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 Co-Chairs	Barron Henderson (GitHub: @barronh) Lu Hu (GitHub: @luhu0) Jingqiu Mao (Github: @jingquimao)
Oxidants and Chemistry Working Group email list	geos-chem-oxidants [at] g.harvard.edu
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--Bob Y. (talk) 18:29, 21 August 2015 (UTC)

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

User Group	Description	Contact Person	Date Added
NOAA CSL	JPL Kinetic Review Update/C-N balance/stoichiometry update	Kelvin Bates	01 Jul 2023
University of York	Nitrate Photolysis	Mat Evans Matthew Rowlinson	08 Jun 2022
University of York	Halogen reverse reactions	Mat Evans Hansen Cao	01 Jun 2022
University of York	Chlorine chemistry	Mat Evans Amy Lees	01 Oct 2022
Harvard University and MPIC-Mainz	Further development of The Kinetic PreProcessor (KPP)	Bob Yantosca (GCST)	03 Jun 2022
Harvard University	Adding an adaptive solver capability into KPP	Haipeng Lin	03 Jun 2022
GCST	Migrating the Hg chemistry mechanism to KPP	Bob Yantosca (GCST)	03 Jun 2022
GCST	Adding a CO-CO2-CH4-OCS chemistry mechanism with KPP	Bob Yantosca (GCST)	03 Jun 2022
U Montana	Formic acid and acetic acid formation in fire smoke	Wade Permar Lu Hu	21 May 2022
U Montana	Formic acid and acetic acid formation in fire smoke	Wade Permar Lu Hu	21 May 2022
U Montana	Furans chemistry in MCM and in GEOS-Chem	Lixu Jin Lu Hu	21 May 2022
U Wollongong	Evaluation of aromatic oxidation products using new observational constraints	Stephen MacFarlane	9 June 2022
UNSW, Sydney	Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen	Maria Paula Perez-Pena	25 June 2021
University of California, Riverside	Updates to DMS oxidation scheme	William Porter	26 August 2020
Harvard University	Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids	Viral Shah Jonathan Moch	5 May 2019
U Alaska Fairbanks	Monoterpene oxidation and its impact on SOA formation	Yiqi Zheng Jingqiu Mao	21 April 2019
NIA / LaRC	Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis	Hongyu Liu	5 May 2015
MIT	Simulating the global reactive carbon budget	Sarah Safieddine	12 April 2017
Harvard University	Halogen extension to include explicit phase partitioning and mass transfer	Sebastian D. Eastham	12 April 2017
FSU	Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry	Chris Holmes	May 2017
FSU	Methane and methyl chloroform lifetimes	Chris Holmes	May 2017
FSU	Arctic halogen & ozone chemistry	Chris Holmes	May 2017

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

Working group telecom on the 13/3/2019

There was a telecon to discuss issues with the chemistry. The notes from the meeting are here Media:Chemistry_WG_March_2019..pdf . Mat Evans

Carbon balance

Script for evaluating carbon balance

Barron Henderson wrote:

[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated).

Currently, this done using an off-line script described in a linked note. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.

Longer term, the same technique would ideally be built-in to the standard KPP as an optional report. I discussed it with Michael Long and we both think that KPP has most of the capability for atom conservation (if not all). It may simply be a matter of defining the chemical formulas in the *.spc file.

--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)

Fixes for carbon creating reactions

This update was included in v11-02c and approved on 21 Sep 2017.

Sarah Safieddine wrote:

Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.

Reaction # in globchem.dat v9-02	Unbalanced Reaction	Rate constant	Issue (R=Reactants, P=Products)	Fix and corrected reaction (in green)
453	R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2	K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)	Creates carbon: R=4C P=4.26C	Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron). R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.093B3O2 + 0.32ETO2 Use Barron's fix to correct ALK4 lumping issue instead.
453	R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2	2.7E-12 exp(350/T)	Creates carbon: R=4C, P=4.8C	Fix, as suggested by Matt: R4N1 + NO → 2NO2 + 0.570RCHO + 0.86ALD2 + 0.57CH2O
453	ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2	2.8E-12 exp(300/T)	Creates carbon: R=3C, P=3.04	Fix as suggested by Mat: ditch the R4N2 channel ATO2 + NO → NO2 + CH2O + MCO3
803	RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH	4.07E+08 exp(-7694/T)	Creates carbon: R=5C, P=7C There was a fix proposed on the isoprene scheme wiki page but still not enough	Fix as suggested by Sarah: remove CH2O RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH This reaction was replaced with RIO2 → 0.5HPALD + 0.5DHPCARP in the isoprene chemistry updates added in v11-02c
453	ISNOOB + NO3 → R4N2 + GLYX + 2NO2	2.3E-12	Creates carbon: R=5C, P=6C	Fix as suggested by Barron: Replace R4N2 by PROPNN ISNOOB + NO3 → PROPNN + GLYX + 2NO2 This reaction was replaced with ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG in the isoprene chemistry updates added in v11-02c
453	ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2	2.6E-12 exp(380/T)	Creates carbon: R=5C, P=5.64C	Same as above ISNOOB + NO → 0.06R4N2 + '0.94PROPNN' + 0.94GLYX + 1.88NO2 This reaction was replaced with ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG in the isoprene chemistry updates added in v11-02c
453	ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX	2.6E-12 exp(380/T)	Creates carbon: R=5C, P=5.574C	Fix by Barron: ISNOHOO + NO → 0.081R4N2 + 0.919PROPNN + 0.934HO2 + 0.919GLYX This reaction was replaced with ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG in the isoprene chemistry updates added in v11-02c
472	MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP	2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4	Creates carbon: R=4C, P=4.85C	Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2 MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85MAOP + 0.85NO2
719	ATO2 + MCO3 → MEK + ACTA	1.87E-13 exp(500/T)	Creates carbon: R=5C, P=6C	From the WIKI: replace MEK with MGLY ATO2 + MCO3 → MGLY + ACTA
817	Br + ALD2 → HBr + MCO3 + CO	1.3E-11 exp(-360/T)	Creates carbon: R=2C, P=3C	Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below) Br + ALD2 → HBr + MCO3
818	Br + ACET → HBr + ATO2 + CO	1.66E-10exp(-7000/T)	Creates carbon: R=3C, P=4C	Remove CO, same as above Br + ACET → HBr + ATO2
819	Br + C2H6 → HBr + ETO2 + CO	2.36E-10 exp(-6411/T)	Creates carbon: R=2C, P=3C	Remove CO, same as above Br + C2H6 → HBr + ETO2
820	Br + C3H8 → HBr + A3O2 + CO	8.77E-11 exp(-4330/T)	Creates carbon: R=3C, P=4C	Remove CO, same as above Br + C3H8 → HBr + A3O2

--Melissa Sulprizio (talk) 19:59, 27 July 2017 (UTC)

Identification of carbon leaking reactions

Sarah Safieddine wrote:

76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as {CO2} in the document ROC_SI.docx, Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.

--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)

Fixes to correct ALK4 lumping issue

These fixes were included in v11-02a and approved on 12 May 2017.

Barron Henderson wrote:

I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).

Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.

If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.

I have extensive notes on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.

1. Increase MO2 stoichiometry from 0.18 to 0.19
2. Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).
3. Modify the carbon count for ALK4 (i.e. the MolecRatio field in the GEOS-Chem species database) from 4 to 4.3.

Fixes 1 and 2—which can be applied to the KPP globchem.eqn file—will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.

--Bob Yantosca (talk) 20:21, 31 January 2017 (UTC)

JPL Released 18th Rate Coefficient Evaluation

This update was included in v11-02a and approved on 12 May 2017.

JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page (Updates in JPL Publication 15-10) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10.

J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.

---B. Henderson 2016-05-03 15:25 (EDT)

Working Group Tele-con on the 2nd December 2011

ChemTelecon20111202 Mat Evans

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)

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)

Previous issues that have now been resolved

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)

Acetone photolysis

This discussion has been moved to our FAST-J photolysis mechanism wiki page.

--Bob Y. 15:20, 20 May 2014 (EDT)

Documentation

• Updated chemical reactions that will be used in GEOS-Chem v8-02-04 and higher.
• Updated chemical reactions now used in GEOS-Chem v8-02-01 through GEOS-Chem v8-02-03.
  • All typos have now been corrected in the present file.
• Format of FAST-J input file jv_spec.dat

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