Scientific Publications 2007
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
D
2007. "Vibrational Recognition of Adsorption Sites for CO onPlatinum and Platinum-Ruthenium Surfaces." Journal of the American Chemical Society 129(36):11045-11052. doi:10.1021/ja067944u 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. We have studied the vibrational properties of CO adsorbed on platinum and platinum-ruthenium surfaces using density-functional perturbation theory within the Perdew-Burke-Ernzerhof generalizedgradient approximation. The calculated C-O stretching frequencies are found to be in excellent agreement with spectroscopic measurements. The frequency shifts that take place when the surface is covered with ruthenium monolayers are also correctly predicted. This agreement for both shifts and absolute vibrational frequencies is made more remarkable by the frequent failure of local and semilocal exchange-correlation functionals in predicting the stability of the different adsorption sites for CO on transition metal surfaces. We have investigated the chemical origin of the C-O frequency shifts introducing an orbital-resolved analysis of the force and frequency density of states, and assessed the effect of donation and backdonation on the CO vibrational frequency using a GGA + molecular U approach. These findings rationalize and establish the accuracy of density-functional calculations in predicting absolute vibrational frequencies, notwithstanding the failure in determining relative adsorption energies, in the strong chemisorption regime.
2007. "Selective CO Methanation Catalysts for Fuel Processing Applications." Applied Catalysis. A, General 326(2):213-218. Abstract Abstract Selective CO methanation as a strategy for CO removal in micro fuel processing applications was investigated over Ru-based catalysts. Ru loading, pretreatment and reduction conditions, and choice of support were shown to affect catalyst activity, selectivity, and stability. Even operating at a gas-hourly-space-velocity as high as 13,500 hr-1, a 3%Ru/Al2O3 catalyst was able to lower CO in a reformate to less than 100 ppm over a wide temperature range from 240oC to 285 oC, while keeping hydrogen consumption below 10%.
2007. "High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design." Journal of Molecular Biology 366(4):1209-1221. Abstract Recent efforts to redesign or de novo design the sequence and structure of proteins using computational techniques have met with significant success. Most, if not all, of these computational methodologies attempt to model atomic-level interactions, and hence high-resolution structural characterization of the designed proteins is critical for evaluating the atomic-level accuracy of the underlying design force-fields. We previously used our computational protein design protocol, RosettaDesign, to completely redesign the sequence of the activation domain of human procarboxypeptidase A2. With 68% of the wild-type sequence changed, the designed protein, AYEdesign, is over 10 kcal / mol more stable than the wild-type protein. Here, we describe the high-resolution crystal structure and solution NMR structure of AYEdesign, which show that the experimentally determined backbone and side-chains conformations are effectively superimposable with the computational model at atomic resolution. To isolate the origins of the remarkable stabilization, we design and characterize a new series of procarboxypeptidase mutants that gain significant thermodynamic stability with a minimal number of mutations – one mutant gains over 5 kcal/mol of stability over the wild-type protein with only four amino-acid changes. We explore the relationship between force-field resolution and conformational sampling by comparing the experimentally determined free energies of the overall design and these focused subsets of mutations to those predicted using force fields of different resolution and both fixed and flexible backbone sampling protocols.
2007. "Electron Transport via Polaron Hopping in Bulk TiO2: a density functional theory characterization." Physical Review. B, Condensed Matter and Materials Physics 75(19):Art. No. 195212. doi:10.1103/PhysRevB.75.195212 Abstract In this work we describe our use of Marcus theory to model the electron transfer process in TiO2. Electron transport is described by a polaron model, whereby a photo-excited electron is localized at a Ti4+ site and hops to an adjacent Ti4+ site. We obtained the relevant parameters in Marcus theory (namely the activation energy ΔG*, the reorganization energy λ, and the electronic coupling matrix elements Vab) for selected crystallographic directions in rutile and anatase, using periodic DFT+U and Hartree-Fock cluster calculations. The DFT+U method was necessary to correct for the ubiquitous electron self-interaction problem? in DFT. Our results give non-adiabatic activation energies of similar magnitude in rutile and anatase, all near 0.3 eV. The electronic coupling matrix element, Vab, was determined to be largest for electron transfer parallel to the c direction in rutile, with a value of 0.20 eV, while the other directions investigated in both rutile and anatase gave Vab values near 0 eV. The results are indicative of adiabatic transfer (thermal hopping mechanism) in rutile and of diabatic transfer (tunneling mechanism) in anatase. This work was supported by the Office of Basic Energy Sciences of the Department of Energy, in part by the Chemical Sciences program and in part by the Engineering and Geosciences Division. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.
2007. "Molecular Dynamics Characterization of Rutile-Anatase Interfaces." Journal of Physical Chemistry C 111(26):9290-9298. doi:10.1021/jp0713211 Abstract We report molecular dynamics (MD) simulations of interfaces between rutile and anatase surfaces of TiO2. These interfaces are important for understanding mixed-phase catalysts, such as the Degussa P25 catalyst, and in particular as a first step toward characterizing electron/hole transport in these photo-active materials. Construction of these interfaces was possible with near-coincidence-site lattice (NCSL) theory. The results suggest adhesion energies for the most stable structures typically near -2 J/m2, and the interfaces appear energetically favorable due to an increase of six-coordinate Ti atoms (Ti6c). Two other notable observations emerge from this work. First, the interfaces are characterized as slightly disordered, with the disorder limited to a narrow region at the interface, in agreement with experiment. Second, formation of rutile octahedral structures was observed at the anatase side of the interface due to surface rearrangement. This appears as the beginning of an anatase-to-rutile phase transition. This work was supported 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. KMR acknowledges the support of the Geosciences program of the DOE Office of Basic Energy Sciences, and the Stanford Environmental Molecular Sciences Institute jointly funded by the National Science Foundation (NSF) and the DOE Office of Biological and Environmental Research.
2007. "Atomistic Simulation of Nafion Membrane: 2. Dynamics of Water Molecules and Hydronium Ions." Journal of Physical Chemistry B 111:13006-13013. doi:10.1021/jp0761057 Abstract We have performed a detailed and comprehensive analysis of the dynamics of water molecules and hydronium ions in hydrated Nafion using classical molecular dynamics simulations with the DREIDING force field. In addition to calculating diffusion coefficients as a function of hydration level, we have also determined mean residence time of H2O molecules and H3O+ ions in the first solvation shell of SO3- groups. The diffusion coefficient of H2O molecules increases with increasing hydration level and is in good agreement with experiment. The mean residence time of H2O molecules decreases with increasing membrane hydration from 1 ns at a low hydration level to 75 ps at the highest hydration level studied. These dynamical changes are related to the changes in membrane nanostructure reported in the first part of this work. Our results provide insights into slow proton dynamics observed in neutron scattering experiments and are consistent with the Gebel model of Nafion structure.
2007. "Atomistic Simulation of Nafion Membrane: I. Effect of Hydration on Membrane Nanostructure." Journal of Physical Chemistry B 111(28):8069-8079. doi:10.1021/jp0726992 Abstract We used classical molecular dynamics simulation with the DREIDING force field to study the changes in the nanostructure of Nafion membrane brought about by systematically changing the hydration level. We calculated the relative percentages of free, weakly bound and bound water in hydrated Nafion membranes. At low hydration levels, coordination of hydronium ions by multiple sulfonate groups prevents vehicular transport and impedes structural transport of protons through steric hindrance to hydration of the hydronium ions. Our results provide insights into the nanostructure of hydrated Nafion and are in excellent agreement with experimental observations by neutron scattering of changes in the percentage of non diffusing hydrogen atoms.
2007. "Radiation Effects in a Model Ceramic for Nuclear Waste Disposal." JOM. The Journal of the Minerals, Metals and Materials Society 59(4):32-35. Abstract The safe immobilization of nuclear waste in geological repositories is one of the major scientific challenges facing humanity today. Crystalline ceramics hold the promise of locking up actinides from nuclear fuel and excess weapons plutonium in their structure thereby isolating them from the environment. In this paper, we discuss the atomistic details of radiation damage in a model ceramic, zircon.
2007. "Atomistic modeling of amorphous silicon carbide using a bond-order potential." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 255(1):130-135. doi:10.1016/j.nimb.2006.11.045 Abstract Molecular dynamics simulations were performed with a Brenner-type bond-order potential to study the melting of silicon carbide (SiC), the structure of amorphous SiC produced by quenching from the melt, and the evolution of the amorphous state after isochronal annealing at elevated temperatures. The simulations reveal that SiC melts above 3700 K with an enthalpy of fusion of about 0.6 eV/atom. The density of the quenched liquid is about 2820 kg/m3, in excellent agreement with the experimental value for SiC amorphized by neutron irradiation. In addition to the loss of long-range order, the quenched liquid shows short-range disorder as measured by the C homonuclear bond ratio. Upon annealing, there is partial recovery of shortrange order.
2007. "Molecular dynamics simulation of amorphization in forsterite by cosmic rays." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 255(1):172-176. doi:10.1016/j.nimb.2006.11.021 Abstract We have examined cosmic ray interactions with silicate dust grains by simulating a thermal spike in a 1.25 million atom forsterite (Mg2SiO4) crystal with periodic boundaries. Spikes were generated by giving a kinetic energy of 1 or 2 eV to every atom within a cylinder of radius 1.73 nm along the [001] direction. An amorphous track of radius ~3 nm was produced for the 2 eV/atom case, but practically no amorphization was produced for 1 eV/atom because of effective dynamic annealing. Chemical segregation was not observed in the track. These results agree with recent experimental studies of ion irradiation effects in silicates, and indicate that cosmic rays can cause the amorphization of interstellar dust.
2007. "Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling." Analytical Chemistry 79(16):6081-6093. doi:10.1021/ac070064t Abstract We have developed an efficient and robust high-pressure capillary LC-MS method for the identification of large numbers of metabolites in biological samples using both positive and negative ESI modes. Initial efforts focused on optimizing the separations conditions for metabolite extracts using various LC stationary phases in conjunction with multiple mobile phase systems, as applied to the separation of 45 metabolite standards. The optimal mobile and stationary phases of those tested were determined experimentally (in terms of peak shapes, theoretical plates, retention of small, polar compounds, etc.), and both linear and exponential gradients were applied in the study of metabolite extracts from the cyanobacterium Cyanothece sp. ATCC 51142. Finally, an automated dual-capillary LC system was constructed and evaluated for the effectiveness and reproducibility of the chromatographic separations using the above samples. When coupled with a commercial LTQ-Orbitrap MS, ~900 features were reproducibly detected from Cyanothece sp. ATCC 51142 metabolite extracts. In addition, 12 compounds were tentatively identified, based on accurate mass, isotopic distribution, and MS/MS information.
2007. "Quantitative Proteomic Approaches for Studying Phosphotyrosine Signaling." Expert Review of Proteomics 4(1):13-23. doi:doi:10.1586/14789450.4.1.13 Abstract Protein tyrosine phosphorylation is a fundamental mechanism for controlling many aspects of cellular processes, as well as aspects of human health and diseases. Compared to phosphoserine (pSer) and phosphothreonine (pThr), phosphotyrosine (pTyr) signaling is more tightly regulated, but often more challenging to characterize due to significantly lower level of tyrosine phosphorylation (a relative abundance of 1800:200:1 was estimated for pSer/pThr/pTyr in vertebrate cells[1]). In this review, we outline the recent advances in analytical methodologies for enrichment, identification, and accurate quantitation of tyrosine phosphorylated proteins and peptides using antibody-based technologies, capillary liquid chromatography (LC) coupled with mass spectrometry (MS), and various stable isotope labeling strategies, as well as non-MS-based methods such as protein or peptide array methods. These proteomic technological advances provide powerful tools for potentially understanding signal transduction at the system level and provide a basis for discovering novel drug targets for human diseases. [1] Hunter, T. (1998) The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: its role in cell growth and disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 353, 583–605
2007. "Heats of Formation of Krypton Fluorides and Stability Predictions forKrF₄ and KrF₆ from High Level Electronic Structure Calculations." Inorganic Chemistry 46(23):10016-10021. doi:10.1021/ic701313h 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. Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for KrF⁺, KrF-, KrF₂, KrF₃⁺, KrF₄, KrF₅⁺, and KrF₆ from coupled-cluster theory (CCSD(T)) calculations with effective core potential correlation-consistent basis sets for krypton. To achieve near chemical accuracy (±1 kcal/mol), three corrections were added to the complete basis set binding energies based on frozen core coupled-cluster theory energies: a correction for corevalence effects, a correction for scalar relativistic effects, and a correction for first-order atomic spin-orbit effects. Vibrational zero point energies were computed at the coupled-cluster level of theory. The calculated value for the heat of formation of KrF₂ is in excellent agreement with the experimental value. Contrary to the analogous xenon fluorides, KrF₂, KrF₄, and KrF₆ are predicted to be thermodynamically unstable with respect to loss of F₂. An analysis of the energetics of KrF₄ and KrF₆ with respect to fluorine atom loss together with calculations of the transition states for the intramolecular loss of F₂ show that fluorine atom loss is the limiting factor determining the kinetic stabilities of these molecules. Whereas KrF₄ possesses a marginal energy barrier of 10 kcal/mol toward fluorine atom loss and might be stable at moderately low temperatures, the corresponding barrier in KrF₆ is only 0.9 kcal/mol, suggesting that it could exist only at very low temperatures. Although the simultaneous reactions of either two or four fluorine atoms with KrF₂ to give KrF₄ or KrF₆, respectively, are exothermic, they do not represent feasible synthetic approaches because the attack of the fluorine ligands of KrF₂ by the fluorine atoms, resulting in F₂ abstraction, is thermodynamically favored over oxidative fluorination of the krypton central atom. Therefore, KrF₆ could exist only at very low temperatures, and even the preparation of KrF₄ will be extremely difficult.
2007. "Structure, Magnetism and Conductivity in Epitaxial Ti-doped -Fe2O3 Hematite: Experiment and density functional theory calculations." Physical Review. B, Condensed Matter and Materials Physics 75(10):, doi:10.1103/PhysRevB.75.104412 Abstract We explore the feasibility of growing epitaxial Ti-doped -Fe2O3 in which Ti(IV) substitutes for Fe(III) preferentially in one magnetic sublattice, but not the other. Such a structure has been predicted by first-principles theory to be energetically likely, and is expected to yield interesting and useful magnetic and electronic properties. However, we find that a majority of Ti dopants disperse and occupy random cation sites in both magnetic sublattices. Density functional theory predicts that the magnetically ordered and magnetically random structures are nearly isoenergetic.
2007. "Electron, hole and exciton self-trapping in germanium doped silica glass from DFT calculations with self-interactions correction." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 255(1 (SP ISS)):188-194. Abstract We performed density functional theory (DFT) calculations of electron, hole and exciton self-trapping in germanium doped silica glass to understand the refractive index change in these glasses induced by UV irradiation. The local structure relaxation and excess electron density distribution upon trapping of the above species were calculated. The results show that both trapped exciton and electron are highly localized on germanium ion and, to some extent, on its oxygen neighbors. Exciton self-trapping is found to lead to the formation of Ge E’ center and non-bridging hole center. Electron trapping changes the GeO4 tetrahedron structure into trigonal bi-pyramid with the majority of the excess electron density located along the equatorial line. Self-trapped hole is localized on bridging oxygen ions that are not coordinated to germanium atoms and leads to elongation of the Si-O bonds and change of the Si-O-Si bond angles. We did comparative study of standard DFT vs. DFT with a hybrid PBE0 exchange and correlation functional. The results show that the two methods give qualitatively similar relaxed structure and charge distribution for the electron and exciton trapping in germanium doped silica glass; however, only using the PBE0 functional reproduces the hole self-trapping. This research is supported by the Divisions of Chemical Science, Office of Basic Energy Sciences, US Department of Energy. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The EMSL is funded by DOE’s Office of Biological and Environmental Research. The pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
