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Add fixes for ALK4 and R4N2 chemistry from Brewer et al. (2023, JGR)
R4N2 was a common product of alkane, isoprene, and monoterpene oxidation and produced organonitrate SOA but we don’t want ALK4 to produce organonitrate SOA as discusses in #1625. A fix from Jared Brewer is included here. NOTE: The KPP fullchem mechanism has not been rebuilt with these fixes to facilitate merging these updates up to the latest GEOS-Chem release. These updates will also need to be added to the custom.eqn file. Signed-off-by: Melissa Sulprizio <[email protected]>
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Original file line number | Diff line number | Diff line change |
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@@ -108,6 +108,7 @@ FP : Fabien Paulot; [email protected] | |
HOTP: Havala Pye; [email protected] | ||
JAF : Jenny Fisher; [email protected] | ||
JAS : Johan Schmidt; [email protected] | ||
JFB : Jared Brewer; [email protected] | ||
JMAO: Jingqiu Mao; [email protected] | ||
JMM : Jonathan Moch [email protected] | ||
JPP : Justin Parrella; [email protected] | ||
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@@ -134,6 +135,7 @@ REFERENCES (alphabetical order) | |
* Bates2019: Bates and Jacob, Atmos. Chem. Phys., doi:10.5194/acp-19-9613-2019, 2019. | ||
* Bates2021a: Bates et al, JGR, https://doi.org/10.1029/2020JD033439, 2021. | ||
* Bates2021b: Bates et al, ACP, https://doi.org/10.5194/acp-2021-605, 2021. | ||
* Brewer2023: Brewer et al., JGR, doi:10.1029/2022JD037257, 2023. | ||
* Browne2011: Browne et al., Atmos. Chem. Phys., doi:10.5194/acp-11-4209-2011, 2011. | ||
* Browne2014: Browne et al., Atmos. Chem. Phys., doi:10.5194/acp-14-1225-2014, 2014. | ||
* Chen2017: Chen et al., Geophys. Res. Lett., doi:10.1002/2017GL073812, 2017. | ||
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@@ -191,6 +193,10 @@ ACTA = IGNORE; {CH3C(O)OH; Acetic acid} | |
AERI = IGNORE; {I; Dissolved iodine} | ||
ALD2 = IGNORE; {CH3CHO; Acetaldehyde} | ||
ALK4 = IGNORE; {>= C4 alkanes} | ||
ALK4N1 = IGNORE; {RO2 from ALKN2} | ||
ALK4N2 = IGNORE; {RO2NO; >= C4 alkylnitrates from ALK4} | ||
ALK4O2 = IGNORE; {RO2 from ALK4} | ||
ALK4P = IGNORE; {CH3CH2CH2CH2OOH; Peroxide from ALK4O2} | ||
AONITA = IGNORE; {Aerosol-phase organic nitrate from aromatic precursors} | ||
AROMRO2 = IGNORE; {generic peroxy radical from aromatic oxidation} | ||
AROMP4 = IGNORE; {Generic C4 product from aromatic oxidation} | ||
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@@ -442,7 +448,7 @@ PRPN = IGNORE; {O2NOCH2CH(OOH)CH3; Peroxide from PRN1} | |
PYAC = IGNORE; {CH3COCOOH; Pyruvic acid} | ||
R4N1 = IGNORE; {RO2 from R4N2} | ||
R4N2 = IGNORE; {RO2NO; >= C4 alkylnitrates} | ||
R4O2 = IGNORE; {RO2 from ALK4} | ||
R4O2 = IGNORE; {RO2 from >= C4 biogenic organics} | ||
R4P = IGNORE; {CH3CH2CH2CH2OOH; Peroxide from R4O2} | ||
RA3P = IGNORE; {CH3CH2CH2OOH; Peroxide from A3O2} | ||
RB3P = IGNORE; {CH3CH(OOH)CH3; Peroxide from B3O2} | ||
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@@ -585,22 +591,30 @@ C3H8 + OH = A3O2 : GC_TBRANCH_2_acabc(7.60d-12, -585.0 | |
A3O2 + NO = NO2 + HO2 + RCHO : GC_RO2NO_B2_aca(2.90d-12, 350.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF} | ||
A3O2 + NO = NPRNO3 : GC_RO2NO_A2_aca(2.90d-12, 350.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF} | ||
PO2 + NO = NO2 + HO2 + CH2O + ALD2 : GCARR_ac(2.70d-12, 350.0d0); | ||
ALK4 + OH = R4O2 : GCARR_ac(9.10d-12, -405.0d0); | ||
ALK4 + OH = ALK4O2 : GCARR_ac(9.10d-12, -405.0d0); {2023/05/14; Brewer2023; JFB} | ||
ALK4O2 + NO = NO2 + 0.320ACET + 0.190MEK + | ||
0.190MO2 + 0.270HO2 + 0.320ALD2 + | ||
0.140RCHO + 0.050A3O2 + 0.180B3O2 + | ||
0.320OTHRO2 : GC_RO2NO_B2_aca(2.70d-12, 350.0d0, 4.5d0); {2023/05/14; Brewer2023; JFB} | ||
ALK4O2 + NO = ALK4N2 : GC_RO2NO_A2_aca(2.70d-12, 350.0d0, 4.5d0); {2023/05/14; Brewer2023; JFB} | ||
ALK4N1 + NO = 2.000NO2 + 0.570RCHO + | ||
0.860ALD2 + 0.570CH2O : GCARR_ac(2.70d-12, 350.0d0); {2023/05/14; Brewer2023; JFB} | ||
R4O2 + NO = NO2 + 0.320ACET + 0.190MEK + | ||
0.190MO2 + 0.270HO2 + 0.320ALD2 + | ||
0.140RCHO + 0.050A3O2 + 0.180B3O2 + | ||
0.320OTHRO2 : GC_RO2NO_B2_aca(2.70d-12, 350.0d0, 4.5d0); {2017/02/23; ALK4 lumping fix; BHH} | ||
R4O2 + NO = R4N2 : GC_RO2NO_A2_aca(2.70d-12, 350.0d0, 4.5d0); | ||
R4N1 + NO = 2.000NO2 + 0.570RCHO + | ||
0.860ALD2 + 0.570CH2O : GCARR_ac(2.70d-12, 350.0d0); {2017/07/27; Fix C creation; SAS,BHH,MJE} | ||
0.860ALD2+ 0.570CH2O : GCARR_ac(2.70d-12, 350.0d0); {2017/07/27; Fix C creation; SAS,BHH,MJE} | ||
ATO2 + NO = NO2 + CH2O + MCO3 : GCARR_ac(2.80d-12, 300.0d0); {2017/07/27; Fix C creation; SAS,BHH,MJE} | ||
KO2 + NO = 0.930NO2 + 0.930ALD2 + | ||
0.930MCO3 + 0.070R4N2 : GCARR_ac(2.70d-12, 350.0d0); | ||
0.930MCO3 + 0.070ALK4N2 : GCARR_ac(2.70d-12, 350.0d0); {2023/05/14; Brewer2023; JFB} | ||
B3O2 + NO = NO2 + HO2 + ACET : GC_RO2NO_B2_aca(2.70d-12, 360.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF} | ||
B3O2 + NO = IPRNO3 : GC_RO2NO_A2_aca(2.70d-12, 360.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF} | ||
PRN1 + NO = 2.000NO2 + CH2O + ALD2 : GCARR_ac(2.70d-12, 350.0d0); | ||
ALK4 + NO3 = HNO3 + R4O2 : GCARR_ac(2.80d-12, -3280.0d0); | ||
ALK4 + NO3 = HNO3 + ALK4O2 : GCARR_ac(2.80d-12, -3280.0d0); {2023/05/14; Brewer2023; JFB} | ||
R4N2 + OH = R4N1 + H2O : 1.60d-12; | ||
ALK4N2 + OH = ALK4N1 + H2O : 1.60d-12; {2023/05/14; Brewer2023; JFB} | ||
ACTA + OH = MO2 + CO2 + H2O : GCARR_ac(3.15d-14, 920.0d0); {2013/02/12; JPL 10-6; BHH,JMAO,EAM} | ||
OH + RCHO = RCO3 + H2O : GCARR_ac(6.00d-12, 410.0d0); | ||
RCO3 + NO2 {+M} = PPN : GCJPLPR_abab(9.00d-28, 8.9d0, 7.7d-12, 0.2d0, 0.6d0); {JPL Eval 17} | ||
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@@ -616,6 +630,8 @@ PO2 + MO2 = HO2 + 0.500ALD2 + 1.250CH2O + | |
0.250ROH : 5.92d-13; | ||
R4O2 + HO2 = R4P : GCARR_ac(7.40d-13, 700.0d0); | ||
R4N1 + HO2 = R4N2 : GCARR_ac(7.40d-13, 700.0d0); | ||
ALK4O2 + HO2 = ALK4P : GCARR_ac(7.40d-13, 700.0d0); {2023/05/14; Brewer2023; JFB} | ||
ALK4N1 + HO2 = ALK4N2 : GCARR_ac(7.40d-13, 700.0d0); {2023/05/14; Brewer2023; JFB} | ||
ATO2 + HO2 = 0.150MCO3 + 0.150OH + | ||
0.150CH2O + 0.850ATOOH : GCARR_ac(8.60d-13, 700.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
KO2 + HO2 = 0.150OH + 0.150ALD2 + | ||
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@@ -637,6 +653,15 @@ R4N1 + MO2 = NO2 + 0.200CH2O + 0.380ALD2 + | |
0.290RCHO + 0.150R4O2 + 0.250RCHO + | ||
0.750CH2O + 0.250MOH + 0.250ROH + | ||
0.500HO2 : 8.37d-14; | ||
ALK4O2 + MO2 = 0.160ACET + 0.100MEK + | ||
0.090MO2 + 0.140HO2 + 0.160ALD2 + | ||
0.070RCHO + 0.030A3O2 + 0.090B3O2 + | ||
0.160OTHRO2 + 0.250MEK + 0.750CH2O + | ||
0.250MOH + 0.250ROH + 0.500HO2 : 8.37d-14; {2023/05/14; Brewer2023; JFB} | ||
ALK4N1 + MO2 = NO2 + 0.200CH2O + 0.380ALD2 + | ||
0.290RCHO + 0.150R4O2 + 0.250RCHO + | ||
0.750CH2O + 0.250MOH + 0.250ROH + | ||
0.500HO2 : 8.37d-14; {2023/05/14; Brewer2023; JFB} | ||
ATO2 + MO2 = 0.300HO2 + 0.300CH2O + | ||
0.300MCO3 + 0.200HAC + 0.200CH2O + | ||
0.500MGLY + 0.500MOH : GCARR_ac(7.50d-13, 500.0d0); | ||
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@@ -694,6 +719,8 @@ RA3P + OH = 0.640OH + 0.360A3O2 + | |
RB3P + OH = 0.791OH + 0.209B3O2 + | ||
0.791ACET : GCARR_ac(8.78d-12, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
R4P + OH = 0.791OH + 0.209R4O2 + 0.791RCHO : GCARR_ac(8.78d-12, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
ALK4P + OH = 0.791OH + 0.209ALK4O2 + | ||
0.791RCHO : GCARR_ac(8.78d-12, 200.0d0); {2023/05/14; Brewer2023; JFB} | ||
RP + OH = RCO3 : GCARR_ac(6.13d-13, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
PP + OH = 0.791OH + 0.209PO2 + 0.791HAC : GCARR_ac(8.78d-12, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
LVOC + OH = OH : GCARR_ac(4.82d-11, -400.0d0); {2017/06/14; Marais2016; EAM} | ||
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@@ -705,16 +732,23 @@ MCO3 + MO2 = ACTA + CH2O : GCARR_ac(2.00d-13, 500.0d0); | |
R4O2 + MCO3 = MO2 + 0.320ACET + 0.190MEK + | ||
0.270HO2 + 0.320ALD2 + 0.130RCHO + | ||
0.050A3O2 + 0.180B3O2 + 0.320OTHRO2 : GCARR_ac(1.68d-12, 500.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
ALK4O2 + MCO3 = MO2 + 0.320ACET + 0.190MEK + | ||
0.270HO2 + 0.320ALD2 + 0.130RCHO + | ||
0.050A3O2 + 0.180B3O2 + 0.320OTHRO2 : GCARR_ac(1.68d-12, 500.0d0); {2023/05/14; Brewer2023; JFB} | ||
ATO2 + MCO3 = MO2 + MCO3 + CH2O : GCARR_ac(1.68d-12, 500.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE} | ||
KO2 + MCO3 = MO2 + ALD2 + MCO3 : GCARR_ac(1.68d-12, 500.0d0); | ||
B3O2 + MCO3 = MO2 + HO2 + ACET : GCARR_ac(1.68d-12, 500.0d0); | ||
R4N1 + MCO3 = MO2 + NO2 + 0.390CH2O + | ||
0.750ALD2 + 0.570RCHO + 0.300R4O2 : GCARR_ac(1.68d-12, 500.0d0); | ||
ALK4N1 + MCO3 = MO2 + NO2 + 0.390CH2O + | ||
0.750ALD2 + 0.570RCHO + 0.300ALK4O2 : GCARR_ac(1.68d-12, 500.0d0); {2023/05/14; Brewer2023; JFB} | ||
PRN1 + MCO3 = MO2 + NO2 + CH2O + ALD2 : GCARR_ac(1.68d-12, 500.0d0); | ||
R4O2 + MCO3 = MEK + ACTA : GCARR_ac(1.87d-13, 500.0d0); | ||
ALK4O2 + MCO3 = MEK + ACTA : GCARR_ac(1.87d-13, 500.0d0); {2023/05/14; Brewer2023; JFB} | ||
ATO2 + MCO3 = MGLY + ACTA : GCARR_ac(1.87d-13, 500.0d0); {2017/07/27; Fix C creation; SAS,BHH,MJE} | ||
KO2 + MCO3 = MEK + ACTA : GCARR_ac(1.87d-13, 500.0d0); | ||
R4N1 + MCO3 = RCHO + ACTA + NO2 : GCARR_ac(1.87d-13, 500.0d0); | ||
ALK4N1 + MCO3 = RCHO + ACTA + NO2 : GCARR_ac(1.87d-13, 500.0d0); {2023/05/14; Brewer2023; JFB} | ||
PRN1 + MCO3 = RCHO + ACTA + NO2 : GCARR_ac(1.87d-13, 500.0d0); | ||
B3O2 + MCO3 = ACET + ACTA : GCARR_ac(1.87d-13, 500.0d0); | ||
MCO3 + ETO2 = MO2 + ALD2 + HO2 : GCARR_ac(1.68d-12, 500.0d0); | ||
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@@ -882,7 +916,7 @@ Cl + C3H8 = HCl + B3O2 : GCARR_ac(6.54d-11, 60.0d0); | |
Cl + C3H8 = HCl + A3O2 : GCARR_ac(8.12d-11, -90.0d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE} | ||
Cl + ACET = HCl + ATO2 : GCARR_ac(7.70d-11, -1000.0d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE} | ||
Cl + ISOP = HCl + 0.5IHOO1 + 0.5IHOO4 : GCARR_ac(7.60d-11, 500.0d0); {2019/11/06; Sherwen2016b;KHB,TS,JAS,SDE} | ||
Cl + ALK4 = HCl + R4O2 : 2.05d-10; {2017/09/22; Sherwen2016b;TS,JAS,SDE} | ||
Cl + ALK4 = HCl + ALK4O2 : 2.05d-10; {2023/05/14; Brewer2023; JFB} | ||
Cl + PRPE {+M} = HCl + PO2 {+M} : GCJPLPR_aa(4.00d-28, 2.8d-10, 0.6d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE} | ||
Br + PRPE = HBr + PO2 : 3.60d-12; {2017/09/22; Sherwen2016b;TS,JAS,SDE} | ||
I + NO {+M} = INO {+M} : GCJPLPR_aba(1.80d-32, 1.0d0, 1.77d-11, 0.6d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE} | ||
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@@ -1462,8 +1496,8 @@ AROMP5 + OH = 0.6MGLY + 0.15ACTA + | |
0.33RCO3 + 0.25CO + 0.52RCOOH : 5.0d-11; {2021/09/29; Bates2021b; KHB,MSL} | ||
AROMP5 + O3 = 0.6MGLY + 0.3ACTA + 0.2HCOOH + | ||
0.5CO + 0.95GLYC + 0.1HO2 + 0.1OH : 8.0d-16; {2021/09/29; Bates2021b; KHB,MSL} | ||
AROMP5 = 0.2HO2 + 0.2R4O2 + | ||
0.2MGLY + 1.2RCHO : 1.5d-3; {2021/09/29; Bates2021b; KHB,MSL} | ||
AROMP5 = 0.2HO2 + 0.2ALK4O2 + | ||
0.2MGLY + 1.2RCHO : 1.5d-3; {2021/09/29; Bates2021b; KHB,MSL}{2023/05/14; Brewer2023; JFB} | ||
// | ||
// KHB -- "we still need to include the dummy species for aromatic oxidation | ||
// to make the complex SOA code work. Hopefully this will be changed | ||
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@@ -1629,12 +1663,17 @@ ETP + hv = OH + HO2 + ALD2 : PHOTOL(80); | |
RA3P + hv = OH + HO2 + RCHO : PHOTOL(81); | ||
RB3P + hv = OH + HO2 + ACET : PHOTOL(82); | ||
R4P + hv = OH + HO2 + RCHO : PHOTOL(83); | ||
ALK4P + hv = OH + HO2 + RCHO : PHOTOL(83); {2023/05/14; Brewer2023; JFB} | ||
PP + hv = OH + HO2 + ALD2 + CH2O : PHOTOL(84); | ||
RP + hv = OH + HO2 + ALD2 : PHOTOL(85); | ||
R4N2 + hv = NO2 + 0.320ACET + 0.190MEK + | ||
0.180MO2 + 0.270HO2 + 0.320ALD2 + | ||
0.130RCHO + 0.050A3O2 + 0.180B3O2 + | ||
0.320OTHRO2 : PHOTOL(98); | ||
ALK4N2 + hv = NO2 + 0.320ACET + 0.190MEK + | ||
0.180MO2 + 0.270HO2 + 0.320ALD2 + | ||
0.130RCHO + 0.050A3O2 + 0.180B3O2 + | ||
0.320OTHRO2 : PHOTOL(98); {2023/05/14; Brewer2023; JFB} | ||
MAP + hv = OH + MO2 : PHOTOL(99); | ||
Br2 + hv = 2.000Br : PHOTOL(23); {2012/06/07; Parrella2012; JPP} | ||
BrO + hv = Br + O : PHOTOL(28); {2014/02/03; Eastham2014; SDE} | ||
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