Scientific Publications 2009
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
Y
2009. "A Targeted Releasable Affinity Probe (TRAP) for In Vivo Photo-Crosslinking." Chembiochem 10(9):1507-1518. doi:10.1002/cbic.200900029 Abstract We have synthesized a targeted and releasable affinity probe (TRAP), consisting of a biarsenical fluorescein linked to benzophenone, and demonstrated the utility of TRAP to stabilize protein binding partners in living bacterial and mammalian systems upon photo-activation of the benzophenone moiety. Moreover, after covalent crosslinking, ligand exchange of the arsenic-sulfur bonds between TRAP and an engineered tetracysteine binding sequence within the target protein permits fluorophore transfer to the crosslinked binding partner, permitting the identification of the proximal binding interface of the isolated protein complex through mass spectrometric fragmentation and sequence identification.
2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides." Analytical Chemistry 81(10):4137-4143. doi:10.1021/ac802605m Abstract Multiplex isobaric tags for relative and absolute quantification (iTRAQ) enable high-throughput quantification of peptides via reporter ion signals in the low mass range of tandem mass spectra. A challenging but highly promising application is to analyze iTRAQ-labeled peptides using a sensitive linear ion trap mass spectrometer (LTQ-MS) and pulsed Q dissociation (PQD), a form of ion trap collision activated dissociation (CAD) designed to allow detection of low mass-to-charge fragment ions. Electron dissociation transfer (ETD), on the other hand, is complementary to PQD and is especially useful for sequencing peptides containing post-translational modifications (PTMs). Here, we developed an integrated workflow for robust and accurate quantitative identification of iTRAQ labeled phosphopeptides that integrates the PQD and ETD fragmentation methods together with PQD optimization, data management and bioinformatics tools. Analysis of the phosphoproteome of human fibroblast cells demonstrated that this hybrid mode is superior to either PQD or ETD alone for phosphopeptide identification and quantitation. The combined PQD/ETD approach can qualitatively identify additional phosphopeptides than ETD alone and PQD information can provide better quantitation of ETD identified iTRAQ-labeled phosphopeptides.
2009. "Single Wall Diesel Particulate Filter (DPF) Filtration Efficiency Studies Using Laboratory Generated Particles." Chemical Engineering Science 64(8):1625-1634. Abstract Diesel offers higher fuel efficiency, but produces higher exhaust particulate matter. Diesel particulate filters are presently the most efficient means to reduce these emissions. These filters typically trap particles in two basic modes: at the beginning of the exposure cycle the particles are captured in the filter holes, and at longer times the particles form a "cake" on which particles are trapped. Eventually the "cake" removed by oxidation and the cycle is repeated. We have investigated the properties and behavior of two commonly used filters: silicon carbide (SiC) and cordierite (DuraTrap® RC) by exposing them to nearly-spherical ammonium sulfate particles. We show that the transition from deep bed filtration to "cake" filtration can easily be identified by recording the change in pressure across the filters as a function of exposure. We investigated performance of these filters as a function of flow rate and particle size. The filters trap small and large particles more efficiently than particles that are ~80 to 200 nm in aerodynamic diameter. A comparison between the experimental data and a simulation using incompressible lattice-Boltzmann model shows very good qualitative agreement, but the model overpredicts the filter’s trapping efficiency.
2009. "Simultaneous MS-IR Studies of Surface Formate Reactivity Under Methanol Synthesis Conditions on Cu/SiO2." Topics in Catalysis 52(10):1440-1447. doi:10.1007/s11244-009-9320-3 Abstract The coverages and surface lifetimes of copper-bound formates on Cu/SiO2 catalysts, and the steady-state rates of reverse water-gas shift and methanol synthesis have been measured simultaneously by mass (MS) and infrared (IR) spectroscopies under a variety of elevated pressure conditions at temperatures between 140 and 160°C. DCOO lifetimes under steady state catalytic conditions in CO2:D2 atmospheres were measured by 12C – 13C isotope transients (SSITKA). The values range from 220s at 160°C to 660s at 140°C. The catalytic rates of both reverse water gas shift (RWGS) and methanol synthesis are ~100-fold slower than this formate removal rate back to CO2+1/2 H2, and thus they do not significantly influence the formate lifetime or coverage at steady state. The formate coverage is instead determined by formate’s rapid production / decomposition equilibrium with gas phase CO2+H2. The results are consistent with formate being an intermediate in methanol synthesis, but with the rate-controlling step being after formate production (for example, its further hydrogenation to methoxy). A 2-3 fold shorter life time (faster decomposition rate) was observed for formate under reactions conditions when both D2 and CO2 are present than in pure Ar or D2+Ar alone, attributed to effects of coadsorbates (produced in D2 and CO2) on adsorbed formate reaction pathways. The carbon which appears in the methanol product spends a longer time on the surface than the formate species, 1.8 times as long at 140°C. The additional delay on the surface is attributed in part to readsorption of methanol on the catalyst, thus obscuring the mechanistic link between formate and methanol.
2009. "Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell-Wall Analogue Peptides: Experimental and Theoretical Studies." Chemistry - a European Journal 15(9):2081-2090. doi:10.1002/chem.200802010 Abstract In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the non-covalent complex between the vancomycin and the cell wall peptide analogue Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac2KDADA). The binding energies between the vancomycin and the peptide were obtained from the RRKM modeling of the time- and energy resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex toward fragmentation increases in the order: [V+Ac2KDADA+H]+2 < [V+Ac2KDADA+H]+ < [V+Ac2KDADA-H]-. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects indicating substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of 1.75 eV and 1.34 eV obtained for the [V+Ac2KDADA-H]- and [V+Ac2KDADA+H]+ , respectively, are in excellent agreement with the results of density functional theory (DFT) calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex as compared to only one charged site in the singly protonated complex. The low binding energy of 0.93 eV obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.
2009. "Selective Removal of Lanthanides from Natural Waters, Acidic Streams and Dialysate." Journal of Hazardous Materials 168(2-3):1233-1238. Abstract The increased demand for the lanthanides in commercial products result in increased production of lanthanide containing ores, increasing public exposure to the lanthanides, both from various commercial products and from production wastes/effluents. This work investigates lanthanide (La, Ce, Pr, Nd, Eu, Gd, Lu) binding properties of self-assembled monolayers on mesoporous silica supports (SAMMS®) that were functionalized with diphosphonic acid (DiPhos), acetamide phosphonic acid (AcPhos), propionamide phosphonic acid (ProPhos), and 1-hydroxy-2-pyridinone (1,2-HOPO) from natural waters (river, ground, and sea waters), acid solutions (to mimic certain industrial process streams), and dialysate and compares their performance to a high surface area activated carbon. The properties include sorption affinity, capacity, and sorption kinetics. Stability and regenerability of SAMMS materials were also investigated. Going from the acid side over to the alkaline side, the AcPhos- and DiPhos-SAMMS maintain their outstanding affinity for lanthanides, which enable the use of the materials in the systems where the pH may fluctuate. While the activated carbon is as effective as 1,2-HOPO-SAMMS for capturing lanthanides in natural (alkaline) waters, it has no affinity in acid solutions (pH 2.4) and low affinity in carbonate-rich dialysate. Over 99% of 100 ug/L of Gd in dialysate was removed by the ProPhos-SAMMS after ten minutes. SAMMS can be regenerated with an acid wash (0.5 M HCl) without losing the binding properties, for a number of regeneration cycles. In acid solutions, PhoPhos- and 1,2-HOPO-SAMMS have differing affinity along the lanthanide series, suggesting their potential for chromatographic lanthanide separations. Thus, SAMMS materials have a great potential to be used as sorbents in large scale treatment of lanthanides, lanthanide separation prior to analytical instruments, and sorbent dialyzers for lanthanide clearances.
2009. "Interaction of D2O with a Thick BaO Film: Formation of and Phase Transitions in Barium Hydroxides." Journal of Physical Chemistry C 113(35):15692-15697. Abstract The interaction of D2O with a thick BaO film (≥ 20 mono-layer equivalent (MLE)) on ultra-thin Al2O3/NiAl(110) was investigated with temperature programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS). Upon D2O exposure of a thick BaO film amorphous barium hydroxide formed at room temperature that readily converted to crystalline Ba(OD)2 phases during annealing in ultra-high vacuum (UHV). The formation of crystalline hydroxide phases depends on the initial D2O exposure at 300 K. Following low D2O exposure at room temperature that results in the formation of amorphous barium hydroxide with no hydrating water, only the a-Ba(OD)2 phase was observed after 400 K annealing. The sample that was exposed to D2O extensively (i.e. hydrated amorphous barium hydroxide formed) showed a series of phase transformations as the sample was annealed to increasingly higher temperatures: amorphous- Ba(OD)2•xD2O (x>1)à b-Ba(OD)2.D2Oà b-Ba(OD)2àa-Ba(OD)2. The results of TPD experiments completely agreed with this phase transformation scheme: hydrating water molecules desorbed first at 425 K, allowing the formation of the b-Ba(OD)2.D2O phase. Desorption of water from b-Ba(OD)2.D2O at around 475 K leads to the formation of b-Ba(OD)2 and its subsequent conversion to a-Ba(OH)2. All the barium hydroxides thermally decomposed at T < 550 K. When the BaO film was exposed to D2O at 425 K crystalline b-Ba(OD)2 formed initially, which lead to the formation of a small amount of a-Ba(OD)2 as well at low D2O exposures. At high D2O exposures the dominant phase was b-Ba(OD)2.xD2O, and no a-phase was seen.
2009. "BaO/Al2O3/NiAl(110) Model NOx Storage Materials: the effect of BaO film thickness on the amorphous-to-crystalline Ba(NO3)2 phase transition." Journal of Physical Chemistry C 113(2):716-723. Abstract The reaction of NO2 with BaO (0.15 – 2 ML and > 30 ML)/Al2O3(12 ML)/NiAl(110) model NOx storage materials was studied. A thick (~12 ML), ordered Al2O3 film was prepared as the support oxide on a NiAl(110) substrate in order to minimize the effect of the intermixing between the two oxide phases (BaO and Al2O3) on the NOx chemistry of BaO. The growth of a thick alumina film, prepared by atomic oxygen deposition onto NiAl(110), follows a layer-by-layer growth mode and the resulting film is much more stable when exposed to NO2 than the ultra-thin alumina films studied before. The interaction of NO2 with the model NOx storage systems at low coverages of BaO show fundamentally different behaviors from a thick BaO film, as nitrite species form at low exposures of NO2, followed by nitrate formation at high NO2 exposures. In contrast, on the thick BaO layer nitrite-nitrate ion pairs form at 300 K under UHV conditions (PNO2 ~ 1 10-9 Torr). However, at elevated NO2 pressures (≥ 1 10-5 Torr) the thick BaO film is gradually converted into amorphous Ba(NO3)2 at 300 K. Raising the temperature of the samples with ΘBaO > 1 ML after NO2 exposure (in the absence of gas phase NO2) leads to the phase transformation of the amorphous Ba(NO3)2 layer into crystalline Ba(NO3)2 particles in the temperature range of 500 – 600 K. No phase transformation is observed in samples with ΘBaO < 1 ML.
2009. "Reaction of NO2 with a pure, thick BaO film: the effect of temperature on the nature of NOx species formed." Journal of Physical Chemistry C 113(6):2134-2140. Abstract The adsorption and reaction of NO2 on a thick (>30 ML), pure BaO film deposited onto an Al2O3/NiAl(110) substrate were investigated in the temperature range of 300 – 660 K using temperature programmed desorption (TPD), infrared reflection absorption spectroscopy (IRAS), and x-ray photoelectron spectroscopy (XPS) techniques. The adsorption of NO2 on BaO at room temperature results in the formation of nitrite-nitrate ion pairs. During thermal desorption the nitrite species decompose first, releasing an NO molecule and leaving an O on the surface, while nitrate species decompose in two steps at higher temperatures: at lower temperature as NO2 only, then, at higher temperature, as NO + O2. In cyclic experiments when the BaO film was exposed to NO2 at 300 K, followed by annealing to 575 K, a large amount of NOx was stored as nitrates, and no saturation was achieved even after the 10th adsorption/anneal cycle. This suggests the gradual conversion of the BaO film into barium nitrate clusters at elevated temperatures. The rate of nitrate formation increases as the sample temperature during NO2 exposure increases up to 610 K, while at even higher temperatures the amount of nitrates formed decreases. NO2 adsorption on the thick BaO film at 610 K results in the formation of strongly bound nitrates as the major NOx species.
2009. "Low-energy networks of the T-cage (H2O)(24) cluster and their use in constructing periodic unit cells of the structure I (sl) hydrate lattice." Journal of the American Chemical Society 131(22):7564-7566. Abstract Hydrate networks are ‘host’ lattices for the storage of ‘guest’ natural gases. To enhance their physical stabilities near ambient conditions, the most stable clathrate hydrates should be identified. Here, we report the lowest energy networks of the tetrakaidecahedral cage (T-cage) (H2O)24 cluster, a constituent of the cubic unit cell of the structure I (sI) hydrate. A four-step screening method was employed to search for the lowest T-cage networks, which were eventually optimized at the MP2 level of theory. The obtained low-energy isomers can furthermore be used to obtain the low-energy hydrogen bonding networks of periodic structures of hydrates thus allowing for the realistic modeling of the accommodation of ‘guest’ molecules in clathrate hydrates. This work was supported by the US Department of Energy's Office of Basic Energy Sciences, Chemical Sciences program. Pacific Northwest National Laboratory is operated by Battelle for DOE.
2009. "On the phase diagram of water with density functional theory potentials: the melting temperature of Ice I-h with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals." Journal of Chemical Physics 130(22):Art. No. 211102. Abstract The melting temperature (Tm) of ice Ih was determined from constant enthalphy (NPH) Born-Oppenheimer Molecular Dynamics (BOMD) simulations to be 417±3 K for the Perdew-Burke-Ernzerhof (PBE) and 411±4 K for the Becke-Lee-Yang-Parr (BLYP) density functionals using a coexisting ice (Ih)-liquid phase at constant pressures of P = 2,500 and 10,000 bar and a density ρ = 1 g/cm3, respectively. This suggests that ambient condition simulations at ρ = 1 g/cm3 will rather describe a supercooled state that is overstructured when compared to liquid water. This work was supported by the US Department of Energy Office of Basic Energy Sciences' Chemical Sciences program. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2009. "Estimation of Interfacial Tension between Organic Liquid Mixtures and Water." Environmental Science & Technology 43(20):7754-7761. doi:10.1021/es901061k Abstract Knowledge of IFT values for chemical mixtures helps guide the design and analysis of various processes, including NAPL remediation with surfactants or alcohol flushing, enhanced oil recovery, and chemical separation technologies, yet available literature values are sparse. A comprehensive comparison of thermodynamic and empirical models for estimating interfacial tension (IFT) of organic chemical mixtures with water is conducted, mainly focusing on chlorinated organic compounds for 14 ternary, three quaternary, and one quinary systems. Emphasis is placed on novel results for systems with three and four organic chemical compounds, and for systems with composite organic compounds like lard oil and mineral oil. Seven models are evaluated: the ideal and nonideal monolayer models (MLID and MLNID), the ideal and nonideal mutual solubility models (MSID and MSNID), an empirical model for ternary systems (EM), a linear mixing model based on mole fractions (LMMM), and a newly developed linear mixing model based on volume fractions of organic mixtures (LMMV) for higher order systems. The two ideal models (MLID and MSID) fit ternary systems of chlorinated organic compounds without surface active compounds relatively well. However, both ideal models did not perform well for the mixtures containing a surface active compound. However, for these systems, both the MLNID and MSNID models matched the IFT data well. It is shown that the MLNID model with a surface coverage value (0.00341 mmol/m2) obtained in this study can practically be used for chlorinated organic compounds. The LMMM results in poorer estimates of the IFT as the difference in IFT values of individual organic compounds in a mixture increases. The EM, with two fitting parameters, provided accurate results for all 14 ternary systems including composite organic compounds. The new LMMV method for quaternary and higher component systems was successfully tested. This study shows that the LMMV may be able to be used for higher component systems and it can be easily incorporated into compositional multiphase flow models using only parameters from ternary systems.
2009. "Numerical and experimental investigation of DNAPL removal mechanisms in a layered porous medium by means of soil vapor extraction." Journal of Contaminant Hydrology 109(1-4):1-13. doi:10.1016/j.jconhyd.2009.07.001 Abstract The purpose of this work is to identify the mechanisms that govern the removal of carbon tetrachloride (CT) during soil vapor extraction (SVE) by comparing multiphase flow simulations with a detailed data set from a well-defined two-dimensional flow cell experiment. The flow cell was packed with two sandy soils including an embedded fine-grained sand layer. Gas concentrations at the outlet of the flow cell and 15 sampling ports inside the flow cell were measured during SVE. A dual-energy gamma radiation system was used to measure an initial NAPL saturation profile in a fine-grained sand layer. Imaging result from a dual-energy gamma radiation system with dyed CT mark along CT migration was used to construct the distribution of initial NAPL saturation in the flow cell for input to numerical simulations. Gas concentration results and photographs during SVE were compared to simulation results using a continuum-based multiphase flow simulator, STOMP (Subsurface Transport Over Multiple Phases). The measured effluent gas concentration decreased quickly at first, and then started to decrease gradually, resulting in long-term tailing. CT mass was removed quickly in coarse sand, followed by a slow removal from the fine-grained sand layer. An analytical solution for a one-dimensional advection and first-order volatilization model matched the tailing well with two fitting parameters. However, given detailed knowledge of the permeability field and initial NAPL distribution, we can predict the tailing and gas concentration profiles at sampling ports using equilibrium NAPL volatilization. NAPL flow occurs in the presence of free NAPL, and must be accounted for to accurately predict NAPL removal during the SVE experiment. The model prediction was accurate within the uncertainty of the measured or literature derived parameters (i.e., dispersivity and soil parameters). This study provides insights into the physical mechanisms of NAPL removal from a low permeability zone, and use of the local equilibrium assumption for NAPL volatilization during SVE. In addition, this study demonstrates that lack of detailed information regarding NAPL distribution and heterogeneity pattern lead overall NAPL removal to a kinetically controlled system at a 2-D flow cell scale.
2009. "First-principles study of defects and phase transition in UO2." Journal of Physics. Condensed matter 21(43):Art. No. 435401. doi:10.1088/0953-8984/21/43/435401 Abstract The electronic properties, structure and phase transformation of UO2 have been studied from first principles by the all-electron projector-augmented-wave (PAW) method. The generalized gradient approximation (GGA)+U formalism has been used to account for the strong on-site Coulomb repulsion among the localized U 5f electrons. GGA+U gives an antiferromagnetic insulating ground state for the effective Hubbard parameter Ueff ≥2.0 eV and this ordering is consistent with experimental measurement. Our results also reveal that by choosing an appropriate Ueff =3.0 eV it is possible to consistently describe structural properties of UO2 and model phase transition processes. The distribution of the local electrostatic potential indicated that the phase transition pressure for UO2 under operant conditions is about 20 GPa. In addition, the formation energies of intrinsic defects, which play a critical role in UO2 fuel under operant conditions, are found to be depended on whether the environment is under U-rich condition or O-rich condition.
2009. "Comparison of Some Representative Density Functional Theory and Wave Function Theory Methods for the Studies of Amino Acids." Journal of Computational Chemistry 30(4):589-6006. doi:10.1002/jcc.21091 Abstract Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-31111G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-31111G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-31111G(d,p), aug-cc-pVDZ, 6-31111G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-31111G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds.
2009. "Contamination from electrically conductive silicone tubing during aerosol chemical analysis." Atmospheric Environment 43(17):2836-2839. Abstract Electrically conductive silicone tubing is used to minimize losses in sampling lines during the analysis of airborne particle size distributions and number concentrations. We report contamination from this tubing using gas chromatography-mass spectrometry (GC-MS) of filter-collected samples as well as by particle mass spectrometry. Comparison of electrically conductive silicone and stainless steel tubing showed elevated siloxanes only for the silicone tubing. The extent of contamination increased with length of tubing to which the sample was exposed, and decreased with increasing relative humidity.
