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

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.

[1]  E. Wynder,et al.  Tobacco and health: a societal challenge. , 1979, The New England journal of medicine.

[2]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[3]  G. Witz.  Biological interactions of alpha,beta-unsaturated aldehydes. , 1989, Free radical biology & medicine.

[4]  G. Witz.  Biological interactions of α,β-unsaturated aldehydes , 1989 .

[5]  D. Dockery,et al.  An association between air pollution and mortality in six U.S. cities. , 1993, The New England journal of medicine.

[6]  E. Grosjean,et al.  Atmospheric chemistry of isoprene and of its carbonyl products , 1993 .

[7]  B. Mannervik,et al.  Detoxication of base propenals and other alpha, beta-unsaturated aldehyde products of radical reactions and lipid peroxidation by human glutathione transferases. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[8]  B. Ostro,et al.  Fine particulate air pollution and mortality in two Southern California counties. , 1995, Environmental research.

[9]  E G Luebeck,et al.  Particulate air pollution and mortality. , 1996, Epidemiology.

[10]  S. Biswal,et al.  The molecular effects of acrolein. , 2000, Toxicological sciences : an official journal of the Society of Toxicology.

[11]  R. Atkinson.  Atmospheric chemistry of VOCs and NOx , 2000 .

[12]  Eger,et al.  Fine particulate air pollution and mortality in 20 U.S. cities, 1987-1994. , 2000, The New England journal of medicine.

[13]  J. Sarnat,et al.  Fine particulate air pollution and mortality in 20 U.S. cities. , 2001, The New England journal of medicine.

[14]  A. Goldstein,et al.  Secondary Atmospheric Photooxidation Products: Evidence for Biogenic and Anthropogenic Sources , 2001 .

[15]  A. Saija,et al.  Study on the mechanisms of the antibacterial action of some plant α,β‐unsaturated aldehydes , 2002, Letters in applied microbiology.

[16]  J. Spengler,et al.  Repeated Exposure to Isoprene Oxidation Products Causes Enhanced Respiratory Tract Effects in Multiple Murine Strains , 2003, Inhalation toxicology.

[17]  R. Kamens,et al.  Particle growth by acid-catalyzed heterogeneous reactions of organic carbonyls on preexisting aerosols. , 2003, Environmental science & technology.

[18]  J. Seinfeld,et al.  Organic atmospheric particulate material. , 2003, Annual review of physical chemistry.

[19]  F. J. Cox,et al.  Formation of oligomers in secondary organic aerosol. , 2004, Environmental science & technology.

[20]  Richard D. Smith,et al.  Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry , 2004, Journal of the American Society for Mass Spectrometry.

[21]  Erik Swietlicki,et al.  Organic aerosol and global climate modelling: a review , 2004 .

[22]  M. Andreae,et al.  Formation of Secondary Organic Aerosols Through Photooxidation of Isoprene , 2004, Science.

[23]  M. Claeys,et al.  Formation of 2-methyl tetrols and 2-methylglyceric acid in secondary organic aerosol from laboratory irradiated isoprene/NOX/SO2/air mixtures and their detection in ambient PM2.5 samples collected in the eastern United States , 2005 .

[24]  Constantinos Sioutas,et al.  Potential Role of Ultrafine Particles in Associations between Airborne Particle Mass and Cardiovascular Health , 2005, Environmental health perspectives.

[25]  Ulrich Pöschl,et al.  Atmospheric aerosols: composition, transformation, climate and health effects. , 2005, Angewandte Chemie.

[26]  J. McCue,et al.  Acrolein in cigarette smoke inhibits T-cell responses. , 2005, The Journal of allergy and clinical immunology.

[27]  James F. Pankow,et al.  Thermodynamics of the formation of atmospheric organic particulate matter by accretion reactions—2. Dialdehydes, methylglyoxal, and diketones , 2005 .

[28]  Robert McLaren,et al.  Reactive uptake of glyoxal by particulate matter , 2005 .

[29]  Robert McLaren,et al.  Heterogeneous reactions of glyoxal on particulate matter: identification of acetals and sulfate esters. , 2005, Environmental science & technology.

[30]  A. Northcross,et al.  Semiempirical model for organic aerosol growth by acid-catalyzed heterogeneous reactions of organic carbonyls. , 2005, Environmental science & technology.

[31]  Jun Zhao,et al.  Heterogeneous reactions of methylglyoxal in acidic media: implications for secondary organic aerosol formation. , 2006, Environmental science & technology.

[32]  James F. Pankow,et al.  Thermodynamics of the formation of atmospheric organic particulate matter by accretion reactions—Part 3: Carboxylic and dicarboxylic acids , 2006 .

[33]  Margaret A. Tolbert,et al.  Acid-catalyzed reactions of hexanal on sulfuric acid particles: Identification of reaction products , 2006 .

[34]  Armin Sorooshian,et al.  Chemical composition of secondary organic aerosol formed from the photooxidation of isoprene. , 2006, The journal of physical chemistry. A.

[35]  Alan G. Marshall,et al.  Truly “exact” mass: Elemental composition can be determined uniquely from molecular mass measurement at ∼0.1 mDa accuracy for molecules up to ∼500 Da , 2006 .

[36]  Yinon Rudich,et al.  Aging of organic aerosol: bridging the gap between laboratory and field studies. , 2007, Annual review of physical chemistry.

[37]  Armin Sorooshian,et al.  Characterization of 2-methylglyceric acid oligomers in secondary organic aerosol formed from the photooxidation of isoprene using trimethylsilylation and gas chromatography/ion trap mass spectrometry. , 2007, Journal of mass spectrometry : JMS.

[38]  Christian Panse,et al.  Ultrahigh mass resolution and accurate mass measurements as a tool to characterize oligomers in secondary organic aerosols. , 2007, Analytical chemistry.

[39]  Axel Metzger,et al.  Gas/particle partitioning of carbonyls in the photooxidation of isoprene and 1,3,5-trimethylbenzene , 2008 .

[40]  John H Seinfeld,et al.  Apportionment of primary and secondary organic aerosols in southern California during the 2005 study of organic aerosols in riverside (SOAR-1). , 2008, Environmental science & technology.

[41]  D. Massi,et al.  Cigarette smoke-induced neurogenic inflammation is mediated by alpha,beta-unsaturated aldehydes and the TRPA1 receptor in rodents. , 2008, The Journal of clinical investigation.

[42]  Annmarie G. Carlton,et al.  Oligomers formed through in-cloud methylglyoxal reactions: Chemical composition, properties, and mechanisms investigated by ultra-high resolution FT-ICR mass spectrometry , 2008 .

[43]  Meinrat O. Andreae,et al.  Aerosol cloud precipitation interactions. Part 1. The nature and sources of cloud-active aerosols , 2008 .

[44]  John C Wenger,et al.  Characterization of polar compounds and oligomers in secondary organic aerosol using liquid chromatography coupled to mass spectrometry. , 2008, Analytical chemistry.

[45]  J. Chow,et al.  Health effects of organic aerosols. , 2008, Inhalation toxicology.

[46]  A. Laskin,et al.  The effect of solvent on the analysis of secondary organic aerosol using electrospray ionization mass spectrometry. , 2008, Environmental science & technology.

[47]  D. Massi,et al.  Cigarette smoke – induced neurogenic inflammation is mediated by α , β-unsaturated aldehydes and the TRPA 1 receptor in rodents , 2008 .

[48]  Pierre Baldi,et al.  No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms , 2009, J. Chem. Inf. Model..

[49]  J. Seinfeld,et al.  Isoprene photooxidation: new insights into the production of acids and organic nitrates , 2009 .

[50]  Christine Wiedinmyer,et al.  A review of Secondary Organic Aerosol (SOA) formation from isoprene , 2009 .

[51]  A. Laskin,et al.  Molecular characterization of nitrogen-containing organic compounds in biomass burning aerosols using high-resolution mass spectrometry. , 2009, Environmental science & technology.

[52]  J. Offenberg,et al.  The formation of secondary organic aerosol from the isoprene + OH reaction in the absence of NO x , 2009 .

[53]  J. Jimenez,et al.  Atmospheric condensed‐phase reactions of glyoxal with methylamine , 2009 .

[54]  Anny Cazenave,et al.  Is coastal mean sea level rising faster than the global mean? A comparison between tide gauges and satellite altimetry over 1993–2007 , 2009 .

[55]  D. R. Worsnop,et al.  Evolution of Organic Aerosols in the Atmosphere , 2009, Science.

[56]  W. J. Cooper,et al.  Appearance of strong absorbers and fluorophores in limonene‐O3 secondary organic aerosol due to NH4+‐mediated chemical aging over long time scales , 2010 .

[57]  D. S. Gross,et al.  Recent Developments in the Mass Spectrometry of Atmospheric Aerosols , 2010, European journal of mass spectrometry.

[58]  J. Seinfeld,et al.  Chemical composition of gas- and aerosol-phase products from the photooxidation of naphthalene. , 2010, The journal of physical chemistry. A.

[59]  Gordon W. Slysz,et al.  High-resolution desorption electrospray ionization mass spectrometry for chemical characterization of organic aerosols. , 2010, Analytical chemistry.

[60]  B. Turpin,et al.  SOA from methylglyoxal in clouds and wet aerosols: Measurement and prediction of key products , 2010 .

[61]  J. Seinfeld,et al.  Characterization and quantification of isoprene-derived epoxydiols in ambient aerosol in the southeastern United States. , 2010, Environmental science & technology.

[62]  M. Claeys,et al.  Characterization of oligomers from methylglyoxal under dark conditions: a pathway to produce secondary organic aerosol through cloud processing during nighttime , 2010 .

[63]  J. Seinfeld,et al.  Role of aldehyde chemistry and NO x concentrations in secondary organic aerosol formation , 2010 .

[64]  P. Mirabel,et al.  Vapor Pressure Measurements of Hydroxyacetaldehyde and Hydroxyacetone in the Temperature Range (273 to 356) K , 2010 .

[65]  E. Da̧bek-Złotorzyńska,et al.  Analysis of the unresolved organic fraction in atmospheric aerosols with ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy: organosulfates as photochemical smog constituents. , 2010, Analytical chemistry.

[66]  Pierre Baldi,et al.  Learning to Predict Chemical Reactions , 2011, J. Chem. Inf. Model..

[67]  A. Laskin,et al.  Nitrogen-containing organic compounds and oligomers in secondary organic aerosol formed by photooxidation of isoprene. , 2011, Environmental science & technology.

[68]  A. Laskin,et al.  Effect of humidity on the composition of isoprene photooxidation secondary organic aerosol , 2011 .

[69]  A. Laskin,et al.  Molecular chemistry of organic aerosols through the application of high resolution mass spectrometry. , 2011, Physical chemistry chemical physics : PCCP.

[70]  E. Gryspeerdt.  Aerosol-cloud-precipitation interactions , 2013 .