Chemistry Working Group

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Oxidants and Chemistry Working Group

All users interested in the GEOS-Chem chemistry scheme and associated processes (photolysis, heterogeneous, deposition) are encouraged to subscribe to the chemistry email list (click on the link in the contact information section below).

Contact information

Oxidants and Chemistry Working Group Chair Mat Evans

Jingqiu Mao

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Current GEOS-Chem Chemistry Projects (please add yours!)

User Group Description Contact Person Date Added
Caltech/Harvard Examining the effects of isoprene nitrates and epoxide on tropical ozone and OH using SHADOZ and OMI measurements Fabien Paulot
Jingqiu Mao
April 28, 2009
Caltech/Harvard Examining the HCHO yield, OH recycling and ozone production with INTEX-A observations from new isoprene chemistry Jingqiu Mao
Fabien Paulot
April 28, 2009
NIA / LaRC Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis Yiqiang Zhang
Hongyu Liu
June 29, 2010
U. Wollongong Tropospheric ozone precursors over Australasia: Using GEOS-Chem to interpret FTIR measurements of CO, NO2 and HCHO Rebecca Buchholz May 19, 2011

Current GEOS-Chem Chemistry Issues (please add yours!)

Isoprene chemistry

I've created a page with some of the recent literature on isoprene chemistry. Please add more papers as they come along! ( MJE Leeds)


rate of HNO4

Ellie Browne found a typo in the globchem.dat (v8-02-01 and beyond)

A   73 9.52E-05  3.2E+00 -10900 1 P   0.60     0.     0.         
       1.38E+15  1.4E+00 -10900 0     0.00     0.     0.         
      HNO4          +                         M                                
=1.000HO2           +1.000NO2           +                   +

This should be corrected as:

A   73 9.52E-05  3.4E+00 -10900 1 P   0.60     0.     0.         
       1.38E+15  1.1E+00 -10900 0     0.00     0.     0.         
      HNO4          +                         M                                
=1.000HO2           +1.000NO2           +                   + 

The difference is within 2%.

--J Mao. 19:04, 30 Aug 2010 (EDT)

HO2 + CH2O

Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)

Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause, Journal of Physical Chemistry A, 109(19), 4303-4311.

According to this paper, this reaction is significant when Temperature is below 220K.

--J Mao. 15:00, 10 Aug 2009 (EDT)

near-IR photolysis of HNO4

1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in calcrate.f. We can therefore comment out this entire IF block:

        ! Prior to 10/27/09:
        ! FastJX has taken near-IR photolysis into account with
        ! cross section at 574nm, so we don't need to add 1e-5 anymore.
        ! According to Jimenez et al., "Quantum yields of OH, HO2 and
        ! NO3 in the UV photolysis of HO2NO2", PCCP, 2005, we also
        ! changed the branch ratio from 0.67(HO2)/0.33(OH) to 0.95/0.05
        ! This will put most weight of near-IR photolysis on HO2 channel.
        ! (jmao, bmy, 10/27/09)
        !! HARDWIRE addition of 1e-5 s-1 photolysis rate to 
        !! HNO4 -> HO2+NO2 to account for HNO4 photolysis in near-IR -- 
        !! see Roehl et al. 'Photodissociation of peroxynitric acid in 
        !! the near-IR', 2002. (amf, bmy, 1/7/02)
        !! Add NCS index to NKHNO4 for SMVGEAR II (gcc, bmy, 4/1/03)
        !IF ( NKHNO4(NCS) > 0 ) THEN
        !   ! Put J(HNO4) in correct spot for SMVGEAR II
        !   NKN     = NKNPHOTRT(PHOTVAL,NCS)
        !   DO KLOOP=1,KTLOOP
        !      RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5
        !   ENDDO

2. We need to change the branch ratio of HNO4 photolysis in ratj.d. Change these lines from:

13 HNO4       PHOTON     OH         NO3                  0.00E+00  0.00     33.3  HO2NO2 
14 HNO4       PHOTON     HO2        NO2                  0.00E+00  0.00     66.7  HO2NO2 


13 HNO4       PHOTON     OH         NO3                  0.00E+00  0.00      5.0  HO2NO2 
14 HNO4       PHOTON     HO2        NO2                  0.00E+00  0.00     95.0  HO2NO2

This is based on Jimenez et al. (Quantum yields of OH, HO2 and NO3 in the UV photolysis of HO2NO2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005) shows that HO2 yield should be 0.95 and OH yield should be 0.05 for wavelength above 290nm.

This way all the near-IR photolysis will have most weight on HO2 channel(Stark et al., Overtone dissociation of peroxynitric acid (HO2NO2): Absorption cross sections and photolysis products, JOURNAL OF PHYSICAL CHEMISTRY A, 2008).

This update has now been added to the chemistry mechanism documentation file.

--J Mao. 11:00, 26 Oct 2009 (EDT)

Previous issues that have now been resolved

Potential issue with reading restart.cspec file

This update was tested in the 1-month benchmark simulation v9-01-02c and approved on 21 Jul 2011.

Jingqiu Mao discovered a mis-indexing problem when using the restart.cspec.YYYYMMDDhh file. Please see this wiki post for more information.

--Bob Y. 16:02, 4 November 2011 (EDT)

Centralizing chemistry time step

This update was tested in the 1-month benchmark simulation v9-01-02q and approved on 18 Oct 2011.

Please see the full discussion on the Centralized chemistry time step wiki page.

--Bob Y. 16:01, 4 November 2011 (EDT)


--Bob Y. 15:41, 27 October 2009 (EDT)