energetics of combination and displacement reactions involving H₂O and Meimid ligands to UO₂R₂ (R ) Ac, NO₃). For both UO₂(NO₃)₂ and UO₂(Ac)₂, the displacement of H₂O by Meimid was predicted to be energetically favorable, consistent with experimental results that suggest Meimid may bind uranyl at physiological pH. Also, log(Knitrate/KAc) calculations supported experimental evidence that the binding stoichiometry of the Meimid ligand is dependent upon the nature of the reactant uranyl complex. These results clearly demonstrate that imidazole binds to uranyl and suggest that binding of histidine residues to uranyl could occur under normal biological conditions.
2007. "Interactions of 1-Methylimidazole with UO₂(CH₃CO₂)₂ andUO₂(NO₃)₂: Structural, Spectroscopic, and TheoreticalEvidence for Imidazole Binding to the Uranyl Ion." Journal of the American Chemical Society 129(3):526-536. doi:10.1021/ja064592i Abstract The first definitive high-resolution single-crystal X-ray structure for the coordination of the 1-methylimidazole (Meimid) ligand to UO₂(Ac)₂ (Ac ) CH₃CO₂) is reported. The crystal structure evidence is confirmed by IR, Raman, and UV-vis spectroscopic data. Direct participation of the nitrogen atom of the Meimid ligand in binding to the uranium center is confirmed. Structural analysis at the DFT (B3LYP) level of theory showed a conformational difference of the Meimid ligand in the free gas-phase complex versus the solid state due to small energetic differences and crystal packing effects. Energetic analysis at the MP2 level in the gas phase supported stronger Meimid binding over H₂O binding to both UO₂(Ac)₂ and UO₂(NO₃)₂. In addition, self-consistent reaction field COSMO calculations were used to assess the aqueous phase energetics of combination and displacement reactions involving H₂O and Meimid ligands to UO₂R₂ (R ) Ac, NO₃). For both UO₂(NO₃)₂ and UO₂(Ac)₂, the displacement of H₂O by Meimid was predicted to be energetically favorable, consistent with experimental results that suggest Meimid may bind uranyl at physiological pH. Also, log(Knitrate/KAc) calculations supported experimental evidence that the binding stoichiometry of the Meimid ligand is dependent upon the nature of the reactant uranyl complex. These results clearly demonstrate that imidazole binds to uranyl and suggest that binding of histidine residues to uranyl could occur under normal biological conditions.