Halogen chemistry mechanism

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Overview

The halogen simulation present in GEOS-Chem v11-2d was build atop of GEOS-Chem v10-01 and brought into the main code branch at v11-01g. This code brings together published halogen developments in GEOS-Chem as described in detail by Sherwen et al [2016b], including the methyl iodide simulation [Bell et al 2002], the iodine simulation from Sherwen et al [2016a], the original bromine simulation in GEOS-Chem [Parrella et al 2012], the UCX simulation including stratospheric halogens [Eastham et al 2014], updates to bromine mechanism [Schmidt et al 2016]. Further updates were made use NASA JPL15-10 halogen cross-sections and rates by Sherwen et al [2017].

The gas-phase chemistry follows Sherwen et al [2016b], with updates made to the heterogenous code to work with structural changes from v10-01 to v11-01.

Key additions vs. v10-01:

  • Addition of 21 new tracers. All halogen tracers are shown below, with new ones in bold. This includes five aerosol tracers for bromine (BrSALA, BrSALC) and iodine (ISALA, ISALC, AERI).
CHCl3 IONO BrNO2 HCFC142b Cl2O2
CH2Cl2 IONO2 BrNO3 CFC11 INO
CH3I I2O2 CHBr3 CFC12 HBr
CH2I2 I2O3 CH2Br2 HCFC22 HCFC141b
CH2ICl I2O4 CH3Br H1211 Cl2
CH2IBr ISALA BrCl H1301 OIO
HOI ISALC HCl H2402 HOBr
I2 AERI CCl4 Cl HCFC123
IBr BrSALA CH3Cl ClO OClO
ICl BrSALC CH3CCl3 HOCl
I Br2 CFC113 ClNO3
IO Br CFC114 ClNO2
HI BrO CFC115 ClOO
  • Emissions of iodocarbons (CH3I, CH2I2, CH2ICl, CH2IBr) have been included following Ordonez et al [2012]. Emissions of inorganic iodine (HOI, I2) has been using the parameterisation from Carpenter et al [2013] and Macdonald et al [2014].
  • Wet deposition of X species (HOCl, ClNO3, HI, HOI, INOy, I2OX, AERI) and dry deposition of Y species (HI, HOI, INOy, I2OX, AERI).

Chlorine

Stratospheric chlorine chemistry is from UCX [Eastham et al 2014]. Tropospheric chlorine chemistry follows that described in Eastham et al [2014] and Schmidt et al [2016], with additions described in Sherwen et al [2016b]. These additions include tropospherically relevant reactions based on the JPL 10-6 compilation [Sander et al., 2011] and IUPAC [Atkinson et al., 2006]. The heterogenous reaction of N2O5 on aerosols was updated to yield products of ClNO2 and HNO3 [Bertram and Thornton, 2009; Roberts et al., 2009] on sea salt and 2HNO3 on other aerosol types. Reaction probabilities are unchanged [Evans and Jacob, 2005].

Bromine

The bromine simulation incorporates the work of Parrella et al [2012] (See wiki article here on incorporation in earlier versions), with updates (especially to heterogenous process) as described in detail by Schmidt et al [2016]. Minor updates to Schmidt et al [2016] are described in Sherwen et al [2016b].

Iodine

The iodine simulation is described in Sherwen et al [2016a], with updates to coupling with bromine and chlorine described in Sherwen et al [2016b]. Notably, the cycling of iodine on aerosol now results in production of ICl and IBr, instead of I2 as in Sherwen et al [2016a].

Key differences from publications

Certain changes were made during implementation of the halogens code in v10-01 into v11-02 that are not described in Sherwen et al (2016b). These include:

  • In combination with UCX [Eastham et al 2014], halogen chemistry is calculated online for both troposphere and stratosphere. In Sherwen et al [2016, 2016b] the troposphere was calculated offline.
  • Updates to heterogeneous chemistry (see detail below).
  • Minor deposition routes included in previous publications were removed for simplicity (Br2, ICl, IBr, I2).
  • Rates were updated following the JPL15-10 complication [Sherwen et al 2017]. Rates were also updated to more consistently use JPL over alternative options (e.g. vs IUPAC).
  • Updates to VOCs (inc. oceanic acetaldehyde source) in the simulation (see “PAN updates”) will decrease Bry mixing ratios and therefore halogen impacts.

Changes in heterogeneous chemistry

Due to updates structuctural changes in GEOS-Chem (aka Flexchem making the smvgear mechanism obsolete), the heterogenous chemistry routines have been updated to allow for use of more complex heterogenous chemistry previously calculated in Calcrate.F [Eastham et al 2014, Schmidt et al. 2016, Sherwen et al 2016b].

This work required a revamp of the heterogeneous chemistry. As a result, all heterogeneous reactions except for direct uptake (e.g. HO2) and those involving sea salt Cl- (which is not explicitly tracked) are now calculated using a second-order rate constant. This should help to make the het-chem easier to extend, as new functions have been implemented which will automatically convert a pseudo-first-order rate constant into a second order constant while performing safety checks and imposing (if requested) limits on depletion rates to avoid instability.

Inclusion of sulfur-halogen chemistry from Chen et al [2016]

Sulfur oxidation by reactive halogens as described by Chen et al [2016] was included in the same development branch (v11-2d) of the GEOS-Chem code ("Sulfur oxidation by reactive halogens").

From Chen et al [2016]:

Sulfur and reactive bromine (Bry) play important roles in tropospheric chemistry and the global radiation budget. The oxidation of dissolved SO2 (S(IV)) by HOBr increases sulfate aerosol abundance and may also impact the Bry budget, but is generally not included in global climate and chemistry models. In this study, we implement HOBr + S(IV) reactions into the GEOS-Chem global chemical transport model and evaluate the global impacts on both sulfur and Bry budgets. Modeled HOBr mixing ratios on the order of 0.1–1.0 parts per trillion (ppt) lead to HOBr + S(IV) contributing to 8% of global sulfate production and up to 45% over some tropical ocean regions with high HOBr mixing ratios (0.6–0.9 ppt). Inclusion of HOBr + S(IV) in the model leads to a global Bry decrease of 50%, initiated by the decrease in bromide recycling in cloud droplets. Observations of HOBr are necessary to better understand the role of HOBr + S(IV) in tropospheric sulfur and Bry cycles.

Text S2 in the supporting document for Chen et al [2016] describes the parameterisation of HOBr + S(IV) reactions now included in GEOS-Chem.

Key differences in Simulation

In addition to changes seen on implementation of halogen chemistry in v10-01 detailed in publications [Eastham et al 2014, Schmidt et al. 2016, Sherwen et al 2016b]. Please find some details on changes to the standard simulation seen (full 1yr benchmark plots are found [ linked here]).

Differences in oxidants

< insert benchmark comparisons of O3 code here - using the gridded O3 dataset from Sofen et al >

Source code and data files

A monthly inventory of Iodocarbon emissions are included from Ordonez et al. [2012]. These files were the result of a project lead by Alfonso Saiz-Lopez and he has kindly allowed for them to be distributed with the main GEOS-Chem code.

These new data files are contained in the HEMCO data directory tree. For detailed instructions on how to download these data files to your disk server, please see our Downloading the HEMCO data directories wiki post.

Known issues

  • The reimplementation into GEOS-Chem v11-2 code is currently only compatible with the standard simulation (e.g. cannot be compiled with a setting of “NO_REDUCED=no”).
  • CH3I is not currently calculated on-line. Instead the emissions of Bell et al [2002] are currently read in from an offline NetCDF.
  • For consistency with published work. Certain reactions that are included in the stratosphere (e.g. ClNO3+HCl, BrNO3+HCl, HOCl+HCl and HOCl+HBr) remain unconsidered in the troposphere.
  • ClNO2 production on sulfate following condensation of HCl is not considered (HCl+N2O5=(sulfate aerosol)>ClNO2) for consistency with Sherwen et al 2016b.
  • The “uptake” reaction of HCl results in destruction of Cl, as there is no aerosol-phase Cl tracer.
  • There are only aerosol-phase bromine tracers for sea-salt, so Bry uptake cannot occur on sulfate.
  • Release of IX by heterogenous iodine cycling (HOI, INOy) leads to net production of Cly and Bry as no aqueous phase Cl/Br is considered in the reaction (e.g. excess Cl-/Br- is assumed).

Previous issues that are now resolved

None yet

References

  1. Bell, N., L. Hsu, D. J. Jacob, M. G. Schultz, D. R. Blake, J. H. Butler, D. B. King, J. M. Lobert, and E. Maier-Reimer (2002), Methyl iodide: Atmospheric budget and use as a tracer of marine convection in global models, J. Geophys. Res-Atmos., 107(D17), ACH 8-1–ACH 8-12, doi:http://dx.doi.org/10.1029/2001jd001151
  2. Eastham, S. D., D. K. Weisenstein, and S. R. H. Barrett (2014), Development and evaluation of the unified tropospheric–stratospheric chemistry extension (UCX) for the global chemistry-transport model GEOS-Chem, Atmos. Environ., 89, 52–63, doi:http://dx.doi.org/10.1016/j.atmosenv.2014.02.001
  3. Parrella, J. P. et al. (2012), Tropospheric bromine chemistry: implications for present and pre-industrial ozone and mercury, Atmos. Chem. Phys., 12(15), 6723–6740, doi:http://dx.doi.org/10.5194/acp-12-6723-2012
  4. Schmidt, J. A. et al. (2016), Modeling the observed tropospheric BrO background: Importance of multiphase chemistry and implications for ozone, OH, and mercury, J Geophys. Res-Atmos., doi:http://dx.doi.org/10.1002/2015JD024229
  5. Sherwen, T. et al. (2016a), Iodine’s impact on tropospheric oxidants: a global model study in GEOS-Chem, Atmos. Chem. Phys., 16(2), 1161–1186, doi:http://dx.doi.org/10.5194/acp-16-1161-2016
  6. Sherwen, T. et al. (2016b), Global impacts of tropospheric halogens (Cl, Br, I) on oxidants and composition in GEOS-Chem, Atmos. Chem. Phys., 16(18), 12239–12271, doi:http://dx.doi.org/10.5194/acp-16-12239-2016
  7. MacDonald, S. M., J. C. Gómez Martín, R. Chance, S. Warriner, A. Saiz-Lopez, L. J. Carpenter, and J. M. C. Plane (2014), A laboratory characterisation of inorganic iodine emissions from the sea surface: dependence on oceanic variables and parameterisation for global modelling, Atmos. Chem. Phys., 14(11), 5841–5852, doi:http://dx.doi.org/10.5194/acp-14-5841-2014
  8. Carpenter, L. J., S. M. MacDonald, M. D. Shaw, R. Kumar, R. W. Saunders, R. Parthipan, J. Wilson, and J. M. C. Plane (2013), Atmospheric iodine levels influenced by sea surface emissions of inorganic iodine, Nat. Geosci., 6(2), 108–111, doi:http://dx.doi.org/10.1038/ngeo1687
  9. Ordóñez, C., Lamarque, J.-F., Tilmes, S., Kinnison, D. E., Atlas, E. L., Blake, D. R., Sousa Santos, G., Brasseur, G., and Saiz-Lopez, A.: Bromine and iodine chemistry in a global chemistry-climate model: description and evaluation of very short-lived oceanic sources, Atmos. Chem. Phys., 12, 1423–1447, doi:http://dx.doi.org/10.5194/acp-12-1423-2012 , 2012
  10. Tomás Sherwen, Mathew John J Evans, Roberto Sommariva, Lloyd D. J. Hollis, Stephen Ball, Paul Monks, Christopher Reed, Lucy Carpenter, James D Lee, Grant Forster, Brian Bandy, Claire Reeves and William Bloss, Effects of halogens on European air-quality, Faraday Discussions, 200, 2017, DOI:http://dx.doi.org/10.1039/c7fd00026j
  11. Chen, Q., J. A. Schmidt, V. Shah, L. Jaeglé, T. Sherwen, and B. Alexander, Sulfate production by reactive bromine: Implications for the global sulfur and reactive bromine budgets, Geophys. Res. Lett., 44, 7069–7078, doi:http://dx.doi.org/10.1002/2017GL073812, 2017
  12. Bertram, T. H. and Thornton, J. A.: Toward a general parameterization of N2O5 reactivity on aqueous particles: the competing effects of particle liquid water, nitrate and chloride, Atmos. Chem. Phys., 9, 8351-8363, https://doi.org/10.5194/acp-9-8351-2009, 2009
  13. Sander, S. P., Friedl, R. R., Abbatt, J. P. D., Barker, J. R., Burkholder, J. B., Golden, D. M., Kolb, C. E., Kurylo, M. J., Moortgat, G. K., Wine, P. H., Huie, R. E., and Orkin, V. L.: Chemical kinetics and photochemical data for use in atmospheric studies, Evaluation Number 17, Tech. rep., NASA Jet Propulsion Laboratory, 2011
  14. Atkinson, R., Baulch, D. L., Cox, R. A., Crowley, J. N., Hampson, R. F., Hynes, R. G., Jenkin, M. E., Rossi, M. J., Troe, J., and IUPAC Subcommittee: Evaluated kinetic and photochemical data for atmospheric chemistry: Volume II – gas phase reactions of organic species, Atmos. Chem. Phys., 6, 3625–4055, doi:http://dx.doi.org/10.5194/acp-6-3625-2006, 2006
  15. Atkinson, R., Baulch, D. L., Cox, R. A., Crowley, J. N., Hampson, R. F., Hynes, R. G., Jenkin, M. E., Rossi, M. J., and Troe, J.: Evaluated kinetic and photochemical data for atmospheric chemistry: Volume III - gas phase reactions of inorganic halogens, Atmos. Chem. Phys., 7, 981–1191, 2007
  16. Atkinson, R., Baulch, D. L., Cox, R. A., Crowley, J. N., Hampson, R. F., Hynes, R. G., Jenkin, M. E., Rossi, M. J., Troe, J., and Wallington, T. J.: Evaluated kinetic and photochemical data for atmospheric chemistry: Volume IV - gas phase reactions of organic halogen species, J. Phys. Chem. Ref. Data, 8, 4141–4496, 2008
  17. Evans, M. J. and Jacob, D. J.: Impact of new laboratory studies of N2O5 hydrolysis on global model budgets of tropospheric nitrogen oxides, ozone, and OH, Geophys. Res. Lett., 32, L09 813, doi:http://dx.doi.org/10.1029/2005GL022469, 2005
  18. Roberts, J. M., Osthoff, H. D., Brown, S. S., Ravishankara, A. R., Coffman, D., Quinn, P., and Bates, T.: Laboratory studies of products of N2O5 uptake on Cl containing substrates, Geophys. Res. Lett., 36, doi:http://dx.doi.org/10.1029/2009GL040448, 2009
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