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COBRA: a computational brewing application for predicting the molecular composition of organic aerosols.

ABSTRACT: Atmospheric organic aerosols (OA) represent a significant fraction of airborne particulate matter and can impact climate, visibility, and human health. These mixtures are difficult to characterize experimentally due to their complex and dynamic chemical composition. We introduce a novel Computational Brewing Application (COBRA) and apply it to modeling oligomerization chemistry stemming from condensation and addition reactions in OA formed by photooxidation of isoprene. COBRA uses two lists as input: a list of chemical structures comprising the molecular starting pool and a list of rules defining potential reactions between molecules. Reactions are performed iteratively, with products of all previous iterations serving as reactants for the next. The simulation generated thousands of structures in the mass range of 120-500 Da and correctly predicted ?70% of the individual OA constituents observed by high-resolution mass spectrometry. Select predicted structures were confirmed with tandem mass spectrometry. Esterification was shown to play the most significant role in oligomer formation, with hemiacetal formation less important, and aldol condensation insignificant. COBRA is not limited to atmospheric aerosol chemistry; it should be applicable to the prediction of reaction products in other complex mixtures for which reasonable reaction mechanisms and seed molecules can be supplied by experimental or theoretical methods.

SUBMITTER: Fooshee DR

PROVIDER: S-EPMC3385869 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

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COBRA: a computational brewing application for predicting the molecular composition of organic aerosols.

Fooshee David R DR Nguyen Tran B TB Nizkorodov Sergey A SA Laskin Julia J Laskin Alexander A Baldi Pierre P

Environmental science & technology 20120518 11

Atmospheric organic aerosols (OA) represent a significant fraction of airborne particulate matter and can impact climate, visibility, and human health. These mixtures are difficult to characterize experimentally due to their complex and dynamic chemical composition. We introduce a novel Computational Brewing Application (COBRA) and apply it to modeling oligomerization chemistry stemming from condensation and addition reactions in OA formed by photooxidation of isoprene. COBRA uses two lists as i ...[more]

PMID: 22568707

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Project description:This study seeks to understand the compositional details of N-containing aromatic compounds (NACs) emitted during biomass burning (BB) and their contribution to light-absorbing organic carbon (OC), also termed brown carbon (BrC). Three laboratory BB experiments were conducted with two U.S. pine forest understory fuels typical of those consumed during prescribed fires. During the experiments, submicron aerosol particles were collected on filter media and subsequently extracted with methanol and examined for their optical and chemical properties. Significant correlations (p < 0.05) were observed between BrC absorption and elemental carbon (EC)/OC ratios for individual burns data. However, the pooled experimental data indicated that the BB BrC absorption depends on more than the BB fire conditions as represented by the EC/OC ratio. Fourteen NAC formulas were identified in the BB samples, most of which were also observed in simulated secondary organic aerosol (SOA) from photo-oxidation of aromatic VOCs with NOX. However, the molecular structures associated with the identical NAC formula from BB and SOA are different. In this work, the identified NACs from BB are featured by methoxy and cyanate groups, and are predominately generated during the flaming phase. The mass concentrations of identified NACs were quantified using authentic and surrogate standards, and their contributions to bulk light absorption of solvent extractable OC were also calculated. The contributions of identified NACs to organic matter (OM) and BrC absorption were significantly higher in flaming-phase samples than those in smoldering-phase samples, and correlated with EC/OC ratio (p < 0.05) for both individual burns and pooled experimental data, indicating that the formation of NACs from BB largely depends on burn conditions. The average contributions of identified NACs to overall BrC absorption at 365 nm ranged from 0.087 ± 0.024 to 1.22 ± 0.54%, 3 - 10 times higher than their mass contributions to OM (0.023 ± 0.0089 to 0.18 ± 0.067%), so the NACs with light absorption identified in this work from BB are likely strong BrC chromophores. Further studies are warranted to identify more light-absorbing compounds to explain the unknown fraction (> 98%) of BB BrC absorption.

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COBRA: a computational brewing application for predicting the molecular composition of organic aerosols.

Publications

COBRA: a computational brewing application for predicting the molecular composition of organic aerosols.

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