Reassessing the atmospheric oxidation mechanism of toluene.

Photochemical oxidation of aromatic hydrocarbons leads to tropospheric ozone and secondary organic aerosol (SOA) formation, with profound implications for air quality, human health, and climate. Toluene is the most abundant aromatic compound under urban environments, but its detailed chemical oxidation mechanism remains uncertain. From combined laboratory experiments and quantum chemical calculations, we show a toluene oxidation mechanism that is different from the one adopted in current atmospheric models. Our experimental work indicates a larger-than-expected branching ratio for cresols, but a negligible formation of ring-opening products (e.g., methylglyoxal). Quantum chemical calculations also demonstrate that cresols are much more stable than their corresponding peroxy radicals, and, for the most favorable OH (ortho) addition, the pathway of H extraction by O2 to form the cresol proceeds with a smaller barrier than O2 addition to form the peroxy radical. Our results reveal that phenolic (rather than peroxy radical) formation represents the dominant pathway for toluene oxidation, highlighting the necessity to reassess its role in ozone and SOA formation in the atmosphere.

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA.

BACKGROUND: It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation. RESULTS: The proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS). CONCLUSION: The use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.

Heterogeneous chemistry of organic acids on soot surfaces.

We have investigated the heterogeneous interaction between a number of carboxylic acids and soot generated from different fuel sources and formation mechanisms. A low-pressure fast flow reactor in conjunction with ion drift-chemical ionization mass spectrometry detection was employed to study uptake of monocarboxylic (benzoic, oleic, and steric) and dicarboxylic (glutaric, maleic, oxalic, and phthalic) acids on deposited soot surfaces formed by combustion of methane, propane, and kerosene. Most acids exhibited irreversible uptake on the soot surfaces and the uptake coefficient was measured in the range of 9 x 10(-4) to 1 x 10(-1) estimated based on the geometric surface areas. Brunauer, Emmett, and Teller surface areas of the deposited soot surfaces were measured and the soot bulk and surface chemical compositions were evaluated with Fourier transform infrared spectroscopy and attenuated total reflection spectroscopy. Plausible uptake mechanisms were discussed on the basis of the measured soot physiochemical properties by comparing the mono and dicarboxylic acids.

Heterogeneous chemistry of butanol and decanol with sulfuric acid: implications for secondary organic aerosol formation.

Recent environmental chamber studies suggest that acid-catalyzed reactions between alcohols and aldehydes in the condensed phase lead to the formation of hemiacetals and acetals, enhancing secondary organic aerosol (SOA) growth. We report measurements of heterogeneous uptake of butanol and decanol on liquid H2SO4 in the range of 62-84 wt % and between 273 and 296 K. Both alcohols exhibit two distinct types of uptake behaviors (partially irreversible vs totally irreversible uptake), depending on the acid concentration and temperature. For the partially irreversible uptake, a fraction of the alcohol was physically absorbed while the other fraction underwent irreversible reaction. For the totally irreversible uptake, the alcohols were completely lost onto the sulfuric acid. The Henry's law solubility constant (H*) was determined from the time-dependent uptake, while the reactive uptake coefficients were calculated from the time-independent irreversible loss. Coexistence of butanol or decanol with octanal or decanal did not show enhanced uptake of the aldehydes in the sulfuric acid. Protonation and dissolution likely account for the reversible uptake, while formation of alkyl sulfate or dialkyl sulfate explains irreversible uptake of the alcohols. The results suggest that heterogeneous uptake of larger alcohols is unlikely of significant importance in the lower atmosphere except in the case of freshly nucleated aerosols that may have high acid concentrations.

Heterogeneous reactions of methylglyoxal in acidic media: implications for secondary organic aerosol formation.

Recent environmental chamber studies have suggested that acid-catalyzed particle-phase reactions of organic carbonyls contribute to the formation of secondary organic aerosol (SOA). We report the first measurements of uptake of methylglyoxal on liquid H2SO4 over the temperature range of 250-298 K and acidic range of 55-85 wt %. From the time-dependent uptake the effective Henry's law solubility constant (H*) was determined. Heterogeneous reactions of methylglyoxal are shown to decrease with acidity and involve negligible formation of sulfate esters. Hydration and polymerization likely explain the measured uptake of methylglyoxal on H2SO4 and the measurements do not support an acid-catalyzed uptake of methylglyoxal. The results imply that heterogeneous reactions of methylglyoxal contribute to organic aerosol formation in less acidic media and hydration and polymerization of methylglyoxal in the atmospheric aerosol-phase are dependent on the hygroscopicity, rather than the acidity of the aerosols.