Computing Publications

2009

Bose S, MF Hochella, YA Gorby, DW Kennedy, DE Mccready, AS Madden, and BH Lower. 2009. "Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1." Geochimica et Cosmochimica Acta 73(4):962-976. Abstract The surface area normalized reduction rates of hematite (α-Fe2O3) nanoparticles, ranging in size from 11 to 99 nm, by S. oneidensis MR-1 with lactate as the sole electron donor were measured. The reduction kinetics of metal-oxide nanoparticles were examined to determine how S. oneidensis utilizes these environmentally-relevant solid-phase electron acceptors. Nanoparticles involved in geochemical reactions show different properties relative to larger particles of the same phase, and their reactivity is predicted to change as a function of size. As evident from whole cell TEM mounts, the mode of nanoparticle adhesion to cells is different between the more aggregated, pseudo-hexagonal to irregular shaped 11, 12, and 99 nm nanoparticles and the less aggregated 30 and 43 nm rhombohedral particles. Due to the aggregation differences, the 11, 12 and 99 nm particles show less cell contact and coverage than the 30 and 43 nm particles, but the former still show significant rates of reduction. This leads to the provisional speculation that S. oneidensis MR-1 employs a pathway of indirect electron transfer in conjunction with the direct-contact pathway, and the relative importance of the bioreduction mechanism employed may depend upon aggregation level, shape of the particles, and/or crystal faces exposed. In accord with the proposed increase in electronic band-gap for hematite nanoparticles with reduction in size, the smallest particles (11 nm) exhibit a one order of magnitude decrease in reduction rate (surface area normalized) when compared with larger (99 nm) nanoparticles, and the 12 nm rate falls in between these two. This effect may also be due to the passivation of the mineral and cell surfaces by Fe(II), or decreasing solubility due to decrease in size.
Elsasser BM, M Valiev, and JH Weare. 2009. "A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction." Journal of the American Chemical Society 131(11):3869-3871. doi:10.1021/ja807940y Abstract The ubiquitous presence of phosphoryl transfer as central step in many metabolic, signaling, energy storage, etc. enzymatic reactions requires that the details of the reaction mechanisms (e.g. reaction paths, transition state stabilization and structure, etc.) that leads to their remarkable rates in protein catalytic environments be understood1. It is expected that most of these reactions proceed through a pathway that includes a penta- coordinated phosphorane species. However, the nature of the bonding and the protonation of the structure in this region and the possibility of stable intermediates as the system passes along the reaction path through the transitions state (TS) are currently topics of considerable debate1a,b,c. Typically nucleophilic substitution reactions are classified in terms of extremes of two bonding situations along the reaction path: in a dissociative mechanism the substrate phosphate bridging bond is broken and the bond to the entering nucleophilic group is not yet formed leaving a metastable metaphosphate (PO3−) intermediate (a DN+AN reaction); in an associative mechanism in the extreme case a metastable pentacoordinated phosphorane species with nearly equivalent bonds is present in the TS, whose subsequent dissociation leads to the product state (an AN+DN reaction). Recently we published a computational study of the phosphoryl transfer step of a major class of enzymes, the serine kinases2a,b involved in signal transduction. These calculations2b support a dissociative mechanism (DNAN,) for this family of enzymes with unstable metaphosphate structure in loose transition state with total bond order of 22%.
Deskins NA, and M Dupuis. 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.
Deskins NA. 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.
Du Y, NA Deskins, Z Zhang, Z Dohnalek, M Dupuis, and I Lyubinetsky. 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. Abstract We report results of the combined experimental and theoretical investigation of the molecular oxygen reaction with a partially hydroxylated TiO₂(110) surface. The consecutive steps of both primary and secondary site-specific reactions have been tracked with high-resolution scanning tunneling microscopy (STM). For the first time, we have directly imaged stable, adsorbed hydroperoxyl (HO₂) species, which is believed to be a key intermediate in many heterogeneous photochemical processes but generally metastable and “elusive” until now. We also found terminal hydroxyl groups, another critical but never directly observed intermediates. A conclusive evidence that O₂ reacts spontaneously with a single bridging OH group as an initial reaction step is provided. The experimental results are supported by density functional theory (DFT) calculations that have determined species energies and configurations. Reported observations provide a basis for a consistent description of the elementary reaction steps and offer molecular-level insight into the underlying reaction mechanisms. In a broader perspective, the results are expected to have far reaching implications for various catalytic systems involving the interconversion of O₂ and H₂O.
Wigginton NS, KM Rosso, AG Stack, and MF Hochella. 2009. "Long-Range Electron Transfer Across Cytochrome-Hematite (a-Fe2O3) Interfaces." Journal of Physical Chemistry C 113(6):2096-2103. Abstract Electrochemical scanning tunneling microscopy (EC-STM) was used to assess the distance dependence of electron tunneling facilitated by a bacterial multiheme cytochrome to a single crystal iron oxide surface. We measured tunneling current-distance (I-s) profiles across the nanoscale space between insulated Au STM tips and the basal (001) surface of a hematite (-Fe2O3) crystal, and compared them to the case in which an intervening small tetraheme cytochrome (STC) from Shewanella oneidensis covalently linked to the Au tip surface. Tunneling profiles were collected at constant surface potentials in solutions having a range of ionic strengths. At short tip-sample separation, the distance dependece of the tunneling current shows a quasi-linear behavior. At longer distances it shows an exponential decay. The different regions are discussed in terms of ordering of interfacial water and ion layers in the electrical double layer associated with the hematite surface. The effective tunneling range and its rate of decay are substantially increased when STC is present in the tunneling junction, suggesting that cytochrome molecules provide enhanced tunneling pathways and stronger electronic coupling to the hematite surface. Based on these results, cytochrome-mediated electron transfer during bacterial metal reduction may be possible at distances further than originally thought. Also, as multiheme cytochromes and other similar molecules gain attention for their promising role in fuel cells and molecular electronics, we show that the solution conditions and surface properties of the substrate must be carefully considered.
Mei D, L Xu, and GA Henkelman. 2009. "Potential Energy Surface of Methanol Decomposition on Cu(110)." Journal of Physical Chemistry C 113(11):4522-4537. Abstract Combining the dimer saddle point searching method and periodic density functional theory calculations, the potential energy surface of methanol decomposition on Cu(110) has been mapped out. Each elementary step in the methanol decomposition reaction into CO and hydrogen occurs via one of three possible mechanisms: OH, CH or CO bond scission. Multiple reaction pathways for each bond scission have been identified in the present work. Reaction pathway calculations were started from an initial (reactant) state with methanol adsorbed in the most stable geometry on Cu(110). The saddle point and corresponding final state of each reaction or diffusion mechanism were determined without assuming the reaction mechanism. In this way, the reaction paths are determined without chemical intuition. The harmonic pre-exponential factor of each identified reaction is calculated from a normal mode analysis of the stationary points. Then, using harmonic transition state theory, the reaction rate of each identified reaction pathway in the entire reaction network is obtained. The most favorable decomposition route for methanol on Cu(110) is found as follows: . The rate-limiting step in this route is the dehydrogenation of methoxy to formaldehyde. Our calculation results are in agreement with previous experimental observations and results. This work was supported by a Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL). The computations were performed using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington.
Hu JZ, JH Kwak, Y Wang, CHF Peden, H Zheng, D Ma, and X Bao. 2009. "Studies of the Active Sites for Methane Dehydroaromatization Using Ultrahigh-Field Solid-State Mo95 NMR Spectroscopy." Journal of Physical Chemistry C 113(7):2936-2942. doi:10.1021/jp8107914 Abstract Abstract It is found that the spin-lattice relaxation time, T1, corresponding to the surface exchanged molybdenum species in Mo/HZSM-5 catalysts is short, i.e., less than about 100ms at 21.1 T while the value of T1 for the crystallite MoO3 molecules is longer, i.e., about 30 s. Such a difference, more than two orders in magnitude, is utilized to differentiate the exchanged Mo species from the agglomerate MoO3 in Mo/HZSM-5 catalyst. An approximately linear correlation between the amount of exchanged species and the aromatics formation rate is obtained. This result significantly strengthens our prior conclusion that the exchanged Mo species are the active centers for the methane dehydroaromatization reaction on Mo/HZSM-5 catalysts (J. Am. Chem. Soc. 2008, 130, 3722-3723). Our results also suggest that one exchanged Mo atom anchors on two ion exchange sites and the exchanged Mo species on catalysts are possibly monomeric. Analyzing the linshapes obtained from both the 95Mo MAS and the static spectra indicates that the exchanged sites are heterogeneous, resulting in a significantly broadened MAS spectrum and essentially a featureless but nearly symmetric static lineshape for the exchanged Mo species. Furthermore, for crystallite MoO3 powder sample, the parameters related to the electric-field-gradient (EFG) tensor, the chemical shift anisotropy (CSA) and the three Euler angles required to align the CSA principal axis system with the quadrupolar principal axis system are determined by analyzing both the 95Mo MAS and the static spectra obtained at ultra-high field of 21.1 T. The new results obtained from this study on crystallite MoO3 powders should help to clarify some of the contradictions in prior literature reports from other groups. Key words: 95Mo NMR, MAS, relaxation, surface exchanged species, HZSM-5, electric-field-gradient (EFG), chemical shift anisotropy (CSA), active centers.
Bylaska EJ, M Holst, and JH Weare. 2009. "Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory." Journal of Chemical Theory and Computation 5(4):937-948. doi:10.1021/ct800350j Abstract Results of the application of an adaptive finite element (FE) based solution using the FETK library of M. Holst to Density Functional Theory (DFT) approximation to the electronic structure of atoms and molecules are reported. The severe problem associated with the rapid variation of the electronic wave functions in the near singular regions of the atomic centers is treated by implementing completely unstructured simplex meshes that resolve these features around atomic nuclei. This concentrates the computational work in the regions in which the shortest length scales are necessary and provides for low resolution in regions for which there is no electron density. The accuracy of the solutions significantly improved when adaptive mesh refinement was applied, and it was found that the essential difficulties of the Kohn-Sham eigenvalues equation were the result of the singular behavior of the atomic potentials. Even though the matrix representations of the discrete Hamiltonian operator in the adaptive finite element basis are always sparse with a linear complexity in the number of discretization points, the overall memory and computational requirements for the solver implemented were found to be quite high. The number of mesh vertices per atom as a function of the atomic number Z and the required accuracy e (in atomic units) was esitmated to be v (e;Z) = 122:37 * Z2:2346 /1:1173 , and the number of floating point operations per minimization step for a system of NA atoms was found to be 0(N3A*v(e,Z0) (e.g. Z=26, e=0.0015 au, and NA=100, the memory requirement and computational cost would be ~0.2 terabytes and ~25 petaflops). It was found that the high cost of the method could be reduced somewhat by using a geometric based refinement strategy to fix the error near the singularities.
Trevisanutto PE, PV Sushko, KM Beck, AG Joly, WP Hess, and AL Shluger. 2009. "Excitation, Ionization, and Desorption: How Sub-band gap Photons Modify the Structure of Oxide Nanoparticles." Journal of Physical Chemistry C 113(4):1274-1279. Abstract Nanoparticles of wide-band-gap materials MgO and CaO, subjected to low-intensity ultraviolet irradiation with 266 nm (4.66 eV) photons, emit hyperthermal oxygen atoms with kinetic energies up to ~ 0.4 eV. We use ab initio embedded cluster methods to study theoretically a variety of elementary photoinduced processes at both ideal and defect-containing surfaces of these nanoparticles and develop a mechanism for the desorption process. The proposed mechanism includes multiple local photoexcitations resulting in sequential formation of localized excitons, their ionization, and further excitations. It is suggested that judicious choice of sub-band-gap photon energies can be used to selectively modify surfaces of nanomaterials.

Next Displaying results 1 - 10 of 703