Scientific Publications 2007
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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.
2007. "HRTEM Study of Diesel Soot Collected from Diesel Particulate Filters ." Carbon 45(1):70-77. doi:10.1016/j.carbon.2006.08.005 Abstract HRTEM study of several soot samples collected on Diesel Particulate Filters (DPF) under conditions relevant to practical applications of DPF technology, revealed nano-structure, to our knowledge, not reported previously for diesel soot. In particular, some of the primary particles were found to have hollow interior, and the outer shell exhibiting evidence of graphitization, with a higher crystallinity compared to the non-hollowed particles. The percentage of such particles varied between different soot samples and tentatively appeared to be related to the oxidation history of the sample. Remarkably, similar effect was not reproduced for a carbon black sample, Printex-U, suggesting that propensity to such oxidation-induced graphitization is related to the original nano-structure of the particle. These initial observations were independently confirmed for the same set of soot samples by two different HRTEM facilities, at NASA-Glenn and PNNL.
2007. "Distribution, Magnitudes, Reactivities, Ratios and Diurnal Patterns of Volatile Organic Compounds in the Valley of Mexico During the MCMA 2002 & 2003 Field Campaigns." Atmospheric Chemistry and Physics 7(2):329-353. Abstract A wide array of volatile organic compound (VOC) measurements was conducted in the Valley of Mexico during the MCMA-2002 and 2003 field campaigns. Study sites included locations in the urban core, in a heavily industrial area and at boundary sites in rural landscapes. In addition, a novel mobile-laboratory-based conditional sampling method was used to collect samples dominated by fresh on-road vehicle exhaust to identify those VOCs whose ambient concentrations were primarily due to vehicle emissions. Four distinct analytical techniques were used: whole air canister samples with Gas Chromatography/Flame Ionization Detection (GC-FID), on-line chemical ionization using a Proton Transfer Reaction Mass Spectrometer (PTR-MS), continuous real-time detection of olefins using a Fast Olefin Sensor (FOS), and long path measurements using UV Differential Optical Absorption Spectrometers (DOAS). The simultaneous use of these techniques provided a wide range of individual VOC measurements with different spatial and temporal scales. The VOC data were analyzed to understand concentration and spatial distributions, diurnal patterns, origin and reactivity in the atmosphere of Mexico City. The VOC burden (in ppbC) was dominated by alkanes (60%), followed by aromatics (15%) and olefins (5%). The remaining 20% was a mix of alkynes, halogenated hydrocarbons, oxygenated species (esters, ethers, etc.) and other unidentified VOCs. However, in terms of ozone production, olefins were the most relevant hydrocarbons. Elevated levels of toxic hydrocarbons, such as 1, 3-butadiene, benzene, toluene and xylenes, were also observed. Results from these various analytical techniques showed that vehicle exhaust is the main source of VOCs in Mexico City and that diurnal patterns depend on vehicular traffic in addition to meteorological processes. Finally, examination of the VOC data in terms of lumped modeling VOC classes and its comparison to the VOC lumped emissions reported in other photochemical air quality modeling studies suggests that some alkanes are underestimated in the emissions inventory, while some olefins and aromatics are overestimated.
2007. "Atomistic Simulations of Hydrated Nafion and Temperature Effects on Hydronium Ion Mobility." Journal of Physical Chemistry B 111(25):7234-7244. doi:10.1021/jp0700276 Abstract The effects of level of hydration and temperature on the nanostructure of an atomistic model of a NafionTM (Du Pont) membrane and the vehicular transport of hydronium ions and water molecules were examined using classical molecular dynamics simulations. Through the determination and analysis of structural and dynamical parameters such as density, radial distribution functions, coordination numbers, means square deviations, and diffusion coefficients, we identify that hydronium ions themselves play a role in modifying the interfacial structure in the membrane at the sulfonate pendants. In the regime of low level of hydration, short hydrogen bonded linkages made of water molecules and also hydronium ions give a more constrained structure to the sulfonate pendants. The diffusion coefficient for water was found to be in good accord with experimental data. The diffusion coefficient for hydronium ions was determined to be much smaller (6 to 10 times) than for water. Temperature was found to have a significant effect on the absolute value of the diffusion coefficients for both water and hydroniums.
2007. " Remodeling of Bacterial RNA Polymerase Supramolecular Complex in Response to Environmental Conditions." Biochemistry 46(11):3023-3035. doi:10.1021/bi0621157 Abstract Directed binding of RNA polymerase to distinct promoter elements controls transcription and promotes adaptive responses to changing environmental conditions. To identify proteins that modulate transcription, we have expressed a tagged alpha-subunit of RNA polymerase in Shewanella oneidensis under controlled growth conditions, isolated the protein complex using newly developed multiuse affinity probes, and used LC-MS/MS to identify proteins in the complex. Complementary fluorescence correlation spectroscopy measurements were used to determine the average size of the RNA polymerase complex in cellular lysates. We find that RNA polymerase exists as a large supramolecular complex with an apparent mass in excess of 1.4 MDa, whose protein composition substantially changes in response to growth conditions. Enzymes that copurify with RNA polymerase include those associated with tRNA processing, nucleotide metabolism, and energy biosynthesis, which we propose to be necessary for optimal transcriptional rates.
2007. "Platinum Monolayer Electrocatalysts for Oxygen Reduction." Electrochimica Acta 52(6):2257-2263. doi:10.1016/j.electacta.2006.05.062 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 synthesized a new class of electrocatalysts for the oxygen reduction reaction, consisting of a monolayer of Pt or mixed monolayer of Pt and another late transition metal (Au, Pd, Ir, Ru, Rh, Re or Os) deposited on a Pd(1 1 1) single crystal or on carbon-supported Pd nanoparticles. Several of these electrocatalysts exhibited very high activity, amounting to 20-fold increase in a Pt mass activity, compared with conventional all-Pt electrocatalysts. Their superior activity reflects a low OH coverage on Pt, caused by the lateral repulsion between the OH adsorbed on Pt and the OH or O adsorbed on neighboring, other than Pt, late transition metal atoms. The origin of this effect was identified through a combination of experimental and theoretical methods, employing electrochemical techniques, X-ray absorption spectroscopy, and periodic, self-consistent density functional theory calculations. This new class of electrocatalysts promises to alleviate some major problems of existing fuel cell technology by simultaneously decreasing materials cost and enhancing performance.
