CMAQ v5.1 SAPRC07tic AE6i

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Brief Description

The SAPRC07tic AE6i gas-phase mechanism was first introduced in v5.0.2 and is based on the work of Xie et al. (2013) to better describe isoprene and its later generation oxidation products. In CMAQ v5.1, the mechanism of Xie et al. is updated to include greater detail for isoprene oxidation under RO2+NO dominant conditions (see Lin et al. 2013) as well as other updates common to SAPRC07t-based mechanisms and AERO6-based mechanisms. SAPRC07tic is designed to work only with the new AERO6i aerosol module which includes speciated predictions of aerosol from isoprene epoxydiols (IEPOX) and MPAN products (HMML and MAE) following Pye et al. (2013), SOA from explicit BVOC organic nitrates, and SOA from glyoxal/methylglyoxal uptake onto particles (previously only considered in clouds). Updates were also made to deposition surrogates. Changes are documented in Pye et al. (2015).

SAPRC07tic Mechanism Updates

Isoprene System

  • Updated high-NOx (RO2+NO) isoprene chemistry to explicitly track MACR peroxy radical from abstraction channel leading to MPAN and form MAE+HMML (Lin et al. 2013).
  • Updated isoprene nitrate reaction rates with OH, NO, O3 (Lee et al. 2014).
  • Added isomerization of MACR+OH peroxy radical (addition channel) (Crounse et al. 2012).
  • Minor update to MACR+OH peroxy radical product yields following Crounse et al. (2012) and references therein
    • MACROO (product from addition channel): ~43-48% of MACR oxidation is addition to external olefinic carbon, ~0-9% is addition to internal olefinic carbon
    • IMACO3 (product from abstraction channel leading to MPAN): ~45-50% of MACR oxidation
  • Tracking of isoprene dinitrates from NO3 reaction for SOA purposes (ISOPNN)

SAPRC07t

  • Added simplified ozone loss due to halogen chemistry over sea-water (Reaction <HAL_Ozone>)
  • implemented the nonaromatic changes found in the supplementary material for the paper by Carter and Gookyoung (2013).
    • modified reaction BR22, BR32, BR43, and IS70, the MECO3, RCO3, BZCO3, and MACO3 reactions with HO2 based on IUPAC (2009) recommendations for HO2 + acyl radical reactions (last accessed Jan. 2015).
    • corrected reaction <BE10>, ACETYLENE + OH, by setting the temperature power for k0 to zero and setting temperature for kinf to -2
    • corrected reaction <BE04>, ETHENE + OH, by setting the temperature power to zero
    • revised GLY reactions with OH and NO3 based IUPAC (2008) recomendation that introduces a new peroxy radical species HCOCO3 (last accessed Jan. 2015). <BP32><BP33>
  • changed the OH + NO2 reaction based on the recommendation of IUPAC (last accessed Jan. 2015).
  • removed species NO2EX, excited NO2, and its reactions (already inactive)
  • Increased acrolein formation from 1,3-butadiene+OH <BT05> from 0.48 to 0.58 per Gookyoung Heo recommendation

Monoterpenes

  • Removed SOA formation counter (TRPRXN) from APIN + NO3 and TERP + NO3 reaction
  • Added explicit monoterpene nitrate (MTNO3) as SOA precursor
  • Updated TERP + NO3 reaction products prioritizing nitrate functionality and conservation of nitrogen
  • APIN no longer forms SOA from NO3 reaction

Complete mechanism

Organic aerosol in AERO6i

  • Added PAH (naphthalene) SOA (Pye and Pouliot 2012)
  • Updated alkane SOA (Pye and Pouliot 2012)
  • Added SOA from uptake of IEPOX and IMAE/HMML on acidic particles (Pye et al. 2013)
  • Replaced Odum 2-product APIN+NO3 and TERP+NO3 SOA with explicit monoterpene nitrate SOA (MTNO3) (Pye et al. 2015)
  • Added isoprene nitrate SOA (from ISOPRENE+NO3 reaction, Pye et al. 2015)
  • Added SOA from glyoxal/methylglyoxal heterogeneous uptake onto particles (Pye et al. 2015, following Liggio et al. 2005 and Fu et al. 2008 with an uptake coefficient of 0.0029)
  • New SOA partitioning routines (see CMAQv5.1_SOA_Update)

Schematic of SOA in aero6i

Figure 1: Schematic of CMAQv5.1 SOA in AERO6i. Pathways in red are new to CMAQv5.1 and present in both AERO6 and AERO6i. Pathways in purple are only available in AERO6i. Species in grey boxes are nonvolatile.


Organic aerosol species in v5.1 aero6i

Table 1: POA species introduced in CMAQ v5.0

POA species description molec wt (g/mol) reference
POCI primary organic carbon in aitken mode 220 Simon and Bhave 2012
POCJ primary organic carbon in accumulation mode 220 Simon and Bhave 2012
ANCOMI non-carbon organic matter (H, O, etc.) attached to POC in aitken mode 220 Simon and Bhave 2012
ANCOMJ non-carbon organic matter (H, O, etc.) attached to POC in accumulation mode 220 Simon and Bhave 2012

Table 2: SOA species in AERO6i. Species in bold are only in aero6i or differ from the species with the same name in aero6

  • SOA species in blue are semivolatile.
  • SOA species in green are low volatility and treated as effectively nonvolatile.
  • SOA species in yellow form due to reactive uptake and are treated as nonvolatile.
  • SOA formed from particle-phase processing is in purple.
SOA species version introduced precursor oxidants semivolatile alpha (mass-based) C* (ug/m3) enthlapy (kJ/mol) number of C molec wt (g/mol) OM/OC Model ref Experimental ref
AALK1 v5.1 long-chain alkanes OH SV_ALK1 0.0334 0.1472 53.0 12 168 1.17 Pye and Pouliot 2012 Presto et al. 2010
AALK2 v5.1 long-chain alkanes OH SV_ALK2 0.2164 51.8774 53.0 12 168 1.17 Pye and Pouliot 2012 Presto et al. 2010
AXYL1 v4.7 XYL/ARO2 excluding naphthalene OH,NO SV_XYL1 0.0310 1.3140 32.0 8 192 2.0 Carlton et al 2010 Ng et al. 2007
AXYL2 v4.7 XYL/ARO2 excluding naphthalene OH,NO SV_XYL2 0.0900 34.4830 32.0 8 192 2.0 Carlton et al. 2010 Ng et al. 2007
AXYL3 v4.7 XYL/ARO2 excluding naphthalene OH,HO2 NA-nonvolatile 0.36 NA NA NA 192 2.0 Carlton et al. 2010 Ng et al. 2007
ATOL1 v4.7 TOL/ARO1 OH,NO SV_TOL1 0.0310 2.3260 18.0 7 168 2.0 Carlton et al. 2010 Ng et al. 2007
ATOL2 v4.7 TOL/ARO1 OH,NO SV_TOL2 0.0900 21.2770 18.0 7 168 2.0 Carlton et al. 2010 Ng et al. 2007
ATOL3 v4.7 TOL/ARO1 OH,HO2 NA-nonvolatile 0.30 NA NA NA 168 2.0 Carlton et al. 2010 Ng et al. 2007
ABNZ1 v4.7 benzene OH,NO SV_BNZ1 0.0720 0.3020 18 6 144 2.0 Carlton et al. 2010 Ng et al. 2007
ABNZ2 v4.7 benzene OH,NO SV_BNZ2 0.8880 111.1100 18 6 144 2.0 Carlton et al. 2010 Ng et al. 2007
ABNZ3 v4.7 benzene OH,HO2 NA-nonvolatile 0.37 NA NA NA 144 2.0 Carlton et al. 2010 Ng et al. 2007
APAH1 v5.1 naphthalene OH,NO SV_PAH1 0.2100 1.6598 18 10 243 2.03 Pye and Pouliot 2012 Chan et al. 2009
APAH2 v5.1 naphthalene OH,NO SV_PAH2 1.0700 264.6675 18 10 243 2.03 Pye and Pouliot 2012 Chan et al. 2009
APAH3 v5.1 naphthalene OH,HO2 NA-nonvolatile 0.73 NA NA NA 243 2.03 Pye and Pouliot 2012 Chan et al. 2009
AISO1 v4.7 isoprene OH,NO3 SV_ISO1 0.2320 116.010 40 5 96 1.6 Carlton et al. 2010 Kroll et al. 2006
AISO2 v4.7 isoprene OH,NO3 SV_ISO2 0.0288 0.6170 40 5 96 1.6 Carlton et al. 2010 Kroll et al. 2006
AISO3 deprecated NA NA NA NA NA NA NA NA NA NA NA
ATRP1 v4.7 APIN+TERP monoterpenes OH,O3P,O3 SV_TRP1 0.1393 14.7920 40 10 168 1.4 Carlton et al. 2010 Griffin et al. 1999
ATRP2 v4.7 APIN+TERP monoterpenes OH,O3P,O3 SV_TRP2 0.4542 133.7297 40 10 168 1.4 Carlton et al. 2010 Griffin et al. 1999
ASQT v4.7 sesquiterpenes OH,O3,NO3 SV_SQT2 1.5370 24.9840 40 15 378 2.1 Carlton et al. 2010 Griffin et al. 1999
AOLGA v4.7 anthropogenic SOA time NA-nonvolatile NA NA NA NA 176.4 2.1 Carlton et al. 2010 Kalberer et al. 2004
AOLGB v4.7 biogenic SOA time NA-nonvolatile NA NA NA NA 252 2.1 Carlton et al. 2010 Kalberer et al. 2004
AORGC v4.7 SOA from cloud processing of glyoxal, methylglyoxal OH NA-nonvolatile NA NA NA NA 177 2.0 Carlton et al. 2008
AGLY v5.1 SOA from aerosol uptake of glyoxal, methylglyoxal NA NA-nonvolatile NA NA NA NA 66.40 2.13 Pye et al. 2015 Liggio et al. 2005
AMTNO3 v5.1 TERP organic nitrates OH/NO,NO3 MTNO3 NA 12.0 40 NA 231 1.9 Pye et al. 2015 Fry et al. 2009
AISOPNN v5.1 ISOP+NO3 organic nitrates NO3 ISOPNN NA 8.9 40 NA 226 3.8 Pye et al. 2015 Rollins et al. 2009
AMTHYD v5.1 AISOPNN+AMTNO3 NA-hydrolysis NA-nonvolatile NA NA NA NA 185 1.54 Pye et al. 2015 Boyd et al. 2015
AIETET v5.1 IEPOX NA-acid catalyzed uptake NA-nonvolatile NA NA NA NA 136.15 2.27 Pye et al. 2013 Eddingsaas et al. 2010
AIEOS v5.1 IEPOX NA-acid catalyzed uptake NA-nonvolatile NA NA NA NA 216.20 3.6 Pye et al. 2013 Eddingsaas et al. 2010
AIDIM v5.1 IEPOX NA-acid catalyzed uptake NA-nonvolatile NA NA NA NA 248.23 2.07 Pye et al. 2013 Eddingsaas et al. 2010
AIMGA v5.1 MAE+HMML NA-acid catalyzed uptake NA-nonvolatile NA NA NA NA 120.10 2.5 Pye et al. 2013 Eddingsaas et al. 2010
AIMOS v5.1 MAE+HMML NA-acid catalyzed uptake NA-nonvolatile NA NA NA NA 200.16 4.17 Pye et al. 2013 Eddingsaas et al. 2010

The reference temperature for table properties (C* and enthalpy) is 298 K.

If more than one gas-phase precursor is named, the first name corresponds to CB05 and the second to SAPRC07.

All SV_* gas-phase semivolatiles use a dry deposition surrogate of ORA (acetic acid, H-law=4.1e3 M/atm) and a wet deposition surrogate of ADIPIC ACID (H-law=2.0e8 M/atm).

Number of carbons is used to conserve carbon upon oligomerization to nonvolatile form.

Summary of changes

New Species

Table 3: New species in SAPRC07tic_ae6i

New Species Phase Description
HCOCO3 gas Peroxy radical from H-abstraction of glyoxal
IMACO3 gas Peroxyacyl radicals formed from methacrolein + OH abstraction channel
IMPAA gas Methacrylicperoxy acid
IMAPAN gas Methacryloyl peroxy nitrate
IMAE gas Methacrylic acid epoxide
IHMML gas Hydroxymethyl-methyl-α-lactone
AIETET aerosol 2-methyltetrols from IEPOX uptake onto particles
AIEOS aerosol IEPOX-derived organosulfate from IEPOX uptake onto particles
ADIM aerosol IEPOX-derived oligomers from IEPOX uptake onto particles
AIMGA aerosol 2-methylglyceric acid from MAE+HMML uptake onto particles
AIMOS aerosol MAE-derived organosulfate from MAE+HMML uptake onto particles
SOAALK gas Alkane SOA precursor, C6 and longer cyclic, C8 and larger linear/branched alkanes, equivalent to ~10% of ALK4 + 70% of ALK5
NAPHTHAL gas PAH SOA precursor/naphthalene, products are the same as ARO2MN with exception of PAHRO2 reaction counter
ARO2MN gas ARO2 minus naphthalene
AH3OP aerosol Hydronium ion (predicted by ISORROPIA)
APAH1,2,3 aerosol PAH (naphthalene) aerosol
AALK1,2 aerosol alkane aerosol
AGLYJ aerosol glyoxal/methylglyoxal aerosol due to uptake on particles
AISOPNNJ aerosol SOA from isoprene dinitrates (C*=8.9 ug/m3)
AMTHYDJ aerosol SOA from hydrolysis of particle-phase organic nitrates
AMTNO3J aerosol SOA from monoterpene nitrates (C*=12 ug/m3)
ISOPNN* gas second generation isoprene dinitrate from NO3 reaction
MTNO3 gas monoterpene(TERP)-derived organic nitrates (exluding alpha-pinene)
TERPNRO2 gas TERP+NO3 peroxy radical

*PROPNN (an existing species) was modified to include isoprene nitrates from NO3 reaction that only have one nitrate (formerly PROPNNB). PROPNNB with two nitrate groups was mapped to ISOPNN.

Removed Species

NO2EX: Excited NO2

AALKJ: Alkane aerosol

PROPNNB: Second generation isoprene nitrate from isoprene+NO3, combined with PROPNN or respeciated as ISOPNN (dinitrate) depending on expected nitrate functionality

New files

  • MECHS/saprc07tic_ae6i/*
  • gas/ebi_saprc07tic_ae6i/*
  • aero/aero6i/*

Significance and Impact

  • Increased isoprene SOA in isoprene source regions at all hours of day
  • Significantly increased SOA at night due to MTNO3 partitioning
  • Increased SOA at all hours due to glyoxal/methylglyoxal uptake
  • Increased formaldehyde and acetaldehyde

Other information

Calculation of OC and OM (for species definition file and combine). Be sure to check the spacing and place on one line before using. 

AOCIJ           ,ugC/m3    ,(AXYL1J[1]+AXYL2J[1]+AXYL3J[1])/2.0+
(ATOL1J[1]+ATOL2J[1]+ATOL3J[1])/2.0+
(ABNZ1J[1]+ABNZ2J[1]+ABNZ3J[1])/2.0 +
(AISO1J[1]+AISO2J[1])/1.6+AISO3J[1]/2.7+
(ATRP1J[1]+ATRP2J[1])/1.4+ASQTJ[1]/2.1+
0.64*(AALK1J[1]+AALK2J[1])+
AORGCJ[1]/2.0+(AOLGBJ[1]+AOLGAJ[1])/2.1+
APOCI[1]+APOCJ[1]+
APAH1J[1]/2.03+APAH2J[1]/2.03+APAH3J[1]/2.03+
AIETETJ[1]/2.27+AIEOSJ[1]/3.6+ADIMJ[1]/2.07+AIMGAJ[1]/2.5+AIMOSJ[1]/4.17+
AMTNO3J[1]/1.9+AISOPNNJ[1]/3.8+AMTHYDJ[1]/1.54+
AGLYJ[1]/2.13

AOMIJ           ,ug/m3  ,AXYL1J[1]+AXYL2J[1]+AXYL3J[1]+
ATOL1J[1]+ATOL2J[1]+ATOL3J[1]+
ABNZ1J[1]+ABNZ2J[1]+ABNZ3J[1]+
AISO1J[1]+AISO2J[1]+ATRP1J[1]+ATRP2J[1]+ASQTJ[1]+
(AALK1J[1]+AALK2J[1])+AORGCJ[1]+
APOCI[1]+APOCJ[1]+APNCOMI[1]+APNCOMJ[1]+
APAH1J[1]+APAH2J[1]+APAH3J[1]+
AIETETJ[1]+AIEOSJ[1]+ADIMJ[1]+AIMGAJ[1]+AIMOSJ[1]+
AMTNO3J[1]+AISOPNNJ[1]+AMTHYDJ[1]+AGLYJ[1]


References

Boyd, C. M.; Sanchez, J.; Xu, L.; Eugene, A. J.; Nah, T.; Tuet, W. Y.; Guzman, M. I.; Ng, N. L., Secondary organic aerosol formation from the b-pinene+NO3 system: effect of humidity and peroxy radical fate. Atmos. Chem. Phys. 2015, 15 (13), 7497-7522. article

Carlton, A. G.; Bhave, P. V.; Napelenok, S. L.; Edney, E. D.; Sarwar, G.; Pinder, R. W.; Pouliot, G. A.; Houyoux, M., Model representation of secondary organic aerosol in CMAQv4.7. Environmental Science & Technology 2010, 44 (22), 8553-8560. article

Carlton, A. G.; Turpin, B. J.; Altieri, K. E.; Seitzinger, S. P.; Mathur, R.; Roselle, S. J.; Weber, R. J., CMAQ Model Performance Enhanced When In-Cloud Secondary Organic Aerosol is Included: Comparisons of Organic Carbon Predictions with Measurements. Environmental Science & Technology 2008, 42 (23), 8798-8802. article

Carter, W. P. L.; Heo, G., Development of revised SAPRC aromatics mechanisms. Atmos. Environ. 2013, 77 (0), 404-414. article

Chan, A. W. H.; Kautzman, K. E.; Chhabra, P. S.; Surratt, J. D.; Chan, M. N.; Crounse, J. D.; Kurten, A.; Wennberg, P. O.; Flagan, R. C.; Seinfeld, J. H.Secondary organic aerosol formation from photooxidation of naphthalene and alkylnaphthalenes: Implications for oxidation of intermediate volatility organic compounds (IVOCs) Atmos. Chem. Phys. 2009, 9 (9), 3049-3060. article

Crounse, J. D.; Knap, H. C.; Ornso, K. B.; Jorgensen, S.; Paulot, F.; Kjaergaard, H. G.; Wennberg, P. O., Atmospheric Fate of Methacrolein. 1. Peroxy Radical Isomerization Following Addition of OH and O-2. J. Phys. Chem. A. 2012, 116 (24), 5756-5762. article

Eddingsaas, N. C.; VanderVelde, D. G.; Wennberg, P. O., Kinetics and products of the acid-catalyzed ring-opening of atmospherically relevant butyl epoxy alcohols. J. Phys. Chem. A. 2010, 114 (31), 8106-8113. article

Fry, J. L.; Kiendler-Scharr, A.; Rollins, A. W.; Wooldridge, P. J.; Brown, S. S.; Fuchs, H.; Dubé, W.; Mensah, A.; dal Maso, M.; Tillmann, R.; Dorn, H. P.; Brauers, T.; Cohen, R. C., Organic nitrate and secondary organic aerosol yield from NO3 oxidation of β-pinene evaluated using a gas-phase kinetics/aerosol partitioning model. Atmos. Chem. Phys. 2009, 9 (4), 1431-1449. article

Fu, T.-M.; Jacob, D. J.; Wittrock, F.; Burrows, J. P.; Vrekoussis, M.; Henze, D. K., Global budgets of atmospheric glyoxal and methylglyoxal, and implications for formation of secondary organic aerosols. J. Geophys. Res. 2008, 113 (D15), D15303. article

Griffin, R. J.; Cocker, D. R.; Flagan, R. C.; Seinfeld, J. H., Organic aerosol formation from the oxidation of biogenic hydrocarbons. J. Geophys. Res. 1999, 104 (D3), 3555-3567. article

Kalberer, M.; Paulsen, D.; Sax, M.; Steinbacher, M.; Dommen, J.; Prevot, A. S. H.; Fisseha, R.; Weingartner, E.; Frankevich, V.; Zenobi, R.; Baltensperger, U., Identification of polymers as major components of atmospheric organic aerosols. Science 2004, 303 (5664), 1659-1662. article

Kroll, J. H.; Ng, N. L.; Murphy, S. M.; Flagan, R. C.; Seinfeld, J. H., Secondary organic aerosol formation from isoprene photooxidation. Environ. Sci. Technol. 2006, 40 (6), 1869-1877. article

Lee, L.; Teng, A. P.; Wennberg, P. O.; Crounse, J. D.; Cohen, R. C., On Rates and Mechanisms of OH and O-3 Reactions with Isoprene-Derived Hydroxy Nitrates. J. Phys. Chem. A. 2014, 118 (9), 1622-1637. article

Liggio, J.; Li, S.-M.; McLaren, R., Reactive uptake of glyoxal by particulate matter. J. Geophys. Res. 2005, 110 (D10), D10304.article

Lin, Y.-H.; Zhang, H.; Pye, H. O. T.; Zhang, Z.; Marth, W. J.; Park, S.; Arashiro, M.; Cui, T.; Budisulistiorini, S. H.; Sexton, K. G.; Vizuete, W.; Xie, Y.; Luecken, D. J.; Piletic, I. R.; Edney, E. O.; Bartolotti, L. J.; Gold, A.; Surratt, J. D., Epoxide as a precursor to secondary organic aerosol formation from isoprene photooxidation in the presence of nitrogen oxides. Proc. Natl. Acad. Sci. USA. 2013, 110 (17), 6718-6723. article

Ng, N. L.; Kroll, J. H.; Chan, A. W. H.; Chhabra, P. S.; Flagan, R. C.; Seinfeld, J. H., Secondary organic aerosol formation from m-xylene, toluene, and benzene. Atmos. Chem. Phys. 2007, 7 (14), 3909-3922. article

Presto, A. A.; Miracolo, M. A.; Donahue, N. M.; Robinson, A. L.Secondary organic aerosol formation from high-NOx photo-oxidation of low volatility precursors: n-alkanes Environ. Sci. Technol. 2010, 44, 2029– 2034. article

Pye, H. O. T., D. J. Luecken, L. Xu, C. M. Boyd, N. L. Ng, K. Baker, B. A. Ayres, J. O. Bash, K. Baumann, W. P. L. Carter, E. Edgerton, J. L. Fry, W. T. Hutzell, D. Schwede, P. B. Shepson, Modeling the current and future roles of particulate organic nitrates in the southeastern United States, Environ. Sci. Technol., 2015. article

Pye, H. O. T., R. W. Pinder, I. Piletic, Y. Xie, S. L. Capps, Y.-H. Lin, J. D. Surratt, Z. Zhang, A. Gold, D. J. Luecken, W. T. Hutzell, M. Jaoui, J. H. Offenberg, T. E. Kleindienst, M. Lewandowski, and E. O. Edney, Epoxide pathways improve model predictions of isoprene markers and reveal key role of acidity in aerosol formation, Environ. Sci. Technol., 2013, 47 (19), 11056-11064. article

Pye, H. O. T. and G. A. Pouliot, Modeling the role of alkanes, polycyclic aromatic hydrocarbons, and their oligomers in secondary organic aerosol formation, Environ. Sci. Technol., 2012, 46 (11), 6041-6047. article

Rollins, A. W.; Kiendler-Scharr, A.; Fry, J. L.; Brauers, T.; Brown, S. S.; Dorn, H. P.; Dubé, W. P.; Fuchs, H.; Mensah, A.; Mentel, T. F.; Rohrer, F.; Tillmann, R.; Wegener, R.; Wooldridge, P. J.; Cohen, R. C., Isoprene oxidation by nitrate radical: alkyl nitrate and secondary organic aerosol yields. Atmos. Chem. Phys. 2009, 9 (18), 6685-6703. article

Simon, H. and P. V. Bhave, Simulating the degree of oxidation in atmospheric organic particles, Environ. Sci. Technol., 2012, 46, 331-339, 2012. article

Xie, Y.; Paulot, F.; Carter, W. P. L.; Nolte, C. G.; Luecken, D. J.; Hutzell, W. T.; Wennberg, P. O.; Cohen, R. C.; Pinder, R. W., Understanding the impact of recent advances in isoprene photooxidation on simulations of regional air quality. Atmos. Chem. Phys. 2013, 13 (16), 8439-8455. article

Contact

Havala Pye, NERL, U.S. EPA

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