CMAQv5.0 Chemistry Notes

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Chemical Mechanisms supported in CMAQv5.0Beta

Aero5 Aero6
CB05CL cb05cl_ae5_aq cb05cl_ae6_aq
CB05TUCL cb05tucl_ae5_aq cb05tucl_ae6_aq
SAPRC99 saprc99_ae5_aq saprc99_ae6_aq
SAPRC07TB saprc07tb_ae5_aq saprc07tb_ae6_aq
SAPRC07TC saprc07tc_ae5_aq saprc07tc_ae6_aq
CB05TUMP Not Available cb05tump_ae6_aq


Golam Sarwar

Changes to the CB05 mechanism include updates in toluene chemistry, updates in homogeneous hydrolysis rate constants for dinitrogen pentoxide (N2O5), and updates in chlorine chemistry. Whitten et al., (2010) developed a new condensed toluene chemistry for the CB05 mechanism. The new toluene chemistry has been implemented into the CB05 mechanism. The International Union of Pure and Applied Chemistry (IUPAC) now suggest using only the bimolecular homogeneous hydrolysis of N2O5 and also recommend a lower rate constant for the reaction. As such, we have assigned a rate constant of zero for the termolecular homogeneous hydrolysis of N2O5 and reduced the rate constant for the bimolecular reaction ( The existing chlorine chemistry contains 21 reactions involving chlorine. It, however, does not include any reaction for toluene and xylene. Greg Yarwood of ENVIRON International Corporation recently developed such reactions which are now included in the mechanism.

Corrected typographical errors in reaction R137 and R138 (CRON changed to CRNO in both reactions) in the CB05TUCL mechanism.

Updated the toluene and xylene reactions with chlorine radical in the in the CB05TUCL mechanism. Products of the TOL + CL and XYL + CL reactions are revised based on the suggestion of Greg Yarwood.

The use of updated CB05 mechanism produces more ozone both in summer and winter. It reduces mean bias of daily maximum 8-hr ozone at high observed ozone (>80 ppbv) in summer. However, it also slightly increases mean bias of daily maximum 8-hr ozone at low observed ozone in summer. It reduces mean bias of daily maximum 8-hr ozone at high observed ozone in winter. It produces less nitric acid and aerosol nitrate in summer. Impact on nitric acid and aerosol nitrate in winter is mixed. In winter, it produces less nitric acid and aerosol nitrate in some areas while more in other areas. Nighttime nitric acid production decreases in winter but daytime production increases in some locations (e.g. Chicago). Average model performance slightly improves for nitric acid and aerosol nitrate in both months. It slightly increases aerosol sulfate production in winter and summer months (≈1.5% increase in winter, ≈0.8% increase in summer). Changes in ammonium are relatively small. Sarwar et al. (2011) describes the impact of the new condensed toluene mechanism on air quality model predictions in more details.


Whitten et al., a new condensed toluene mechanism for Carbon Bond: CB05-TU. Atmospheric Environment, 44, 5346-5355, 2010.

Sarwar, et al., impact of a new condensed toluene mechanism on air quality model predictions in the US, Geosci. Model Dev.,4, 1-11, 2011.

Affected files:

mech.def, RXCM.EXT, RXDT.EXT, GC_cb05tucl_ae5_aq_recon.csv, GC_cb05tucl_ae5_aq_recon.nml, hrdriver.F, hrcalcks.F, hrdata_mod.F, hrg1.F, hrg2.F, hrg3.F, hrg4.F, hrinit.F, hrprodloss.F, hrrates.F, hrsolver.F


Bill Hutzell

The SAPRC07T mechanisms update the SAPRC99 mechanism. They differ from the SAPRC07 mechanism presented by Carter (2010a, and 2010b) because the SAPRC07T mechanisms include species that permit simulating reactive organic compounds (such as propene, ethanol, 1,2,4-trimethylbenzene) and Hazardous Air Pollutants (such as acrolein, 1,3-butadiene, toluene, isomers of xylene). Species in SAPRC07T also represent compounds that are suspected to form Secondary Organic Aerosols either by gas phase or cloud droplet chemistry (such as glycoaldehyde, sesquiterpenes, and alpha-pinene).

Two versions of SAPRC07T are available at The SAPRC07TB version is preferred in CMAQ for reasons given below. The other version is SAPRC07TC. The mechanisms have the same species and give the same predictions but differ in the numerical expressions of reaction rates. SAPRC07TB introduces a new way to express rates. They are defined in the SPECIAL block within the mechanism definitions file and the "?" character denotes their usage by a reaction. The expressions are used to decrease model runtimes and equal the sum of products between standard rate constants and model species. The below insert attempts to show how these new rates expressions are used. To compute their values, the Gear and Rosenbrock solvers for gas phase chemistry were revised and each are supplemented with a new subroutine to accomplish the task. For the assignments to the emissions used by the mechanism, the above website gives the assignments employed by the Speciation Tool.

SPECIAL rate expression block is from mechanism defintion files for SAPRC07TB. 
K<X> and C<Y> refer to reaction labeled X and species 
concentration labeled Y in the REACTIONS block.

RO2NO = K<BR07>*C<NO>;
RO2HO2 = K<BR08>*C<HO2>;
RO2NO3 = K<BR09>*C<NO3>;
RO2RO2 = K<BR10>*C<MEO2> + K<BR11>*C<RO2C> + K<BR11>*C<RO2XC>;
RO2RO3 = K<BR25>*C<MECO3> + K<BR25>*C<RCO3> + K<BR25>*C<BZCO3> +
RO2RO = RO2NO + RO2NO3 + RO2RO3 + 0.5*RO2RO2;
RO2XRO = RO2HO2 + 0.5*RO2RO2;
RO2RO2M = 0.5*RO2RO2;
RO22NN = RO2NO3 + RO2RO3 + 0.5*RO2RO2;
end special

The below extract from the SAPRC07TB mechanism defintion file illustrates
how to use the special rate expressions as in reactions PO35, PO36 and PO37.

<1> NO2 = NO + O3P # 1.0/<NO2_06>;
<2> O3P + O2 + M = O3 # 5.68e-34^-2.60;
<3> O3P + O3 =  # 8.00e-12@2060;
<PO35> zRNO3 = RNO3 - 1*XN # 1.0?RO2NO;
<PO36> zRNO3 = PRD2 + HO2 # 1.0?RO22NN;
<PO37> zRNO3 = 6*XC # 1.0?RO2XRO;


Carter, W.P.L., 2010a. Documentation of the SAPRC-07 chemical mechanism and updated ozone reactivity scales. Report to the California Air Resources Board, January 27, 2010. Available at

Carter, W.P.L., 2010b. Development of the SAPRC-07 Chemical Mechanism. Atmospheric Environment 44, 5336-5345.


Bill Hutzell and Jesse Bash

The mechanism, species and runtime options are described under sections for Multi-Pollutant Modeling Mechanism and Species and Bidirectional Exchange of Hg0