Chemistry Working Group: Difference between revisions

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*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])
*[https://www.jessicahaskinsphd.com/ Jessica Haskins] (Github: [https://github.com/jhaskinsPhD jhaskinsPhD])
*[https://www.kelvinbates.com/ Kelvin Bates] (Github: [https://github.com/kelvinhb @kelvinb])


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!width="150px"|Contact Person
!width="150px"|Contact Person
!width="100px"|Date Added
!width="100px"|Date Added
|-valign="top"
|NASA LARC
|Scheme for higher PN production from aromatics, MEK, monoterpenes, glycolaldehyde, and 1,3-butadiene
|[mailto:katherine.travis@nasa.gov Katherine R. Travis]
|19 Sep 2023
|-valign="top"
|Columbia University
|Automated model reduction isoprene oxidation mechanism
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br>
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt]
|12 Sep 2023


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|University of York
|University of York
|Nitrate Photolysis
|Nitrate Photolysis
|[mailto:mat.evans@york.ac.ul Mat Evans]
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:matthew.rowlinson@york.ac.ul Matthew Rowlinson]
|08 Jun 2022
|08 Jun 2022
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|University of York
|Halogen reverse reactions
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:hansen.cao@york.ac.ul Hansen Cao]
|01 Jun 2022
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|University of York
|Chlorine chemistry
|[mailto:mat.evans@york.ac.ul Mat Evans]<br>
[mailto:al1916@york.ac.uk Amy Lees]
|01 Oct 2022


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|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
|03 Jun 2022
|03 Jun 2022
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|U Montana
|Formic acid and acetic acid formation in fire smoke
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]
|21 May 2022
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|U Montana
|Formic acid and acetic acid formation in fire smoke
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]
|21 May 2022


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|U Wollongong
|U Wollongong
|Evaluation of aromatic oxidation products using new observational constraints
|Evaluation of aromatic oxidation products using new observational constraints
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|9 June 2022
|9 June 2022


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|UNSW, Sydney
|U Wollongong, U Sydney, UNSW
|Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen
|Impacts of photophysical oxidation of aldehydes
|[mailto:m.perez_pena@unsw.edu.au Maria Paula Perez-Pena]
|[mailto:paolos@uow.edu.au Paolo Sebastianelli]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|25 June 2021
|10 June 2024
 
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|UNSW, U Wollongong
|GEOS-Chem simulation of HFO and CF3CHO chemistry
|[mailto:b.killen@unsw.edu.au Beth Killen]<br>[mailto:jennyf@uow.edu.au Jenny Fisher]
|10 June 2024


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|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]
|21 April 2019
|21 April 2019
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|NIA / LaRC
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
|[mailto:hyl@nianet.org Hongyu Liu]
|5 May 2015
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|MIT
|Simulating the global reactive carbon budget
|[mailto:sarahsaf@mit.edu Sarah Safieddine]
|12 April 2017
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|University of York
|Halogen chemistry
|[mailto:ts551@york.ac.uk Tomas Sherwen]
|12 April 2017
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|Harvard University
|Halogen extension to include explicit phase partitioning and mass transfer
|[mailto:seastham@fas.harvard.edu Sebastian D. Eastham]
|12 April 2017


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== Current GEOS-Chem Chemistry Issues (please add yours!) ==
== 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 ]] .  '''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''


=== Carbon balance ===
=== Carbon balance ===
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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.</blockquote>
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.</blockquote>
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
==== Fixes for carbon creating reactions ====
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
'''''Sarah Safieddine wrote:'''''
<blockquote>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.</blockquote>
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!Reaction # in globchem.dat v9-02
!Unbalanced Reaction
!Rate constant
!Issue<br>(R=Reactants, P=Products)
!Fix and corrected reaction (in <span style="color:green">green</span>)
|-valign="top
|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).<br>
<span style="color:green">R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + '''0.093B3O2''' + 0.32ETO2</span><br>
<span style="color:darkorange">'''Use Barron's [[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|fix to correct ALK4 lumping issue]] instead.'''</span>
|-valign="top
|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:<br>
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span>
|-valign="top
|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<br>
<span style="color:green">ATO2 + NO → NO2 + CH2O + MCO3
|-valign="top
|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<br>There was a [[Caltech_isoprene_scheme#Remove_duplicate_GLYX_product_from_RIO2_reaction|fix proposed on the isoprene scheme wiki page]] but still not enough
|Fix as suggested by Sarah: remove CH2O<br>
<span style="color:green">RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH</span><br>
<span style="color:darkorange">This reaction was replaced with '''RIO2 → 0.5HPALD + 0.5DHPCARP''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
|-valign="top
|453
|ISNOOB + NO3 → R4N2 + GLYX + 2NO2
|2.3E-12
|Creates carbon: R=5C, P=6C
|Fix as suggested by Barron: Replace R4N2 by PROPNN<br>
<span style="color:green">ISNOOB + NO3 → '''PROPNN''' + GLYX + 2NO2</span><br>
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
|-valign="top
|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<br>
<span style="color:green">ISNOOB + NO → '''0.06R4N2''' + ''''0.94PROPNN'''' + 0.94GLYX + 1.88NO2</span><br>
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
|-valign="top
|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:<br>
<span style="color:green">ISNOHOO + NO → '''0.081R4N2''' + '''0.919PROPNN''' + 0.934HO2 + 0.919GLYX</span><br>
<span style="color:darkorange">This reaction was replaced with '''ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span>
|-valign="top
|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<br>
<span style="color:green">MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + '''0.85MAOP + 0.85NO2'''</span>
|-valign="top
|719
|ATO2 + MCO3 → MEK + ACTA
|1.87E-13 exp(500/T)
|Creates carbon: R=5C, P=6C
|From the WIKI: replace MEK with MGLY<br>
<span style="color:green">ATO2 + MCO3 → '''MGLY''' + ACTA</span>
|-valign="top
|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>
<span style="color:green">Br + ALD2 → HBr + MCO3</span>
|-valign="top
|818
|Br + ACET → HBr + ATO2 + CO
|1.66E-10exp(-7000/T)
|Creates carbon: R=3C, P=4C
|Remove CO, same as above<br>
<span style="color:green">Br + ACET → HBr + ATO2</span>
|-valign="top
|819
|Br + C2H6 → HBr + ETO2 + CO
|2.36E-10 exp(-6411/T)
|Creates carbon: R=2C, P=3C
|Remove CO, same as above<br>
<span style="color:green">Br + C2H6 → HBr + ETO2</span>
|-valign="top
|820
|Br + C3H8 → HBr + A3O2 + CO
|8.77E-11 exp(-4330/T)
|Creates carbon: R=3C, P=4C
|Remove CO, same as above<br>
<span style="color:green">Br + C3H8 → HBr + A3O2</span>
|}
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)
==== Identification of carbon leaking reactions ====
'''''Sarah Safieddine wrote:'''''
<blockquote>76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as <tt>{CO2}</tt> in the document [http://onlinelibrary.wiley.com/store/10.1002/2017GL072602/asset/supinfo/grl55781-sup-0001-Supplementary.docx?v=1&s=21c96c26c411290d72b64fc4f9ecdc5e806af2c5 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.</blockquote>
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
==== Fixes to correct ALK4 lumping issue ====
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
'''''[[User:Barronh|Barron Henderson]] wrote:'''''
<blockquote>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 [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 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.
#Increase MO2 stoichiometry from 0.18 to 0.19
#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).
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;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.</blockquote>
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)
=== JPL Released 18th Rate Coefficient Evaluation ===
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
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.
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)
=== Working Group Tele-con on the 2nd December 2011 ===
[[ChemTelecon20111202]]
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
=== Isoprene chemistry ===
I've created a page with some of the recent literature on [[Isoprene|isoprene chemistry]]. Please add more papers as they come along! ([[User:mje| 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.
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
== Previous issues that have now been resolved ==
=== Centralizing chemistry time step===
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02q|v9-01-02q]] and approved on 18 Oct 2011.'''''</span>
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
=== Acetone photolysis ===
[[FAST-J_photolysis_mechanism#v9-02_post-release_patch_to_fix_bug_in_acetone_photolysis_pressure_dependency|This discussion has been moved to our ''FAST-J photolysis mechanism'' wiki page]].
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)
== Documentation ==
[[Image:Obsolete.jpg]]
*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf 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.
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jv_spec_format.pdf Format of FAST-J input file <tt>jv_spec.dat</tt>]
--[[User:Bmy|Bob Y.]] 15:41, 27 October 2009 (EDT)

Latest revision as of 14:47, 23 September 2024

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
Oxidants and Chemistry Working Group email list geos-chem-oxidants [at] g.harvard.edu
To subscribe to email list Either
  • Send an email to geos-chem-oxidants+subscribe [at] g.harvard.edu

Or

To unsubscribe from email list Either
  • Send an email to geos-chem-oxidants+unsubscribe [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
NASA LARC Scheme for higher PN production from aromatics, MEK, monoterpenes, glycolaldehyde, and 1,3-butadiene Katherine R. Travis 19 Sep 2023


Columbia University Automated model reduction isoprene oxidation mechanism Benjamin Yang

Dan Westervelt

12 Sep 2023
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 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
Jenny Fisher 		9 June 2022
U Wollongong, U Sydney, UNSW Impacts of photophysical oxidation of aldehydes Paolo Sebastianelli
Jenny Fisher 		10 June 2024
UNSW, U Wollongong GEOS-Chem simulation of HFO and CF3CHO chemistry Beth Killen
Jenny Fisher 		10 June 2024
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
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!)

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.

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