Computing Publications

2013

Arey BW, L Kovarik, O Qafoku, Z Wang, NJ Hess, and AR Felmy. 2013. "Identification of Fragile Microscopic Structures during Mineral Transformations in Wet Supercritical CO2." Microscopy and Microanalysis 19(2):268-275. doi:10.1017/S1431927612014171 Abstract In this study we examine the nature of highly fragile reaction products that form in low water content super critical carbon dioxide (scCO2) using a combination of scanning electron microscopy/focus ion beam (SEM/FIB), confocal Raman spectroscopy, helium ion microscopy (HeIM), and transmission electron microscopy (TEM). HeIM images show these precipitates to be fragile rosettes that can readily decompose even under slight heating from an electron beam. Using the TEM revealed details on the interfacial structure between the newly formed surface precipitates and the underlying initial solid phases. The detailed microscopic analysis revealed that the growth of the precipitates either followed a tip growth mechanism with precipitates forming directly on the forsterite surface if the initial solid was non-porous (natural forsterite) or growth from the surface of the precipitates where fluid was conducted through the porous (nanoforsterite) agglomerates to the growth center. The mechanism of formation of the hydrated/hydroxylated magnesium carbonate compound (HHMC) phases offers insight into the possible mechanisms of carbonate mineral formation from scCO2 solutions which has recently received a great deal of attention as the result of the potential for CO2 to act as an atmospheric greenhouse gas and impact overall global warming. The techniques used here to examine these fragile structures an also be used to examine a wide range of fragile material surfaces. SEM and FIB technologies have now been brought together in a single instrument, which represents a powerful combination for the studies in biological, geological and materials science.
Shao Y, F Ding, J Xiao, J Zhang, W Xu, SK Park, J Zhang, Y Wang, and J Liu. 2013. "Making Li-air batteries rechargeable: material challenges." Advanced Functional Materials 23(8):987-1004. doi:10.1002/adfm.201200688 Abstract A Li-air battery could potentially provide three to five times higher energy density/specific energy than conventional batteries, thus enable the driving range of an electric vehicle comparable to a gasoline vehicle. However, making Li-air batteries rechargeable presents significant challenges, mostly related with materials. Herein, we discuss the key factors that influence the rechargeability of Li-air batteries with a focus on nonaqueous system. The status and materials challenges for nonaqueous rechargeable Li-air batteries are reviewed. These include electrolytes, cathode (electocatalysts), lithium metal anodes, and oxygen-selective membranes (oxygen supply from air). The perspective of rechargeable Li-air batteries is provided.
Song T, CY Ma, IK Chu, CK Siu, and J Laskin. 2013. "Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations." Journal of Physical Chemistry A 117(6):1059-1068. doi:10.1021/jp303562e Abstract In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.
Oehmen CS, and DJ Baxter. 2013. "ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems." Bioinformatics 29(6):797-8. doi:10.1093/bioinformatics/btt013 Abstract BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving the emergence of new fields of biological research. At the same time multicore systems and conventional clusters are more accessible. ScalaBLAST has been designed to run on conventional multiprocessor systems with an eye to extreme parallelism, enabling parallel BLAST calculations using over 16,000 processing cores with a portable, robust, fault-resilient design. ScalaBLAST 2.0 source code can be freely downloaded from http://omics.pnl.gov/software/ScalaBLAST.php.
Kuta J, Z Wang, K Wisuri, MCF Wander, N Wall, and AE Clark. 2013. "The surface structure of α-uranophane and its interaction with Eu(III) – An integrated computational and fluorescence spectroscopy study." Geochimica et Cosmochimica Acta 103:184-196. doi:10.1016/j.gca.2012.10.056 Abstract Uranophane is a rare U(VI) secondary silicate mineral formed in nature by the oxidation of the primary mineral uraninite. It is also relevant to the long-term geochemistry of nuclear waste repositories, where it can be formed under oxidizing conditions and has the potential to act as a secondary barrier to the migration of radionuclides through mineral sorption reactions. A combination of classical molecular dynamics and ab-initio density functional theory (DFT) has been employed to investigate the uranophane|water interface as well as the interfacial reactivity of the U(VI) silicate toward acidic conditions and radionuclide ion sorption. The sorption simulations have been complemented by experimental sorption studies and laser induced fluorescence spectroscopy to help identify the molecular structure of the surface sorbed species. Experimental distances and essential coordination numbers are properly captured by the simulation results within bulk uranophane, while interfacial water is found to orient primarily with the hydrogen-atoms directed towards the negatively charged surface. Sorption sites for water are observed to belong to 3 different groups: (1) those involving uranyl oxygen, (2) involving uranyl and silica hydroxyl oxygen atoms, and (3) involving hydroxyl hydrogen. The pKa of the surface -OH groups have been calculated using a variety of models, including a bond valence approach and utilization of the energetics of deprotonation within DFT. Under basic conditions, deprotonation of the Si-OH groups is likely responsible for uranophane dissolution. Finally, the stability and structure of surface sorbed Eu3+ has been examined, with a stable inner-sphere species being observed.
Merkley ED, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, and JN Adkins. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking ." Journal of the American Society for Mass Spectrometry 24(3):444-449. doi:10.1007/s13361-012-0565-x Abstract Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides can provide insights into protein structure and protein-protein interactions. However, cross-linked peptides are by necessity of low stoichometry and have different physicochemical properties than linear peptides, routine unambiguous identification of the cross-linked peptides has remained difficult. To address this challenge, we demonstrated the use of liquid chromatography and ion mobility separations coupled with mass spectrometry in combination with a heavy-isotope labeling method. The combination of mixed-isotope cross-linking and ion mobility provided unique and easily interpretable spectral multiplet features for the intermolecular cross-linked peptides. Application of the method to two different homodimeric proteins ‒ SrfN, a virulence factor from Salmonella Typhimurium and SO_2176, a protein of unknown function from Shewanella oneidensis‒ revealed several cross-linked peptides from both proteins that were identified with a low false discovery rate (estimated using a decoy approach). A greater number of cross-linked peptides were identified using ion mobility drift time information in the analysis than when the data were summed across the drift time dimension before analysis. The identified cross-linked peptides migrated more quickly in the ion mobility drift tube than the unmodified peptides.
Bogatko SA, EL Cauet, EJ Bylaska, GK Schenter, JL Fulton, and JH Weare. 2013. "The Aqueous Ca2+ System, in Comparison with Zn2+, Fe3+, and Al3+: An Ab Initio Molecular Dynamics Study." Chemistry - A European Journal 19(9):3047-3060. doi:10.1002/chem.201202821 Abstract Results of Ab Initio Molecular Dynamics (AIMD) simulations of a Ca2+ ion in an aqueous environment (64 waters, 38ps=5ps equilibration + 33ps data collection, 300K) are reported. The 1st hydration shell contains 6-7 waters with d(OH) = 0.97Å (identical to our bulk water estimate) and average tilt angle, I = 32º. The 1st maximum in the radial distribution function occurs at GCaO(r) = 2.45Å. Our results compare well with published experimental structural data from X-Ray Absorption (XAFS) and Neutron Diffraction. We also generate simulated XAFS spectra using a 1st principles MD-XAFS procedure and show quantitative agreement with experimental XAFS data from a 0.2m Ca(ClO4)2 aqueous solution. The Ca2+ 1st shell water dipole moment of 3.1D is identical to our bulk water estimate (3.1D). The structured 2nd hydration shell, composed of ~16.5 waters, has a maximum at GCaO(r) =4.6Å. The average 2nd shell dipole moment = 2.9D, is suppressed relative to bulk water values. Detailed H-bond analysis demonstrates the waters in this shell predominately coordinate 1st shell waters with a trigonally structured H-bond network. Two exchanges between the 1st hydration shell and the bulk were observed. These were consistent with a dissociative and dissociative interchange Eigen-Wilkins ligand exchange mechanism. Many transfers between the 2nd shell and bulk are detected for Ca2+ allowing an estimation of the 2nd shell mean residence time (MRT) of 4.6ps. Comparison of the Ca2+ hydration shell structure and dynamics with those of the recently reported Zn2+, Fe3+ and Al3+ cation species show that the 1st and 2nd hydration shell parameters, d(M-OI) distance, CNII, H-bond d(OI-OII) distance and %Tetrahedral structure are correlated with cation charge density, the ratio of cation charge (Z) and size (Rion). However, important exceptions are d(M-OII) and the 2nd shell Mean Residence Time (MRT). These differences are explained in terms of the 1st shell structure parameters (d(M-OI) distance and tilt angle I which are strongly influenced by the valence electronic structure of the Ca2+, Zn2+, Fe3+, and Al3+ cation species. The average 2nd shell dipole moment for all cations are found to be suppressed relative to bulk water.
Turcu RVF, DW Hoyt, KM Rosso, JA Sears, Jr, JS Loring, AR Felmy, and JZ Hu. 2013. "Rotor Design for High Pressure Magic Angle Spinning Nuclear Magnetic Resonance." Journal of Magnetic Resonance 226:64-69. doi:10.1016/j.jmr.2012.08.009 Abstract High pressure magic angle spinning (MAS) nuclear magnetic resonance (NMR) with a sample spinning rate exceeding 2.1 kHz and pressure greater than 165 bar has never been realized. In this work, a new sample cell design is reported, suitable for constructing cells of different sizes. Using a 7.5 mm high pressure MAS rotor as an example, internal pressure as high as 200 bar at a sample spinning rate of 6 kHz is achieved. The new high pressure MAS rotor is re-usable and compatible with most commercial NMR set-ups, exhibiting low 1H and 13C NMR background and offering maximal NMR sensitivity. As an example of its many possible applications, this new capability is applied to determine reaction products associated with the carbonation reaction of a natural mineral, antigorite ((Mg,Fe2+)3Si2O5(OH)4), in contact with liquid water in water-saturated supercritical CO2 (scCO2) at 150 bar and 50 C. This mineral is relevant to the deep geologic disposal of CO2, but its iron content results in too many sample spinning sidebands at low spinning rate. Hence, this chemical system is a good case study to demonstrate the utility of the higher sample spinning rates that can be achieved by our new rotor design. We expect this new capability will be useful for exploring solid-state, including interfacial, chemistry at new levels of high-pressure in a wide variety of fields.
Zhu H, JH Kwak, CHF Peden, and J Szanyi. 2013. "In situ DRIFTS-MS studies on the oxidation of adsorbed NH3 by NOx over a Cu-SSZ-13 zeolite." Catalysis Today 205:16-23. doi:10.1016/j.cattod.2012.08.043 Abstract DRIFT spectroscopy combined with mass spectrometry was used to investigate the oxidation of adsorbed ammonia by NO2, NO+O2 and NO2+O2 on a copper ion exchanged SSZ 13 (Cu-SSZ-13) zeolite. Compared with both NO2 and NO, the adsorption of ammonia is much stronger on the Cu-SSZ-13 zeolite. Two adsorbed ammonia species were found over the Cu-SSZ-13 zeolite studied here; notably ammonia on Brönsted acid sites (proton) and ammonia on Lewis acid sites (copper ions). These adsorbed ammonia species present different activity profiles and selectivity to N2 during NH3 oxidation. The results obtained suggest that ammonia adsorbed onto copper ions in Cu-SSZ-13 are more active at low temperatures than proton-adsorbed NH3, and give rise to a higher selectivity to N2. The formation of N2O is associated primarily with the reaction of NOx with proton-adsorbed NH3 via the formation and subsequent thermal decomposition of NH4NO3. Financial support was provided by the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Portions of this work were performed in the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). The EMSL is a national scientific user facility supported by the US DOE, Office of Biological and Environmental Research. PNNL is a multi-program national laboratory operated for the US DOE by Battelle.
Kovarik L, A Genc, CM Wang, A Qiu, CHF Peden, J Szanyi, and JH Kwak. 2013. "Tomography and High-Resolution Electron Microscopy Study of Surfaces and Porosity in a Plate-Like γ-Al2O3." Journal of Physical Chemistry C 117(1):179?186. doi:10.1021/jp306800h Abstract Morphological and surface characteristics of gamma-Al2O3 are topics of high relevance in the field of catalysis. Using tomography and high-resolution S/TEM imaging, we have studied the surface characteristics of a model gamma-Al2O3 synthesized in the shape of platelets and macroscopically defined by (110)Al2O3 and (111)Al2O3 surface facets. We show that the dominant (110)Al2O3 surface of the synthesized gamma-Al2O3 is not atomically flat but undergoes a significant reconstruction, forming nanoscale (111)Al2O3 terraces. In addition to high resolution imaging, tomographic analysis was carried out, enabling an examination of the pores/voids, which were found to be mostly enclosed within the bulk and inaccessible to gasses or metals. Tomographic analysis shows that the surfaces of the pores are defined exclusively by (100)Al2O3 and (111)Al2O3 facets. The importance of these findings is discussed in the context of relative surface energies of low index surfaces and ethanol desorption characteristics.

Next Displaying results 1 - 10 of 1494