CMAQ v5.1 CB05 updates

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Brief Description

Multiple changes were made in the v5.02 release version of CB05, now referred to as CB05e51. These include:

  • Updates to reactions of NOy species and an expanded description of alkyl nitrates in order to better characterize the NOx cycling and removal through different pathways,
  • Incorporation of new research on the atmospheric reactivity of products of isoprene photooxidation, including both high NOx and high HOx pathways,
  • Addition of several high priority HAPs to the standard version of CB05e51 as active species or tracers following protocol in CMAQ-MP, and
  • Other changes to update the mechanism and make it compatible with updates to aerosol chemistry.

Minor changes were made to the previous model release version CB05tucl to make it compatible with aerosol updates. The name remains CB05tucl.

CB05e51 Mechanism Updates

Description of changes

NOy updates/additions

Peroxyacylnitrate updates: Modifications to peroxyacylnitrates were largely updates to be consistent with IUPAC, and to represent PANs from methacrolein by existing species OPAN:

  1. Added MEO2+NO3 model species as products of PAN photolysis
  2. Added ALD2+XO2+HO2+NO3 model species as products of PANX photolysis
  3. Corrected PAN thermal formation and degradation N values (add N=1.41, following Bridier et al., (1991)
  4. PANX formation rate corrected, as it is set equal to PAN. PANX decay rate set equal to PPN (based on IUPAC)
  5. Added explicit production of methacrolein acylperoxy radical and PAN to account for high NO2 formation of PANs and SOA precursor. CXO3 from isoprene reactions is replaced by MACO3.
  6. Added decay reactions of MAPAN with OH

NOx updates:

  1. The OH+NO2 reaction rate was updated to a Troe expression following IUPAC (
  2. A small yield of HNO3 was added to the reaction of HO2+NO following IUPAC (

Alkyl nitrate updates/additions:

  1. Replaced the one alkyl nitrate in CB05 with 7 species to better represent the variety of chemical and physical fates of alkyl nitrates
    1. 5 species are predominanently from anthropogenic sources, with distribution of functional groups and products were determined based on the top 5 alkanes and alkenes listed in the NEI inventory (Simon et al., 2010).
    2. 2 species represent biogenic (isoprene and terpene) sources. Biogenic nitrate products were based on reaction products from Lee et al., (2014), with some reaction rates and NOx recycling from Jenkin et al., (2015) and photolysis rates with QY of unity based on Muller et al., (2014).
  2. Added heterogeneous hydrolysis rate of alkyl nitrates based on formulation by B. Koo (Environ, 2015) based on Liu et al., (2012), with a 6 hr lifetime at high RH, and partitioning to aerosol from Rollins et al. (2013). (For reactions added to mech.def file, see Integration of gas and heterogeneous chemistry)

Isoprene extensions

The high HOx pathways for isoprene oxidation have been modified to explicitly account for production of isoprene epoxydiol, which can form SOA and modify the gas phase concentrations. The high NOx pathways have been modified to explicitly account for methacrolein PAN (MAPAN) which can form SOA via methyacrylic acid epoxide or hydroxymethylmethyl-a-lactone (Lin et al.,2013)

high HOx pathway:

  1. Separated out initial reaction of ISOP+OH to produce peroxy radical (explicitly represented isoprene peroxy radicals (ISOPO2).
  2. Added ISOPO2 reactions with NO, HO2, and C2O3
  3. ISOPO2+C2O3 and ISOPO2+ NO reactions are based on CB6r2, using XO2_CB05=(XO2+XO2H)CB6 HO2_CB05=(HO2+XO2H)CB6, GLY=PAR+FORM GLYD=ALD2
  4. ISOPO2+HO2 reaction was added, forming 100% yield of ISOPX (isoprene hydroperoxide)
  5. ISOPX + OH forms IEPOX (isoprene epoxydiol) plus OH with yield of 90%, with rate and products from CB6r2 (same treatment as in SAPRC07tic)
  6. IEPOX +OH forms IEPOXO2, which reacts with rate and products from CB6r2
  7. Changed products of OH+ISPD reaction

high NOx pathway:

  1. Represented CXO3 in O3+ISOP and IPSPD reactions as MACO3. This required separation of the C2O3 in ISPD photolysis into C2O3 and CXO3 as in the original condensed isoprene mechanism (Carter, 1996). This did not get changed in the transition from CB4 to CB05
  2. Added reaction of model species MACO3 and NO2 to make methacrolein peroxyacylnitrate (MAPAN)
  3. Add reaction of MAPAN with OH (unlike PAN, because it has a double bond)

Explicit representation of hazardous air pollutants (HAPS)

Several high priority HAPs were added to the standard version of CB05e51 as active species or tracers following protocol in CMAQ-MP; including:

  1. 1,3-butadiene was added as tracer for OH, and produces acrolein
  2. Toluene was added as tracer
  3. Xylene isomers were added as tracers, their reactivity is still included in model species XYL
  4. Alpha and beta-pinene were added as tracers
  5. Naphthalene was added as an active species, uses the same reaction rate and products as XYL, but produces PAHRO2 which forms SOA. Because it forms SOA, it is treated as an active species integral to the model.
  6. Removed naphthalene from previous lumped species XYL. All other species previously represented by XYL are now lumped into XYLMN, which retains the same reaction rate and product yields. The name change signifies that it no longer includes naphthalene

Other changes

  1. Updated ethanol chemistry, using yield from IUPAC (
    1. k1 --> converts NO to NO2, and 80%(2*HCHO+HO2) and 20% (hydroxyacetaldehyde+HO2)
    2. k2--> ALD2+HO2, k3--> ALD2+HO2 (100% reaction with O2)
  2. Included 44% yield of OH from model species C2O3 and CXO3 with HO2 consistent with IUPAC (
  3. Added emissions of SOAALK with acts as a tracer for SOA formation from alkanes; see SOA updates

New species

New Species Description
NTRALK, NALKO2 first generation, monofunctional alkylnitrate formed from PAR; peroxy radical from NTRALK+OH
NTROH, NOHO2 first generation, hydroxynitrate formed from PAR; peroxy radical from NTROH+OH
NTRCN, NCNO2 second generation difunctional carbonylnitrate; peroxy radical from NTRCN+OH
NTRCNOH, NCNOHO2 second generation hydroxycarbonylnitrate; peroxy radical from NTRCNOH+OH
NTRPX second generation multifunctional hydroperoxide nitrate formed through HO2 pathways
NTRM first generation isoprene nitrate
NTRI second generation isoprene nitrate
MACO3 peroxyacyl radical from methacrolein (makes MAPAN)
MAPAN peroxyaceylnitrate from methacrolein
ISOPX isoprene hydroperoxide
IEPOX, IEPOXO2 isoprene epoxydiol and peroxy radical formed from IEPOX+OH
XO2T operator to produce biogenic nitrate from terpene
XYLMN model species XYL without naphthalene
NAPH explicit naphthalene
PAHRO2 tracer for SOA precursor from naphthalene (NAPH)
BUTADIENE13 explicit 1,3-butadiene as reactive tracer; produces acrolein
AROLEIN acrolein as reactive tracer
TOLU explicit toluene as reactive tracer
MXYL, OXYL, PXYL explicit meta, ortho, para isomers of xylene as reactive tracers
APIN, BPIN explicit alpha and beta pinene as reactive tracers
HG, HGIIGAS, HGIIAER explicit reactive, gaseous and aerosol mercury, with HG as reactive tracer
CLNO2 nitrylchloride

Removed Species

NO2EX: Excited NO2

NTR: lumped alkylnitrate

XYL: naphthalene is now treated explicitly and removed from XYL. All other species previously represented in XYL are now included in new model species XYLMN

CB05tucl Mechanism Updates

Description of changes

Only minor modifications have been made to CB05tucl, in order to ensure compatibility with other updates in CMAQv5.1, including:

  • ClNO2 was added as a reactive species and first order ozone depletion parameterized from marine halogen chemistry was included.
  • integration of heterogeneous and homogeneous chemistry, including oligomerization reactions, POA aging, HONO production from NO2, and heterogeneous N2O5 reaction to produce HNO3

All other reaction rates, photochemical properties, product yields, etc. have remained as previously released in CMAQ v5.0.2, although other changes in CMAQv5.1 (changes in actinic flux, PBL, cloud descriptions) will impact predicted concentrations with this mechanism.

New Species

CLNO2: nitryl chloride

Removed Species

NO2EX: Excited NO2

Significance and Impact

The changes to CB05e51 allow alkyl nitrates to be more reactive and release NO2, while at the same time increasing the deposition of the more soluble alkyl nitrates. The alkylnitrate concentrations are decreased both through reaction and deposition. The PAN corrections result in less overall PAN through small formation rate and smaller degradation rate. The additional NO2 that becomes available from the degradation of nitrates and from the decreased PAN forms slightly more ozone.

Extensions for updated SOA, including the isoprene and naphthalene changes, allow for a more kinetic/mechanistic representation of SOA formation (see SOA updates) and compatiblity with heterogeneous changes (see Integration of gas and heterogeneous chemistry; CMAQv5.1 ClNO2 chemistry).

Affected files


  • cloud/acm_ae6 (added Henry's Law constants for alkyl nitrates to hlconst.F)
  • depv/m3dry (added dry deposition for alkyl nitrates to m3dry.F)
  • aero/aero6 (added hydrolysis to AEROSOL_CHEMISTRY.F)
  • gas/ebi_cb05e51_ae6_aq (modified ebi solver files to match mechanism)
  • MECHS/cb05e51_ae6_aq


  • gas/ebi_cb05tucl_ae6_aq (modified ebi solver files to match mechanism)
  • MECHS/cb05tucl_ae6_aq


Bridier, I., et al., 1991, Kinetic and theoretical studies of the reactions acetylperoxy + nitrogen dioxide + acetyl peroxynitrate + M between 248 and 393 K and between 30 and 760 torr, The Journal of Physical Chemistry 95(9): 3594-3600.

Carter, W.P.L., 1996, Condensed atmospheric photooxidation mechanisms for isoprene, Atmos. Env., 30(24): 4275-4290.article

Jenkin, M.E. et al., 2015, The MCM v3.3 degradation scheme for isoprene, Atmos. Chem. Phys. Disc., 15: 9709-9766.

Lee, L., et al., 2014, On Rates and Mechanisms of OH and O3 Reactions with Isoprene-Derived Hydroxy Nitrates, The Journal of Physical Chemistry A 118(9): 1622-1637.

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

Liu, S. et al., 2012, Hydrolysis of organonitrate functional groups in aerosol particles, Aerosol Sci. Tech., 46: 1359-1369.

Muller, J.P., et al., 2014, Fast photolysis of carbonyl nitrates from isoprene, Atmos. Chem. Phys., 14, 2497–2508.

Rollins, A.W. et al., 2013, Gas/particle partitioning of total alkyl nitrates observed with TD-LIF in Bakersfield, J. Geophys. Res., 118(12): 6651-6662.article

Simon, H., et al., 2010, The development and uses of EPA's SPECIATE database, Atmospheric Pollution Research 1(4): 196-206


Deborah Luecken, National Exposure Research Laboratory, U.S. EPA