Computing: Spokane cluster Publications

2008

Nichols P, EJ Bylaska, GK Schenter, and WA De Jong. 2008. "Equatorial and Apical Solvent Shells of the UO?²? Ion." Journal of Chemical Physics 128(12):124507. doi:10.1063/1.2884861 Abstract First principles molecular dynamics simulations of the hydration shells surrounding UO₂²⁺ ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree very well known results from X-ray data. The average U=O bond length was found to be 1.77Å . The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44Å (2.46Å - 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59Å. The equatorial second shell contained 10 water molecules hydrogen-bonded to the five first shell molecules. Above and below the UO₂²⁺ ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO₂²⁺; oriented in such way as to have their protons pointed towards the cation. While the number of apical waters varied greatly, an average of 5-6 waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond (ps) time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.

2007

Feaver AM, S Sepehri, PJ Shamberger, AC Stowe, T Autrey, and G Cao. 2007. "Coherent Carbon Cryogel-Ammonia Borane Nanocomposites for Improved Hydrogen Storage." Journal of Physical Chemistry B 111(26):7469-7472. doi:10.1021/jp072448t Abstract Ammonia borane has been adsorbed into mesoporous carbon cryogels in an effort to manipulate the hydrogen release properties. TEM studies showed that ammonia borane was incorporated into the cyrogel structure. Thermochemical analysis of the dehydrogenation indicated that the hydrogen release properties of ammonia borane were enhanced when incorporated into cryogels. Dehydrogenation occured at lower temperatures and the non-hydrogen volatile products were controlled, liimiting borazine formation.
Bylaska EJ, M Valiev, JR Rustad, and JH Weare. 2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10):Art.no.104505. Abstract First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300oC. The predicted six waters in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen-bonds to 12 second shell waters in agreement with the putative structure used to analyze the X-ray data, but in disagreement with results reported from conventional molecular dynamics using two- and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shell and the average radii of these shells also agreed very well with the results of the X-ray analysis. Water transfers into and out of the 2nd solvation shell were observed to occur on a picosecond (ps) time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating waters (20 ps). Limited simulations with 128 waters (5 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen-bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum was found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region,
Stowe AC, WJ Shaw, JC Linehan, B Schmid, and T Autrey. 2007. "In situ solid state B-11 MAS-NMR studies of the thermal decomposition of ammonia borane: mechanistic studies of the hydrogen release pathways from a solid state hydrogen storage material." Physical Chemistry Chemical Physics. PCCP 9(15):1831-1836. doi:10.1039/b617781f Abstract The mechanism of hydrogen release from solid state ammonia borane (AB) has been investigated via in situ solid state 11B{1H} MAS-NMR techniques in external fields of 7.06 T and 18.8 T at a decomposition temperature of 88 oC, well below the reported melting point. The decomposition of AB is well described by an induction, nucleation and growth mechanistic pathway. During the induction period, little hydrogen is released from AB; however, a new species identified as a mobile phase of AB is observed in the 11B NMR spectra. Subsequent to induction, at reaction times when hydrogen is initially being released, three additional species are observed: the diammoniate of diborane (DADB), [(NH3)2BH2]+[BH4]-, and two BH2N2 species believed to be the linear (NH3BH2NH2BH3) and cyclic dimer (NH2BH2)2 of aminoborane. At longer reaction times the sharper features are replaced by broad, structureless peaks of a complex polymeric aminoborane (PAB) containing both BH2N2 and BHN3 species. We propose the following mechanistic model for the induction, nucleation and growth for AB decomposition leading to formation of hydrogen: (1) an induction period that yields a mobile phase of AB caused by disruption of the dihydrogen bonds, (2) nucleation that yields reactive DADB from the mobile AB and (3) growth that includes a bimolecular reaction between DADB and AB to release the stored hydrogen. Support for this work by the U.S. Department of Energy, Office of Science, Basic Energy Sciences is gratefully acknowledged. A portion of the research described in this paper was performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.
Gibbs GV, DF Cox, KM Rosso, NL Ross, RT Downs, and MA Spackman. 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.
Valiev M, J Yang, J Adams, SS Taylor, and JH Weare. 2007. "Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations." Journal of Physical Chemistry B 111(47):13455-13464. doi:10.1021/jp074853q Abstract Protein kinases catalyze the transfer of the γ-phosphoryl group from ATP, a key regulatory process governing signalling pathways in eukaryotic cells. The structure of the active site in these enzymes is highly conserved implying common catalytic mechanism. In this work we investigate the reaction process in cAPK protein kinase (PKA) using a combined quantum mechanics and molecular mechanics approach. The novel computational features of our work include reaction pathway determination with nudged elastic band methodology and calculation of free energy profiles of the reaction process taking into account finite temperature fluctuations of the protein environment. We find that the transfer of the γ-phosphoryl group in the protein environment is an exothermic reaction with the reaction barrier of 15 kcal/mol.
Wang J, JR Rustad, and WH Casey. 2007. "Calculation of Water-Exchange Rates on Aqueous Polynuclear Clustersand at Oxide-Water Interfaces." Inorganic Chemistry 46(8):2962-2964. doi:10.1021/ic070079+ 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 rates of a wide variety of reactions in aqueous coordination compounds can be correlated with lifetimes of water molecules in the inner-coordination shell of the metal. For simple octahedral metal ions, these lifetimes span ~10²⁰ but are unknown, and experimentally inaccessible, for reactive sites in interfacial environments. Using recent data on nanometer-sized aqueous aluminum clusters, we show that lifetimes can be calculated from reactiveflux molecular dynamics simulations. Rates scale with the calculated metal-water bond lengths. Surprisingly, on all aluminum(III) mineral surface sites investigated, waters have lifetimes in the range of 10⁻⁸-10⁻power10 s, making the surface sites as fast as the most reactive ions in the solution.

2006

Yanina S, KM Rosso, and P Meakin. 2006. "Defect Distribution and Dissolution Morphologies on Low-Index Surfaces of alpha-Quartz ." Geochimica et Cosmochimica Acta 70(5):1113-1127. doi:10.1016/j.gca.2005.11.019 Abstract The dissolution of prismatic and rhombohedral quartz surfaces by KOH/H2O solutions was investigated by atomic force microscopy. Rates of dissolution of different classes of surface features (e.g., steps, voids, dislocation etch pits) were measured. The prismatic surface etched almost two orders of magnitude faster than the rhombohedral surface, mostly due to the difference in the number and the rate of dissolution of extended defects, such as dislocations. Because of the presence of imperfect twin boundaries, defect densities on the prismatic surface were estimated at 50 – 100 µm2, whereas the rhombohedral surface possessed only ~0.5 – 1.0 µm2, mostly in the form of crystal voids. Crystal voids etched almost one order of magnitude faster on the prismatic surface than on the rhombohedral surface due to differences in the number and the density of steps formed by voids on the different surfaces. In the absence of extended defects, both surfaces underwent step-wise dissolution at similar rates. Average rates of step retreat were comparable on both surfaces (~3 – 5 nm/h on the prismatic surface and ~5 – 10 nm/h on the rhombohedral surface). Prolonged dissolution left the prismatic surface reshaped to a hill-and-valley morphology, whereas the rhombohedral surface dissolved to form coalescing arrays of oval-shaped etch pits.

2004

Rosso KM, DMA Smith, and M Dupuis. 2004. "Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions." Journal of Physical Chemistry A 108(24):5242-5248. Abstract Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions

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