Difference between revisions of "Chemistry Working Group"

From Geos-chem
Jump to: navigation, search
(Current GEOS-Chem Chemistry Issues (please add yours!))
(Contact information)
 
(133 intermediate revisions by 16 users not shown)
Line 1: Line 1:
<big><big><strong>Oxidants and Chemistry Working Group</strong></big></big>
 
 
 
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|contact information section]] below).
 
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|contact information section]] below).
  
Line 6: Line 4:
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
|-
+
|-valign="top"
|'''Oxidants and Chemistry Working Group Co-Chairs'''
+
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs
|[http://www.env.leeds.ac.uk/~lecmje/lecmje Mat Evans] and [http://www.gfdl.noaa.gov/jingqiu-mao Jingqiu Mao]
+
|width="600px"|
|-
+
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])
|'''Oxidants and Chemistry Working Group email list'''
+
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])
|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
+
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])
|-
+
 
|'''To subscribe to email list'''
+
|-valign="top"
|Send email to [mailto:geos-chem-oxidants-join@seas.harvard.edu <tt>geos-chem-oxidants-join@seas.harvard.edu</tt>]
+
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list
|-
+
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt>
|'''To unsubscribe from email list'''
+
 
|Send email to [mailto:geos-chem-oxidants-leave@seas.harvard.edu <tt>geos-chem-oxidants-leave@seas.harvard.edu</tt>]
+
|-valign="top"
 +
!bgcolor="#CCCCCC"|To subscribe to email list
 +
|Either
 +
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt>
 +
Or
 +
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]
 +
*Click on '''Subscribe to this group'''
 +
 
 +
|-valign="top"
 +
!bgcolor="#CCCCCC"|To unsubscribe from email list
 +
|Either
 +
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt>
 +
Or
 +
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]
 +
*Click on the '''My Settings''' button
 +
*Click on '''Leave this group'''
 +
 
 
|}
 
|}
 +
 +
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)
  
 
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
 
== Current GEOS-Chem Chemistry Projects (please add yours!) ==
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|- bgcolor="#cccccc"
 
|- bgcolor="#cccccc"
!User Group
+
!width="200px"|User Group
!Description
+
!width="600px"|Description
!Contact Person
+
!width="150px"|Contact Person
!Date Added
+
!width="100px"|Date Added
|-
+
 
|Caltech/Harvard
+
|-valign="top"
|Examining the effects of isoprene nitrates and epoxide on tropical ozone and OH using SHADOZ and OMI measurements
+
|University of York
|[mailto:paulot@caltech.edu Fabien Paulot] <br>[mailto:jmao@seas.harvard.edu Jingqiu Mao]
+
|Nitrate Photolysis
|April 28, 2009
+
|[mailto:mat.evans@york.ac.ul Mat Evans]
|-
+
|08 Jun 2022
|Caltech/Harvard
+
 
|Examining the HCHO yield, OH recycling and ozone production with INTEX-A observations from new isoprene chemistry
+
|-valign="top"
|[mailto:jmao@seas.harvard.edu Jingqiu Mao ] <br>[mailto:paulot@caltech.edu Fabien Paulot]
+
|Harvard University and<br>MPIC-Mainz
|April 28, 2009
+
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]
|-
+
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)
 +
|03 Jun 2022
 +
 
 +
|-valign="top"
 +
|Harvard University
 +
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]
 +
|[mailto:hplin@seas.harvard.edu Haipeng Lin]
 +
|03 Jun 2022
 +
 
 +
|-valign="top"
 +
|GCST
 +
|Migrating the Hg chemistry mechanism to [https://kpp.readthedocs.io KPP]
 +
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
 +
|03 Jun 2022
 +
 
 +
|-valign="top"
 +
|GCST
 +
|Adding a CO-CO2-CH4-OCS chemistry mechanism with [https://kpp.readthedocs.io KPP]
 +
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)
 +
|03 Jun 2022
 +
 
 +
|-valign="top"
 +
|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
 +
 
 +
|-valign="top"
 +
|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
 +
 
 +
|-valign="top"
 +
|U Montana
 +
|Furans chemistry in MCM and in GEOS-Chem
 +
|[mailto:lixu.jin@umontana.edu Lixu Jin]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]
 +
|21 May 2022
 +
 
 +
|-valign="top"
 +
|U Wollongong
 +
|Evaluation of aromatic oxidation products using new observational constraints
 +
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]
 +
|9 June 2022
 +
 
 +
|-valign="top"
 +
|UNSW, Sydney
 +
|Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen
 +
|[mailto:m.perez_pena@unsw.edu.au Maria Paula Perez-Pena]
 +
|25 June 2021
 +
 
 +
|-valign="top"
 +
|University of California, Riverside
 +
|Updates to DMS oxidation scheme
 +
|[mailto:wporter@ucr.edu William Porter]
 +
|26 August 2020
 +
 
 +
|-valign="top"
 +
|Harvard University
 +
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids
 +
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]
 +
|5 May 2019
 +
 
 +
|-valign="top"
 +
|U Alaska Fairbanks
 +
|Monoterpene oxidation and its impact on SOA formation
 +
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]
 +
|21 April 2019
 +
 
 +
|-valign="top"
 
|NIA / LaRC
 
|NIA / LaRC
 
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
 
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis
|[mailto:yiqiang.zhang@nianet.org Yiqiang Zhang ] <br>[mailto:hyl@nianet.org Hongyu Liu]
+
|[mailto:hyl@nianet.org Hongyu Liu]
|June 29, 2010
+
|5 May 2015
|-
+
 
|U. Wollongong
+
|-valign="top"
|Tropospheric ozone precursors over Australasia: Using GEOS-Chem to interpret FTIR measurements of CO, NO2 and HCHO
+
|MIT
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz ]
+
|Simulating the global reactive carbon budget
|May 19, 2011
+
|[mailto:sarahsaf@mit.edu Sarah Safieddine]
|-
+
|12 April 2017
|University of York
+
 
|Role of iodine chemistry in the troposphere
+
|-valign="top"
|[mailto:mat.evans@york.ac.uk Mat Evans ] [mailto:lucy.carpenter@york.ac.uk Lucy Carpenter]
+
|University of York
|12th April, 2012
+
|Halogen chemistry
 +
|[mailto:ts551@york.ac.uk Tomas Sherwen]
 +
|12 April 2017
 +
 
 +
|-valign="top"
 +
|Harvard University
 +
|Halogen extension to include explicit phase partitioning and mass transfer
 +
|[mailto:seastham@fas.harvard.edu Sebastian D. Eastham]
 +
|12 April 2017
 +
 
 +
|-valign="top"
 +
| US EPA
 +
|Alkane chemistry and product yields as a function of temperature/pressure.
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
 +
 
 +
|-valign="top"
 +
| US EPA
 +
|Carbon and Nitrogen Balance and checking software.
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
 +
 
 +
|-valign="top"
 +
| US EPA
 +
|Update DSMACC for v11 GEOS-Chem Chemistry and Emissions to facilitate chemical experiments
 +
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
 +
|4 May 2017
 +
 
 +
|-valign="top"
 +
| FSU
 +
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 +
 
 +
|-valign="top"
 +
|FSU
 +
|Methane and methyl chloroform lifetimes
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 +
 
 +
|-valign="top"
 +
|FSU
 +
|Arctic halogen & ozone chemistry
 +
|[mailto:cdholmes@fsu.edu Chris Holmes]
 +
|May 2017
 
|}
 
|}
  
 
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
 
== Current GEOS-Chem Chemistry Issues (please add yours!) ==
  
=== Working Group Tele-con on the 2nd December 2011 ===
+
=== Working group telecom on the 13/3/2019 ===
[[ChemTelecon20111202]]
+
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]'''''
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
+
  
=== Bug in subroutine ARSL1K ===
+
=== Carbon balance ===
  
''NOTE: This update is slated for inclusion in [[GEOS-Chem v9-01-03]]''
+
==== Script for evaluating carbon balance ====
  
A bug in routine ARSL1K became problematic in the implementation of Justin Parrella's [[Bromine_chemistry_mechanism|tropospheric bromine chemistry mechanism]] for [[GEOS-Chem v9-01-03]]. In the bromine chemistry mechanism, a sticking coefficient of 0.0 is passed to the function ARSL1K for non-sulfate, non-sea salt aerosol. The IF statement modified in [[GEOS-Chem_v8-02-04#Div-by-zero_error_encountered_in_arsl1k.f|GEOS-Chem v8-02-04]] resulted in the reaction rate being set to the default value of 1.0d-3. A 1-month benchmark for July 2005 indicated that the simulated BrO was a little more than twice the expected zonal mean. Modifying the default value from 1.0d-3 to 1.0d-30 resulted in reasonable simulated BrO values.
+
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''
  
'''''[mailto:mat.evans@york.ac.uk Mat Evans] wrote:'''''
+
<blockquote>[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 [http://www.evernote.com/l/ATuCIZsKADFPPKnKQBlk07TFevitHHQ1Q_o/ linked note]. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.
  
:I've re-run two 2 month simulation. One with the error handling value of 1e-3 (standard) and one with it being 1e-30. There are 5127 time and space points where the model traps the problem and invokes the 1e-3 or 1e-30 value. There are 30*24*2*37*72*46 (roughly 200 million) time and space points when the error could have occurred so we are looking at a relatively infrequent event.
+
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>
  
:The simulations show virtually no difference between the two simulations.
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
  
:mean and stddev ratio of all grid boxes with and without the fix are shown below
+
==== Fixes for carbon creating reactions ====
    NOx    0.999996  0.000409291
+
    Ox      1.00000  1.27233e-05
+
    O3      1.00000  1.52284e-05
+
    PAN    0.997849  0.0111997
+
    CO      1.00000  4.21768e-06
+
    ALK4    0.990514  0.0351941
+
    ISOP    0.999979  0.0108033
+
    H2O2    0.992067  0.0264659
+
    DST1    1.00000  0.00000
+
    HO2    0.999996  0.00309464
+
    OH      1.00003  0.00767954
+
  
:So although there are some differences they are very minor. For completeness we should put this in as a bug fix (make the error value 1d-30 rather than 1d-3). But it is not a major problem.
+
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
  
--[[User:Melissa Payer|Melissa Payer]] 17:52, 14 May 2012 (EDT)
+
'''''Sarah Safieddine wrote:'''''
  
=== GLCO3, GLPAN bug in standard mechanism ===
+
<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>
  
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03a|v9-01-03a]] and approved on 08 Dec 2011.'''''
+
{| 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>)
  
'''''[mailto:fabienpaulot@gmail.com Fabien Paulot] wrote:'''''
+
|-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>
  
:I think there is a relatively serious bug in the standard chemistry. GLPAN and GLCO3 are set to inactive but their production and loss reactions are active. As a result they never reach equilibrium and this results in an artificial loss of NOx.
+
|-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>
  
:If this is the only cause of the imbalance between sources and sinks of NOx in my simulations, this would account for ~5% of NOy losses. I don't see that problem in a simulation with a different chemistry that among other changes does not feature those reactions. So hopefully that's it.
+
|-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
  
:To fix the error, I made the following modifications in <tt>globchem.dat</tt>:
+
|-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>
  
:#I set GLPAN and GLCO3 rxns from active to dead.  These rxns were causing an artificial loss of NOx.
+
|-valign="top
:#I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions. 
+
|453
:#I have made GLYX active.  I'm not sure why it's not active by default.
+
|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>
  
:and to <tt>ratj.d</tt>:
+
|-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>
  
:# I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in <tt>globchem.dat</tt>
+
|-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>
  
--[[User:Bmy|Bob Y.]] 14:51, 10 November 2011 (EST)<br>
+
|-valign="top
--[[User:Melissa Payer|Melissa Payer]] 10:49, 15 December 2011 (EST)
+
|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>
  
=== Isoprene chemistry ===
+
|-valign="top
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]])
+
|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>
  
=== HO2 + CH2O ===
+
|-valign="top
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
+
|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>
  
Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation
+
|-valign="top
processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause,
+
|818
Journal of Physical Chemistry A, 109(19), 4303-4311.
+
|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>
  
According to this paper, this reaction is significant when Temperature is below 220K.
+
|-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>
  
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
+
|-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>
  
== Previous issues that have now been resolved ==
+
|}
 +
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)
  
=== rate of HNO4 ===
+
==== Identification of carbon leaking reactions ====
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat ([[GEOS-Chem v8-02-01]] and beyond)
+
<pre>
+
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          +                  +
+
</pre>
+
This should be corrected as:
+
<pre>
+
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          +                  +
+
</pre>
+
The difference is within 2%.
+
  
--[[User:Jmao|J Mao.]] 19:04, 30 Aug 2010 (EDT)<br>
+
'''''Sarah Safieddine wrote:'''''
--[[User:Bmy|Bob Y.]] 16:12, 4 November 2011 (EDT)
+
  
=== near-IR photolysis of HNO4 ===
+
<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>
  
'''''This update was added to [[GEOS-Chem v8-02-04]].'''''
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)
  
1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in <tt>calcrate.f</tt>.  We can therefore comment out this entire IF block:
+
==== Fixes to correct ALK4 lumping issue ====
+
        !---------------------------------------------------------------------
+
        ! 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
+
        !  PHOTVAL = NKHNO4(NCS) - NRATES(NCS)
+
        !  NKN    = NKNPHOTRT(PHOTVAL,NCS)
+
        !
+
        !  DO KLOOP=1,KTLOOP
+
        !      RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5
+
        !  ENDDO
+
        !ENDIF
+
        !---------------------------------------------------------------------
+
  
 +
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
  
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>.  Change these lines from:
+
'''''[[User:Barronh|Barron Henderson]] wrote:'''''
  
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00    33.3  HO2NO2
+
<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).
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    66.7  HO2NO2
+
  
to:
+
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.
  
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
+
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.
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.
+
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.
  
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).
+
#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.
  
This update has now been added to the [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf chemistry mechanism documentation file].
+
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:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)<br>
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)
--[[User:Bmy|Bob Y.]] 16:08, 4 November 2011 (EDT)
+
  
=== yield of isoprene nitrates ===
+
=== JPL Released 18th Rate Coefficient Evaluation ===
  
'''''This update was added to [[GEOS-Chem v8-03-02]] as a post-release patch, and standardized in [[GEOS-Chem v9-01-01]].'''''
+
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
  
[mailto:paulot@caltech.edu Fabien Paulot] found a problem in current chemistry scheme. In [[GEOS-Chem v8-02-01]] and beyond, isoprene nitrates are produced twice: one through channel A and one through 10% loss in channel B. This makes the loss of NOx larger than it should be (18.7% vs. 10%) and also reduces the yield of MVK/MACR/CH2O by about 13%.  
+
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.  
  
A  453 2.70E-12  0.0E+00    350 1 B   0.00    0.     0.        
+
: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.
        5.00E+00  0.0E+00      0 0    0.00    0.     0.        
+
      RIO2          +    NO                                             
+
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
+
+0.220MACR          +0.560CH2O          +                  + 
+
         
+
A  453 2.70E-12  0.0E+00    350 1 A  0.00    0.     0.        
+
        5.00E+00  0.0E+00      0 0    0.00    0.     0.        
+
      RIO2          +    NO                                             
+
=1.000HNO3          +                  +                  +           
+
  
So it should be corrected as (no channel A):
+
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)
  
A  453 2.70E-12  0.0E+00    350 0 0  0.00    0.    0.       
+
=== Working Group Tele-con on the 2nd December 2011 ===
      RIO2          +    NO                                             
+
[[ChemTelecon20111202]]
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
+
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''
+0.220MACR          +0.560CH2O          +                  +     
+
+
D  453 2.70E-12  0.0E+00    350 1 A  0.00    0.    0.       
+
        5.00E+00  0.0E+00      0 0    0.00    0.    0.       
+
      RIO2          +    NO                                             
+
=1.000HNO3          +                  +                  + 
+
  
--[[User:Jmao|J Mao.]] 18:04, 30 Aug 2010 (EDT)<br>
+
=== Isoprene chemistry ===
--[[User:Bmy|Bob Y.]] 16:05, 4 November 2011 (EDT)
+
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]])
  
=== Potential issue with reading restart.cspec file ===
+
=== HO2 + CH2O ===
 +
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)
  
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02c|v9-01-02c]] and approved on 21 Jul 2011.'''''
+
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.
  
Jingqiu Mao discovered a mis-indexing problem when using the <tt>restart.cspec.YYYYMMDDhh</tt> file.  Please see [[Restart files#Potential issue with reading restart.cspec_file|this wiki post]] for more information.
+
According to this paper, this reaction is significant when Temperature is below 220K.
  
--[[User:Bmy|Bob Y.]] 16:02, 4 November 2011 (EDT)
+
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)
 +
 
 +
== Previous issues that have now been resolved ==
  
 
=== Centralizing chemistry time step===
 
=== Centralizing chemistry time step===
  
'''''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 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.
 
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
  
 
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
 
--[[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 ==
 
== 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_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.

Latest revision as of 15:16, 22 July 2022

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

Or

--Bob Y. (talk) 18:29, 21 August 2015 (UTC)

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

User Group Description Contact Person Date Added
University of York Nitrate Photolysis Mat Evans 08 Jun 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
University of York Halogen chemistry Tomas Sherwen 12 April 2017
Harvard University Halogen extension to include explicit phase partitioning and mass transfer Sebastian D. Eastham 12 April 2017
US EPA Alkane chemistry and product yields as a function of temperature/pressure. Barron H. Henderson 4 May 2017
US EPA Carbon and Nitrogen Balance and checking software. Barron H. Henderson 4 May 2017
US EPA Update DSMACC for v11 GEOS-Chem Chemistry and Emissions to facilitate chemical experiments Barron H. Henderson 4 May 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

Obsolete.jpg

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