Caltech isoprene scheme

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This page is for documentation of the isoprene chemistry mechanism (cf. Fabien Paulot) included in GEOS-Chem v9-02. This update was tested in the 1-month benchmark simulation v9-02g and approved on 24 Mar 2013.

Implementation of the Paulot isoprene scheme

This chemistry is largely base on Paulot et al.(2009a, ACP) for high-NOx regime and Paulot et al.(2009b, Science) for low-NOx regime. Other additions include:

  1. Isomerization of RIO2 base on Peeters et al. (2009, 2010) an Crounse et al. (2011).
  2. Isomerization of MRO2 base on Crounse et al. (2012).
  3. Nighttime isoprene oxidation based on Rollins et al. (2009) and Xie et al. (2012).
  4. Updates to the reactions of isoprene nitrates + O3 base on Lockwood et al. (2010).

Evaluation of this chemical mechanism is described here. If you have any questions, please let us know (Fabien Paulot, Jingqiu Mao ).

--Bob Y. 13:47, 12 May 2014 (EDT)

Species information

The following tables list the species that comprise the Paulot isoprene chemistry mechanism:

Species

Species Formula Note
A3O2 CH3CH2CH2OO primary RO2 from C3H8
ACET CH3C(O)CH3 acetone
ACTA CH3C(O)OH acetic acid
ALD2 CH3CHO acetaldehyde
ALK4 RH ≥C4 alkanes
ATO2 CH3C(O)CH2O2 RO2 from acetone
ATOOH CH3C(O)CH2OOH ATO2 peroxide
B3O2 CH3CH(OO)CH3 secondary RO2 from C3H8
C2H6 C2H6 ethane
C3H8 C3H8 propane
CH2O CH2O formaldehyde
CH4 CH4 methane
CO CO carbon monoxide
CO2 CO2 carbon dioxide
DHMOB HOCH2C(CH3)(OH)C(=O)CHO See Paulot et al., ACP (2009)
DIBOO Dibble peroxy radical
EOH C2H5OH ethanol
ETHLN CHOCH2ONO2 Ethanal nitrate
ETO2 CH3CH2OO ethylperoxy radical
ETP CH3CH2OOH ethylhydroperoxide
GLYC HOCH2CHO glycoaldehyde (hydroxyacetaldehyde)
GLYX CHOCHO glyoxal
H2 H2 hydrogen atom
H2O H2O water vapor
H2O2 H2O2 hydrogen peroxide
HAC HOCH2C(O)CH3 hydroxyacetone
HCOOH HCOOH formic acid
HC5 HOCH2CH=C(CH3)CHO Hydroxycarbonyl with 5C
HC5OO Peroxy radical from HC5 (old IAO2?)
HNO2 HONO nitrous acid
HNO3 HNO3 nitric acid
HNO4 HNO4 pernitric acid
HO2 HO2 hydroperoxyl radical
IALD HOCH2C(CH3)=CHCHO hydroxy carbonyl alkenes from isoprene
IAP HOCH2C(CH3)(OOH)CH(OH)CHO peroxide from IAO2
IEPOX Isoprene epoxide
IEPOXOO RO2 from IEPOX
INO2 O2NOCH2C(OO)(CH3)CH=CH2 RO2 from ISOP+NO3
INPN O2NOCH2C(OOH)(CH3)CH=CH2 peroxide from INO2
ISN1 nighttime isoprene nitrate
ISNOOA peroxy radical from ISN1
ISNOOB peroxy radical from ISN1
ISNOHOO peroxy radical from ISN1
ISNP HOCH2C(OOH)(CH3)CH(ONO2)CH2OH peroxide from ISOPNBO2 and ISOPNDO2
ISOP CH2=C(CH3)CH=CH2 isoprene
ISOPNB C5H9NO4 Isoprene nitrate Beta
ISOPND C5H9NO4 Isoprene nitrate Delta
KO2 RO2 from >3 ketones RO2 from >3 ketones
M for three body reactions
MACR CH2=C(CH3)CHO methacrolein
MACRN HOCH2C(ONO2)(CH3)CHO Nitrate from MVK
MAN2 HOCH2C(ONO2)(CH3)CHO RO2 from MACR+NO3
MAO3 CH2=C(CH3)C(O)OO peroxyacyl from MVK and MACR
MAOP CH2=C(CH3)C(O)OOH peroxide from MAO3
MAOPO2 CH2OH-CHOO*CH3C(O)OOH Peroxy radical from MAOP (addition on the double bond)
MAP CH3C(O)OOH peroxyacetic acid
MCO3 CH3C(O)OO peroxyacetyl radical
MEK RC(O)R >3 ketones
MGLY CH3COCHO methylglyoxyal
MNO3 CH3ONO2 methylnitrate
MOBA HOC(=O)C(CH3)=CHCHO 5C acid from isoprene
MOBAOO RO2 from MOBA
MO2 CH3O2 methylperoxy radical
MOH CH3OH methanol
MP CH3OOH methylhydroperoxide
MRO2 HOCH2C(OO)(CH3)CHO RO2 from MACR+OH
MRP HOCH2C(OOH)(CH3)CHO peroxide from MRO2
MVK CH2=CHC(=O)CH3 methylvinylketone
MVKN HOCH2CH(ONO2)C(=O)CH3 Nitrate from MACR
N2 N2 nitrogen
N2O N2O nitrous oxide
N2O5 N2O5 dinitrogen pentoxide
NH2 NH2 ammonia radical
NH3 NH3 ammonia
NO NO nitric oxide
NO2 NO2 nitrogen dioxide
NO3 NO3 nitrate radical
O2 O2 molecular oxygen
O2CH2OH O2CH2OH produced by CH2O+HO2
O3 O3 ozone
OH OH hydroxyl radical
PAN CH3C(O)OONO2 peroxyacetylnitrate
PMN CH2=C(CH3)C(O)OONO2 peroxymethacryloyl nitrate (MPAN)
PO2 HOCH2CH(OO)CH3 RO2 from isoprene
PP HOCH2CH(OOH)CH3 peroxide from PO2
PPN CH3CH2C(O)OONO2 peroxypropionylnitrate
PRN1 O2NOCH2CH(OO)CH3 RO2 from propene + NO3
PRPE C3H6 ≥C4 alkenes
PRPN O2NOCH2CH(OOH)CH3 peroxide from PRN1
PROPNN CH3C(=O)CH2ONO2 Propanone nitrate
PYAC CH3COCOOH Pyruvic acid
R4N1 RO2 from R4N2 RO2 from R4N2
R4N2 RO2NO ≥C4 alkylnitrates
R4O2 RO2 from ALK4 RO2 from ALK4
R4P CH3CH2CH2CH2OOH peroxide from R4O2
RA3P CH3CH2CH2OOH peroxide from A3O2
RB3P CH3CH(OOH)CH3 peroxide from B3O2
RCHO CH3CH2CHO >C2 aldehydes
RCO3 CH3CH2C(O)OO peroxypropionyl radical
RCOOH C2H5C(O)OH >C2 organic acids
RIO1 HOCH2C(OO)(CH3)CH=CHOH RO2 from isoprene oxidation products
RIO2 HOCH2C(OO)(CH3)CH=CH2 RO2 from isoprene (named as ISOPO2 in the literature)
RIP HOCH2C(OOH)(CH3)CH=CH2 peroxide from RIO2 (named as ISOPOOH in the literature)
ROH C3H7OH >C2 alcohols
RP CH3CH2C(O)OOH peroxide from RCO3
VRO2 HOCH2CH(OO)C(O)CH3 RO2 from MVK+OH
VRP HOCH2CH(OOH)C(O)CH3 peroxide from VRO2
DMS (CH3)2S dimethylsulfide
SO2 SO2 sulfur dioxide
SO4 SO4 sulfate radical
MSA CH4SO3 methanesulfonic acid
DRYDEP generic entry for dry dep
DRYPMNN Dry deposition for the different species
DRYALPH
DRYLIMO
DRYISOPND
DRYISOPNB
DRYRIP
DRYIEPOX
DRYMACRN
DRYMVKN
DRYPROPNN
DRYHCOOH
DRYACTA
EMISSION generic entry to do emissions

--Bob Y. 13:46, 12 May 2014 (EDT)

Species emitted and deposited

Species emitted Species deposited
NO NO2
NO2 O3
CO PAN
ALK4 HNO3
ISOP CH2O
ACET N2O5
PRPE H2O2
C3H8 PMN
C2H6 PPN
MEK R4N2
ALD2
CH2O PMNN
HNO3 IEPOX
O3 RIP
ISOPND
ISOPNB
PROPNN
MACRN
MVKN
HCOOH
ACTA
HAC
ALD2

--Bob Y. 13:46, 12 May 2014 (EDT)

Henry's law constant

This is effective Henry's law constant for water near neutral pH, mainly from Wesley et al. (1989). So the value would be different when you put in wetscav_mod.F.

Species H*(moles L-1 atm-1 ) ΔH/R (K) Reactivity factor (f0) Reference
NO2 0.01 0.1
Ox 0.01 1.0
PAN 3.6 1.0
HNO3 1.0d+14 0.0
H2O2 1.0d+5 1.0
PMN as PAN
PPN as PAN
R4N2 as PAN
CH2O 6.0e+3 1.0 Karl et al., 2010
GLYX 360000 -7200 1.0 Schweitzer et al., 1998
MGLY 3700 -7500 1.0 Ito et al., 2007
GLYC 41000 -4600 1.0 Ito et al., 2007
MPAN as PAN
N2O5 as HNO3
HCOOH 1.67d+5 -6100 1.0 Ito et al., 2007
ACTA 1.14d+4 -6300 1.0 Ito et al., 2007
ISOPND 1.7d+4 -9200 1.0 Ito et al., 2007
ISOPNB 1.7d+4 -9200 1.0 Ito et al., 2007
MVKN+MACRN 1.7d+4 -9200 1.0 Ito et al., 2007
PROPNN 1.0d+3 1.0 NITROOXYACETONE IN SANDER TABLE
RIP 1.7e6 1.0 Marais et al., 2012
IEPOX 1.3e8 1.0 Marais et al., 2012
MAP 8.4d+2 -5300 1.0 R. Sander
MVK 4.4d1 1.0 from R.Sander
MACR 6.5d0 1.0 from R.Sander
MOBA 23000 -6300 1.0 Ito et al., 2007
HAC 2.9e3 1.0 Ito et al., 2007
ALD2 1.5e1 1.0 R. Sander
SO2 1.0d+5 0.0

Karl, T., Harley, P., Emmons, L., Thornton, B., Guenther, A., Basu, C., Turnipseed, A., and Jardine, K.: Efficient Atmospheric Cleansing of Oxidized Organic Trace Gases by Vegetation, Science, 330, 816-819, 10.1126/science.1192534, 2010.

Reactions

The following tables list information about new reactions in the Paulot isoprene chemistry mechanism:

New reactions

No Reaction Rate Constant Reference Note
Reactions with OH
ISOP + OH = RIO2 3.1E-11exp(350/T) Sander et al. 2012 from JPL
MACR + OH = 0.53MAO3 +0.47MRO2 8.0E-12exp(380/T) Paulot 2009a MAO3(=MCO3 in the paper); MRO2(=MACROO in the paper)
MVK+OH = VRO2 2.6E-12exp(610/T)
PMN + OH = HAC + CO + NO2 2.90E-11 MCM v3.2 rates and products all from MCM, originally from Orlando et al. (2002)
GLYC + OH = 0.732CH2O +0.361CO2 + 0.505CO + 0.227OH + 0.773HO2 + 0.134GLYX + 0.134HCOOH FRAC=1-11.0729*exp(-1/73T) Rate=8.00E-12*FRAC Paulot 2009a Butkovskaya 2006 companion paper and Paulot 2009
GLYC + OH = HCOOH + OH + CO FRAC=1-11.0729*exp(-1/73T) Rate=8.00E-12*(1-FRAC) Paulot 2009a Butkovskaya 2006 companion paper and Paulot 2009
GLYX+ OH = HO2+2CO 3.1E-12exp(340/T) IUPAC2008 JMAO
HAC + OH = MGLY +HO2 FRAC=1-23.7*exp(1/60T) Rate=2.15E-12exp(305/T)*FRAC Paulot 2009a Butkovskaya JPC A (a,b)2006 and Paulot 2009a
HAC + OH = 0.5HCOOH + OH +0.5ACTA +0.5CO2 + 0.5CO + 0.5MO2 FRAC=1-23.7*exp(1/60T) Rate=2.15E-12exp(305/T)*(1-FRAC) Paulot 2009a Butkovskaya JPC A (a,b)2006 and Paulot 2009a
PRPN + OH =0.209PRN1+0.791OH+0.791PROPNN 8.78E-12exp(200/T) Branching ratio is determined by alpha and beta Hydrogen position (Kwok et al., 1995).
ETP + OH =0.64OH+0.36ETO2+0.60ALD2 5.18E-12exp(200/T) Branching ratio is determined by alpha and beta Hydrogen position (Kwok et al., 1995).
RA3P + OH =0.64OH+0.36A3O2+0.64RCHO 5.18E-12exp(200/T) Branching ratio is determined by alpha and beta Hydrogen position (Kwok et al., 1995).
RB3P + OH =0.791OH+0.209B3O2+0.791ACET 8.78E-12exp(200/T) Branching ratio is determined by alpha and beta Hydrogen position (Kwok et al., 1995).
R4P + OH =0.791OH+0.209R4O2+0.791RCHO 8.78E-12exp(200/T) Branching ratio is determined by alpha and beta Hydrogen position (Kwok et al., 1995).
RP + OH = RCO3 6.13E-13exp(200/T) same as MAP+OH
PP + OH =0.791OH+0.209PO2+0.791HAC 8.78E-12exp(200/T) Branching ratio is determined by alpha and beta Hydrogen position (Kwok et al., 1995).
RIP + OH = 0.387RIO2 + 0.613OH + 0.613HC5 4.75E-12exp(200/T) Paulot 2009b branching ratio is derived below
RIP + OH = OH + IEPOX 1.9E-11exp(390/T) Paulot 2009b the yield of IEPOX is > 70% assumed to be 100%
IEPOX + OH = IEPOXOO 5.78e-11exp(-400/T) Paulot 2009b
IAP + OH = 0.654OH + 0.654DHMOB + 0.346HC5OO 5.31E-12 exp(200/T)
VRP + OH =0.791OH+0.791MEK+0.209VRO2 8.78E-12exp(200/T)
MRP + OH = MRO2 1.84E-12exp(200/T) This channel is for the abstraction of peroxide H (OOH), which is slow and ignored in MCM v3.2
MRP + OH = CO2 + HAC + OH 4.40E-12exp(380/T) This second channel is for the abstraction of aldehydic H, much faster! The rate is from MACR + OH.
MAOP + OH = MAO3 6.13E-13exp(200/T) same as MAP+OH
MAOP + OH = MAOPO2 3.60E-12exp(380/T)
OH + MAP = 1.0MCO3 6.13E-13exp(200/T) From J. Orlando (unpublished results), how confident is this temperature dependence?
HC5 + OH =HC5OO 3.35E-11exp(380/T) Paulot 2009a
ISOPND + OH =ISOPNDO2 2.64E-11exp(380/T) Paulot 2009a
ISOPNB + OH =ISOPNBO2 3.61E-12exp(380/T) Paulot 2009a
ISNP + OH =0.612OH+0.612R4N1++0.193ISOPNBO2+0.193ISOPNDO2 4.75E-12exp(200/T) replace the old ISNP+OH
MVKN + OH = 0.650HCOOH+NO3+0.650MGLY+0.350CH2O+0.350PYAC 1.5E-12exp(380/T) Paulot 2009a
MACRN + OH = 1.0MACRNO2 1.39E-11exp(380/T)
DHMOB + OH = 1.5CO + 1.0HO2 + 0.5HAC + 0.5MEK 2.52E-11exp(410/T)
MOBA + OH =MOBAOO 2.79E-11exp(380/T)
ETHLN + OH =CH2O +CO2+NO2 1.00E-11
PROPNN+ OH =NO2+MGLY 1.00E-15 Paulot 2009a IUPAC says < 1e-12;Experiment suggests it is slower than than 1e-13-1e-15
ATOOH + OH = ATO2 + H2O 2.66E-12exp(200/T) Vaghjiani and Ravishankara (1989) Abstraction of peroxide H, follow MP + OH
ATOOH + OH = MGLY + OH +H2O 1.14E-12exp(200/T) Vaghjiani and Ravishankara (1989) Abstraction of alpha H, follow MP + OH
R4N2+OH = R4N1+H2O 1.6E-12 IUPAC06 JMAO: use the one from HO + 1-C4H9ONO2 → products
RO2 + NO reactions
RIO2 + NO = 0.883NO2 + 0.783HO2 + 0.660CH2O + 0.400MVK + 0.260MACR + 0.070ISOPND + 0.047ISOPNB + 0.123HC5 + 0.1DIBOO 2.7E-12 exp(350/T) Paulot 2009a HNO3 channel deleted since nitrate is treated explicitly;paulothn2009;neglect methylfuran formation (increase the yield of other products)
VRO2 + NO = 0.88NO2 + 0.35HO2 + 0.35CH2O + 0.53MCO3 + 0.53GLYC + 0.35MGLY + 0.12MVKN 2.7E-12 exp(350/T) Paulot 2009a
MRO2 + NO = 0.85NO2 + 0.85HO2 + 0.122MGLY + 0.728HAC + 0.728CO + 0.122CH2O + 0.15MACRN 2.7E-12 exp(350/T) Paulot 2009a This is modified based on Chuong et al. (2004).It was equally yield for MGLY and HAC in Paulot 2009 ACP, according to Peeters decomposition scheme.
MAN2 + NO = 1.5NO2 + 0.5CH2O + 0.5MGLY + 0.5PROPNN + 0.5CO + 0.5OH 2.7E-12 exp(350/T) Tyndall ETO2+NO
IEPOXOO + NO = 0.725HAC+0.275GLYC+0.275GLYX +0.275MGLY +0.125OH +0.825HO2+0.200CO2+0.375CH2O +0.074HCOOH +0.251CO +NO2 2.7E-12exp(350/T) FP: No peroxide was observed
MAOPO2 + NO = 1.0HAC+1.0CO2+1.0OH+1.0NO2 K* (1-YN) where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00)
MAOPO2 + NO = 1.0HNO3 K* YN where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00) Not treated explicitly
HC5OO + NO = NO2 + 0.216GLYX + 0.234MGLY + 0.234GLYC + 0.216HAC + 0.290DHMOB + 0.170MOBA + 0.090RCHO + HO2 + 0.090CO K* (1-YN) where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00)
HC5OO +NO=HNO3 K* YN where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=5.00E00)
ISOPNDO2 + NO = 0.070MACRN + 0.310HCOOH + 0.440HAC + 0.130ETHLN + 0.650CH2O + 1.340NO2 + 0.150GLYC + 0.310NO3 + 0.150PROPNN + 0.340MEK + 0.350HO2 K* (1-YN) where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00) Paulot 2009a
ISOPNDO2+NO=HNO3 K* YN where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=5.00E00) Nitrates from ISOPND could not be observed in this experiment
ISOPNBO2 + NO = 0.6GLYC + 0.6HAC + 0.4CH2O + 1.6NO2 + 0.26MACRN + 0.4HO2 + 0.14MVKN K* (1-YN) where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00) Paulot 2009a
ISOPNBO2 + NO = HNO3 K* YN where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=5.00E00) Nitrates from ISOPND could not be observed in this experiment
MACRNO2 + NO = 0.08ACTA + 0.08CH2O + 0.15NO3 + 0.07HCOOH + 0.070MGLY + 0.850HAC + 0.85NO2 + 0.93CO2 + 1.0NO2 2.7E-12exp(350/T) no nitrate yield (acyl)
DIBOO + NO =HO2+NO2+0.520GLYC +0.520MGLY +0.480HAC+0.480GLYX K* (1-YN) where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00) Dibble, 2004 Note that the yield of DIBOO Is likely overestimate (~30%)
DIBOO + NO =HNO3 K* YN where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=5.00E00)
MOBAOO + NO =RCHO+CO2+HO2+NO2 K* (1-YN) where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=4.00E00)
MOBAOO + NO =HNO3 K* YN where YN is returned from fyrno3.f K=2.7E-12 exp(350/T) (Xcarbn=5.00E00)
MAN2 + NO = 1.5NO2 + 0.5CH2O + 0.5MGLY + 0.5PROPNN + 0.5CO + 0.5OH 2.7E-12 exp(350/T)
MCO3+NO = MO2 + NO2 + CO2 8.10E-12 exp(270/T) JPL06
RCO3+NO = NO2+ETO2 6.70E-12 exp(340/T) IUPAC06 Products follow C2H5CO3+NO
MAO3 + NO = NO2 + 0.5CH2O + 0.5CO + CO2 + 0.5MO2 + 0.5MCO3 6.70E-12 exp(340/T)
ATO2+NO = 0.96NO2 + 0.960CH2O +0.960MCO3 + 0.04R4N2 2.80E-12 exp(300/T)
RO2 + HO2 reactions
RIO2 + HO2= 0.88RIP + 0.12OH + 0.047MACR + 0.073MVK + 0.12HO2 + 0.12CH2O 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 Paulot 2009b Rate is from Saunders et al. (2003)
VRO2 + HO2 = 0.1VRP + 0.68OH + 0.578GLYC + 0.578MCO3 + 0.187MEK + 0.102HO2 + 0.102CH2O + 0.102MGLY + 0.033RCHO 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4 ??? crounse2010
MRO2 + HO2 = 1.0MRP 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4 isomerization of MRO2 is included in another reaction.
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 assume 15% recycling of OH, the rest goes to ISNP
IEPOXOO + HO2 = 0.725HAC + 0.275GLYC + 0.275GLYX + 0.275MGLY + 1.125OH + 0.825HO2 + 0.200CO2 + 0.375CH2O + 0.074HCOOH + 0.251CO 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 Paulot 2009b
DIBOO + HO2 = 0.15HO2 + 0.15OH + 0.078GLYC + 0.078MGLY + 0.072HAC + 0.072GLYX + 0.85R4P 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 assume 15% recycling of OH, rest goes to R4P
MAOPO2 + HO2 = 1.0HAC+1.0CO2+2.0OH 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4
HC5OO + HO2 = 0.1IAP + 0.9OH + 0.9MGLY + 0.9GLYC + 0.9HO2 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 90% recycling, no experimental data. Somewhat based upon the high recycling rate observed for MVK/MACR
ISOPNDO2 + HO2 = 0.035MACRN + 0.155HCOOH + 0.22HAC + 0.065ETHLN + 0.325CH2O + 0.170NO2 + 0.075GLYC + 0.155NO3 + 0.075PROPNN + 0.170MEK + 0.175HO2 + 0.5OH + 0.5ISNP 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 Assume 50% recycling from HO2+RO2 (no experimental data - check Ng et al. for better estimates)
ISOPNBO2 + HO2 = 0.3GLYC + 0.3HAC + 0.2CH2O + 0.13MACRN + 0.07MVKN + 0.3NO2 + 0.2HO2 + 0.5OH + 0.5ISNP 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 Assume 50% recycling from HO2+RO2 (no experimental data - check Ng et al. for better estimates)
MACRNO2 + HO2 = 0.08ACTA + 0.08CH2O + 0.15NO3 + 0.07HCOOH + 0.07MGLY + 0.85HAC + 0.85NO2 + 0.93CO2 + 1.0OH 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4 Assume 100% recycling. No experiment data. Inferred from the very high recycling observed for MAO2+HO2
MOBAOO + HO2=0.15OH + 0.15HO2 + 0.15RCHO + 0.15CO2 + 0.85R4P 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 Paulot 2009a assume 15% recycling of OH, rest goes to R4P
MCO3 + HO2 = 0.15 ACTA + 0.15 O3 + 0.44 OH + 0.44 MO2 + 0.41 MAP 5.2e-13exp(980/T) IUPAC(Feb2009)
RCO3 + HO2 = 0.410RP + 0.150RCOOH + 0.150O3 + 0.440OH + 0.440ETO2 4.3E-13exp(1040/T) MCM v3.2 Branching ratio is from MCMv3.2
ATO2 + HO2 = 0.15MCO3 + 0.15OH + 0.15CH2O + 0.85ATOOH 8.60E-13 exp(700/T) Dillon et al. (2008) Tyndall, Dillon et al. (ACP 2008) cycling 15%,reduce the recyling by 5% compared to previous version to be fully consistent with Dillon et al.
KO2 + HO2 = 0.15OH + 0.15ALD2 + 0.15 MCO3 + 0.85ATOOH 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4 MCM assuming 15% recycling of OH
MAO3 + HO2 = 0.44OH +0.15O3 + 0.59CH2O + 0.39MO2 + 0.41MAOP + 0.39CO 4.3E-13exp(1040/T) use MCM, 44% OH channel, 15% O3 channel, 41% peroxide channel.
RO2 + MO2/RO2 reactions
RIO2 + MO2 = 1.1HO2 + 1.22CH2O + 0.280MVK + 0.180MACR + 0.3HC5 + 0.24MOH + 0.24ROH 8.37E-14
HC5OO + MO2 = 0.50HO2 + 0.33CO + 0.09H2 + 0.18HAC + 0.13GLYC + 0.29MGLY + 0.25MEK + 0.95CH2O + 0.25MOH + 0.25ROH + 0.5HO2 8.37E-14 Tyndall MO2+MO2 Atkinson97 RO2+RO2; HC5OO=old IAO2
MRO2 + MO2 = 0.595HAC + 0.255MGLY + 0.595CO + 1.255CH2O + 1.7HO2 + 0.150ROH 8.37E-14
VRO2 + MO2 = 0.14HO2 + 0.14CH2O + 0.36MCO3 + 0.36GLYC + 0.14MGLY + 0.25MEK + 0.75CH2O +0.25MOH + 0.25ROH + 0.5HO2 8.37E-14
MAN2 + MO2 = 0.375PROPNN + 0.375CO + 0.375HO2 + 0.375MGLY + 0.375CH2O + 0.375NO2 + 0.250CH2O + 0.250R4N2 8.37E-14
MAOPO2 + MO2 = 0.7HAC +0.7CO2+0.7OH+1.0CH2O+0.7HO2+0.3ROH 8.37E-14
RIO2 + RIO2 = 1.28HO2 + 0.92CH2O + 0.56MVK + 0.36MACR + 0.48ROH + 0.5HC5 1.54E-13
MAOPO2 + MAOPO2 = 2.0HAC+2.0CO2+2.0OH 8.37E-14
MCO3 + MO2 = CH2O + MO2 + HO2 1.80E-12 exp(500/T)
MCO3 + MO2 = ACTA + CH2O 2.00E-13 exp(500/T)
RCO3 + MO2 = CH2O+HO2 + ETO2 1.68E-12 exp(500/T)
RCO3 + MO2 = RCOOH + CH2O 1.87E-13 exp(500/T)
MAO3 + MO2 = CH2O + HO2 + CH2O + MCO3 1.68E-12 exp(500/T)
MAO3 + MO2 = RCOOH + CH2O 1.87E-13 exp(500/T)
RO2 + MCO3 reactions
MAOPO2 + MCO3 = 1.0HAC + 2.0CO2 + OH + MO2 1.68E-12exp(500/T)
MAOPO2 + MCO3 = 1.0ACTA+1.0MEK 1.87E-13 exp(500/T)
R4O2 + MCO3 = MO2 + 0.32ACET + 0.19MEK + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2 1.68E-12 exp(500/T)
R4O2 + MCO3 = 1.0ACTA+1.0MEK 1.87E-13 exp(500/T)
ATO2 + MCO3 = MCO3 + CH2O + MO2 1.68E-12 exp(500/T) IUPAC06
ATO2 + MCO3 = MGLY+ACTA 1.87E-13exp(500/T) IUPAC06 replace MEK with MGLY
HC5OO + MCO3 = 0.216GLYX + 0.234MGLY + 0.234GLYC + 0.216HAC + 0.29DHMOB + 0.17MOBA + 0.09RCHO + HO2 + 0.09CO + MO2 1.68E-12 exp(500/T) HC5OO=old IAO2, this radical channel use the same as HC5OO+NO without NO2 yield.
HC5OO + MCO3 = MEK +ACTA 1.87E-13 exp(500/T)
VRO2 + MCO3 = 0.4HO2 + 0.4CH2O + 0.6MCO3 + 0.6GLYC + 0.4MGLY + 1.0MO2 1.68E-12 exp(500/T) this radical channel use the same as VRO2+NO without NO2 and MVKN yield. And carbon balance.
VRO2 + MCO3 = MEK +ACTA 1.87E-13 exp(500/T)
MRO2 + MCO3 = 0.850HO2 + 0.143MGLY + 0.857HAC + 0.857CO + 0.143CH2O +1.0MO2 1.68E-12 exp(500/T) this radical channel use the same as MRO2+NO without NO2 and MACRN yield.
MRO2 + MCO3 = MEK +ACTA 1.87E-13 exp(500/T)
MAN2 + MCO3 = 0.5PROPNN + 0.5CO + 0.5HO2 + 0.5MGLY + 0.5CH2O + 0.5NO2 + CO2 + MO2 1.68E-12 exp(500/T)
MAN2 + MCO3 = RCHO + ACTA + NO2 1.87E-13 exp(500/T)
RIO2 + MCO3 = 0.887HO2 + 0.747CH2O + 0.453MVK + 0.294MACR + 0.140HC5 + 0.113DIBOO + CO2 + MO2 1.68E-12 exp(500/T) Follow RIO2+NO without the yield of nitrate and NO2 and then rescale it.
RIO2 + MCO3 = MEK +ACTA 1.87E-13 exp(500/T)
MCO3 + MCO3 = 2MO2 2.50E-12 exp(500/T) Tyndall2001
RCO3 + MCO3 = MO2 + ETO2 2.50E-12 exp(500/T) Tyndall2001
MAO3 + MCO3 = MO2 + MCO3 + CH2O 2.50E-12 exp(500/T) Tyndall2001
RO2 + NO2 equilibrium
MCO3+NO2+M = PAN LPL: 9.70E-29(300/T)^5.6; HPL:9.3E-12(300/T)^1.5; Fc: 0.6 JPL06
PAN = MCO3+NO2 9.30E-29 exp(14000/T) IUPAC06 equilibrium with the one above
RCO3+NO2 = PPN LPL: 9.00E-28(300/T)^8.9; HPL:7.70E-12(300/T)^0.2; Fc: 0.6 JPL06
PPN = RCO3+NO2 9e-29*exp(14000/T) JPL06
MAO3+NO2 = PMN LPL: 9.00E-28(300/T)^8.9; HPL:7.70E-12(300/T)^0.2; Fc: 0.6 JPL06
PMN = MAO3+NO2 9e-29*exp(14000/T) JPL06
MACRNO2+NO2= PMNN LPL: 9.00E-28(300/T)^8.9 HPL:7.70E-12(300/T)^0.2 Fc: 0.6
PMNN =MACRNO2 + NO2 9e-29*exp(14000/T)
Reactions with O3
ISOP + O3 = 0.244MVK + 0.325MACR + 0.845CH2O + 0.110H2O2 + 0.522CO + 0.204HCOOH + 0.199MCO3 + 0.026HO2 + 0.270OH + 0.128PRPE + 0.051MO2 1.00E-14 *EXP(-1970/T) MCM v3.2 rate is from JPL 11, products from MCM, assuming CH2OO is dominated by reactions with H2O. ISOP + O3 in standard chem is not carbon-balanced.
MVK + O3 = 0.202OH + 0.202HO2 + 0.352HCOOH + 0.535CO + 0.050ALD2 + 0.950MGLY + 0.050CH2O 8.5 E-16exp(-1520/T) MCM? Rate is from IUPAC06
MACR + O3 = 0.261OH + 0.202HO2 + 0.326HCOOH + 0.569CO + 0.880MGLY + 0.120CH2O 1.4 E-15exp(-2100/T) MCM?
HC5 + O3 = 0.6MGLY + 0.1OH + 0.12CH2O + 0.28GLYC + 0.3O3 + 0.4CO + 0.2H2 + 0.2HAC + 0.2HCOOH 6.16E-15 exp(-1814/T) HC5=old IALD??
ISOPNB + O3 = 0.610MVKN + 0.390MACRN + 0.27OH + CH2O 1.06E-16 Lockwood et al., 2010 ACP use 1,2 for beta channel
ISOPND + O3 = 0.5PROPNN + 0.5ETHLN + 0.27OH + 0.5GLYC + 0.5HAC 5.3E-17 Lockwood et al., 2010 ACP use 1,4 for delta channel
MOBA + O3 =OH +HO2+CO2+MEK 2.00E-17 Paulot 2009a Weak constraint on the rate constant - no constraint on the products
PMN + O3 = NO2 + 0.6CH2O + HO2 8.20E-18 ?
Isomerization reactions
RIO2 = 2.0HO2 + 1.0CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.500HAC + 1.0OH 4.07E+08 exp(-7694/T) Peeters et al. (2009, 2010) Isomerization rate is adjusted according to Crounse et al. (2010), products follow Stavrakou et al. (2010).
MRO2 = 1.0CO + 1.0HAC + 1.0OH 2.90E+07 exp(-5297/T) Crounse et al. (2012) 1,4-H-shift isomerization rate dominates over 1,5-H-shift.
Nighttime isoprene chemistry
ISOP + NO3 = INO2 3.3E-12exp(-450/T) Sander et al. 2012 from JPL
MACR + NO3 = MAN2 2.30E-15 IUPAC06
MACR + NO3 = MAO3 + HNO3 1.10E-15 IUPAC06 IUPAC06 total rate is 3.4E-15, so use the ratio from Lurmann et al.,1986
INO2 + NO = 0.70ISN1 + 0.035MVK + 0.035MACR + 0.07*CH2O + 0.80HO2 + 1.3NO2 + 0.23HC5 2.7E-12 exp(350/T) Rollins et al. (2009) ISN1 is the NIT1 in Rollins et al. (2009)
INO2 + NO3 = 0.70ISN1 + 0.035MVK + 0.035MACR + 0.07CH2O + 0.80HO2 + 1.3NO2 + 0.23*HC5 2.3E-12
INO2 + HO2 = INPN 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 Xie et al. (2012)
INPN + OH = 1.0OH + 1.0NO2 + 1.0MEK 1.9E-11exp(390/T)
INPN + OH = 0.36INO2 + 0.64R4N2 + 0.64OH 5.18E-12exp(200/T)
INO2 + MO2=0.35*ISN1 + 0.0175*MVK + 0.0175*MACR + 0.15*NO2 + 0.40*HO2 + 0.035*HCHO + 0.115*HC5 + 0.25*ISN1 + 0.25*ISOPND + 0.5*HCHO + 0.5*HO2 + 0.25*HCHO + 0.25*MEOH 1.30E-12
INO2 + MCO3 = MO2 + 0.70ISN1 + 0.035MVK + 0.035MACR + 0.07CH2O + 0.80HO2 + 0.3NO2 + 0.23HC5 1.68E-12 exp(500/T)
INO2 + MCO3 = RCHO + ACTA + NO2 1.87E-13 exp(500/T)
INO2 + INO2 = 0.3NO2 + 0.70ISN1 + 0.035MVK + 0.035MACR + 0.07CH2O + 0.8 HO2 + 0.23HC5 + 0.5ISN1 + 0.5ISOPND 1.20E-12
ISN1 + NO3 = 0.6*ISNOOA + 0.4* ISNOOB + 0.6*HNO3 3.15E-13*exp(-448/T) Xie et al. (2012) ISNOOA and ISNOOB correspond to NIT1NO3OOA and NIT1NO3OOB in Xie et al. (2012)
ISNOOA + NO3 = NO2 + R4N2 + CO +HO2 4.00E-12
ISNOOA + NO = NO2 + R4N2 + CO +HO2 6.70E-12*exp(340/T)
ISNOOA + HO2 = 0.75RP + 0.25RCOOH + 0.25O3 5.20E-13*exp(980/T)
ISNOOA + NO2 = MPAN LPL: 9.00E-28(300/T)^8.9; HPL:7.70E-12(300/T)^0.2; Fc: 0.6
ISNOOB + NO3=R4N2 + GLYX + NO2 + NO2 2.30E-12
ISNOOB + NO = 0.94R4N2 + 0.94GLYX + 0.94 NO2 + 0.94 NO2 2.60E-12*exp(380/T)
ISNOOB + HO2 = INPN 2.06E-13*exp(1300/T)
ISNOOB + MO2 = 0.7R4N2 + 0.7GLYX + 0.7NO2 + 0.25HCHO + 0.25MOH + 0.5HO2 + 0.5HCHO 2.0E-13
ISN1 + O3 = 0.3R4N2 + 0.45CO + 0.15OH + 0.45 HO2 + 0.7 GLYX + 0.7 OH + 0.7NO2 + 0.7MGLY 4.15E-15*exp(-1520/T)
ISN1 + OH = 0.345ISNOOA + 0.655ISNOHOO 7.48E-12*exp(410/T) ISNOHOO is NIT1OHOO in Xie et al. (2012).
ISNOHOO + NO = 0.934R4N2 + 0.934HO2 + 0.919GLYX 2.60E-12*exp(380/T)
ISNOHOO + HO2 = INPN 2.06E-13*exp(1300/T)
ISNOHOO + MO2 = 0.7R4N2 + 0.7 GLYX + 0.7HO2 + 0.25 HCHO + 0.25MOH + 0.5 CH2O + 0.5 HO2 2.0E-13
Photolysis reactions
O3 + H2O = 2.0OH JO1D JPL2011 Assume steady state of O1D. The rate is calculated in calcrate.F with the quenching from N2 and O2 taken into account.
NO2 = NO + O3 JNO2
H2O2 = 2OH JH2O2
MP = CH2O + HO2 + OH J_ROOH
CH2O = HO2 + HO2 + CO
CH2O = H2 + CO
HNO3 = OH + NO
HNO4 = OH + NO3 J_HO2NO2*0.05 Chemistry_Issues#near-IR_photolysis_of_HNO4
HNO4 = HO2 + NO2 J_HO2NO2*0.95 Chemistry_Issues#near-IR_photolysis_of_HNO4
NO3 = NO2 + O3
NO3 = NO + O2
N2O5 = NO3 + NO2
N2O5 = NO3 + NO + O3 0 turned off
ALD2 = MO2 + HO2 + CO
ALD2 = CH4 + CO
PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2
RCHO = ETO2 + HO2 + CO
ACET = MCO3 + MO2
ACET = 2.0MO2 + CO
MEK = 0.85MCO3 + 0.85ETO2 + 0.15MO2 + 0.15RCO3
GLYC = CH2O + 2.0HO2 + CO
GLYX = 0.5H2 + CO + 0.5CH2O + 0.5CO
GLYX = 2.0CO + 2.0HO2
MGLY = MCO3 + CO +HO2 J_MGLY
MGLY = ALD2 + CO 0 turned off
MVK = PRPE + CO J_MVK*0.6
MVK = MCO3 + CH2O + CO + HO2 J_MVK*0.2
MVK = MO2 + MAO3 J_MVK*0.2
MACR = MAO3 + HO2 J_MACR*0.5
MACR = CO + HO2 + CH2O + MCO3 J_MACR*0.5
HAC = MCO3 + CH2O + HO2
INPN = OH + HO2 + RCHO + NO2 J_ROOH
PRPN = OH + HO2 + RCHO + NO2 J_ROOH
ETP = OH + HO2 + ALD2 J_ROOH
RA3P = OH + HO2 + RCHO J_ROOH
RB3P = OH + HO2 + ACET J_ROOH
R4P = OH + HO2 + RCHO J_ROOH
PP = OH + HO2 + ALD2 + CH2O J_ROOH
RP = OH + HO2 + ALD2 J_ROOH
RIP = OH + HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.29HC5 J_ROOH
IAP = OH + HO2 + 0.67CO + 0.190H2 + 0.36HAC + 0.26GLYC + 0.580MGLY J_ROOH
ISNP = OH + HO2 + RCHO + NO2 J_ROOH
VRP = OH + 0.3HO2 + 0.3CH2O + 0.7MCO3 + 0.7GLYC + 0.3MGLY J_ROOH
MRP = OH + HO2 + HAC + CO + CH2O J_ROOH
MAOP = OH + CH2O + MCO3 J_ROOH
R4N2 = NO2 + 0.320ACET + 0.190MEK + 0.180MO2 + 0.270HO2 + 0.320ALD2 + 0.130RCHO + 0.050A3O2 + 0.180B3O2 + 0.320ETO2 J_MeNO3
MAP = OH + MO2 J_ROOH
MACRN = NO2 + HAC + MGLY + 0.5CH2O + HO2 + 0.5CO J_ONIT1
MVKN = GLYC + NO2 + MCO3 J_ONIT1
ISOPNB = HC5 + NO2 + HO2 J_ONIT1
ISOPND = HC5 + NO2 + HO2 J_ONIT1
PROPNN = CH2O + NO2 + CO + MO2 J_ONIT1
ATOOH = OH + CH2O +MCO3 J_ROOH

--Bob Y. 13:48, 12 May 2014 (EDT)

RIP+OH

Follow SAR rules assuming a C(OOH) = 2* C(OH) = 7 (for the abstraction of the H alpha of the peroxide group). (see Kwok 1995 paper)

Assume that the abstraction of the peroxide H has a constant rate @298K of 3.6e-12

This gives for RIP:

43% 3.6e-12 (1,2)
28% 3.6e-12+7*1.94e-12 (4,3)
29% 3.6e-12+7*0.937e-12 (1,4)+(4,1) (I neglected 3,4 and 2,1)
9.3e-12@298K (4.75e-12*exp(200/T))
0.387 not recycling

Therefore 0.387=3.6/9.3. RIP + OH = 0.387RIO2 + 0.613OH + 0.613HC5.

Updates to the Paulot isoprene scheme

NO3 aerosol reactive uptake coefficient

This update was tested in the 1-month benchmark simulation v9-02g and approved on 24 Mar 2013.

The NO3 aerosol reactive uptake coefficient (gamma) has been increased from 1.0E-04 (Jacob et al., 2000) to 0.1 following Mao et al. (2013, submitted). In globchem.dat, we now have:

A  415 6.20E+01  1.0E-01      0 0 K   0.00     0.     0.         
      NO3           +                                                     
=1.000HNO3          +                   +                   +             
+                   +                   +                   +             
+                   +                   +                   +             
+                   +                   +                   +

--Melissa Sulprizio 12:44, 11 July 2013 (EDT)

There are two reasons for this modification.

  1. First, a few recent papers show potential high gamma(NO3) on all types of aerosols.
  2. Second, gamma(NO3) is supposed to increase at lower temperature (driven by its Henry's law constant), while most laboratory measurements are conducted at 298 K.

From the tests I have done so far, ozone seems to be insensitive to gamma(NO3) in the range of 0.0001-0.1.

--Jmao 13:11, 11 July 2013 (EDT)

Update One - RO2+HO2 Reaction Rate

This update was tested in the 1-month benchmark simulation v9-02g and approved on 24 Mar 2013. This update is included in Adjoint v35k.

Update applied to all >C2 RO2 species reaction with HO2. These include, in the standard scheme, R4O2, R4N1, KO2, RIO2, RIO1, IAO2,ISN1, VRO2, MRO2, MVN2, MAN2, B3O2, INO2, PRN1, A3O2, PO2.

Old RO2+HO2 reaction rate: k = 7.40E-13*EXP(700/T)

New RO2+HO2 reaction rate: k = 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], where n=no. of carbon atoms

Comparison of new and old RO2+HO2 reaction rates for C4 RO2 and C5 RO2:

Ro2 ho2 rate.jpg

Benchmarking for this update can be viewed at: (Benchmarking results for RO2+HO2 reaction)

Note: this is applied to RIO2, VRO2, MRO2, MAN2, INO2, HC5OO, ISOPNBO2, ISOPNDO2, MACRNO2, DIBOO, MOBAOO in the new isoprene chemistry, but not MAO3, MCO3, RCO3 radicals (acetyl peroxy type radicals.

--Bob Y. 13:49, 12 May 2014 (EDT)

Update Two - Transport of RIP

RIP = isoprene peroxide species formed at low-NOx (i.e. via the RO2+HO2 pathway)

This benchmark is done to understand the muted influence of the increased rate of the RO2+HO2 reaction on CH2O. Is this because the ultimate yield of CH2O is similar for all levels of NOx and RIP is not transported, leading to the realization of the ultimate yield of CH2O in the same grid box as its emission source?

Both schemes are run with initial concentrations of species set to zero. As RIP is added as an additional transported species this was viewed as the most effective way of comparing the two model runs.

Benchmarking for this update can be viewed at: (Benchmarking results for transporting RIP)

--Bob Y. 13:50, 12 May 2014 (EDT)

Updates 02/04/2013

These reactions are updated from the beta-version of Paulot scheme.

Old reaction Old rate New reaction New rate Note
KO2+HO2 =OH +ALD2 +MCO3 7.40E-13 exp(700/T) KO2 + HO2 = 0.15OH +0.15ALD2 +0.15 MCO3 + 0.85 ATOOH 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4 Assuming 15% recycling of OH, consistent with MCM. Rate is also from Saunders et al. (2003).
MRO2 +HO2 =0.020MRP+0.980OH +0.980HO2+0.294CH2O+0.686HAC +0.294MGLY +0.686CO 7.40E-13 exp(700/T) MRO2 + HO2 = 1.0MRP 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4 Isomerization of MRO2 is already taken into account in another reaction.
MAN2 + HO2 = 0.5PROPNN + 0.5CO + 0.5HO2 + 0.5MGLY + 0.5CH2O + 0.5NO2 + OH 7.40E-13 exp(700/T) 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 assuming 15% recycling
INO2 + HO2 = 0.5INPN + 0.5ISOPND + 0.5OH + 0.5HO2 7.40E-13 exp(700/T) INO2 + HO2 = INPN 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 See nighttime chemistry
MAO3 + HO2 = 0.87OH +0.03O3 + 0.435CH2O + 0.435MO2 + 0.1MAOP + 0.030RCOOH + 0.283HAC + 0.152ATO2 + 0.870CO2 + 0.435CO 4.3E-13exp(1040/T) MAO3 + HO2 = 0.44OH +0.15O3 + 0.59CH2O + 0.39MO2 + 0.41MAOP + 0.39CO 4.3E-13exp(1040/T) use MCM, 44% OH channel, 15% O3 channel, 41% peroxide channel.
PMN + OH = 1.000PMNO2 3.20E-11 PMN + OH = HAC + CO + NO2 2.90E-11 from MCM
PMNO2 + NO = 0.6CO2 + 0.6HAC + 0.6NO3 + 0.4CH2O + 0.4HO2 + 0.4PYPAN + 0.900NO2 K* (1-YN) where YN isreturned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.0E00) we now remove all reactions from PMN following MCM.
PMNO2 + NO=PMNN K* YN where YN is returned from fyrno3.f ; K=2.7E-12 exp(350/T) (Xcarbn=4.0E00)
PMNO2 + HO2 = 0.6CO2 + 0.6HAC + 0.6NO3 + 0.4CH2O + 0.4HO2 + 0.4PYPAN + 0.5R4P + 0.5OH 7.4E-13exp(700/T)
PYPO2 + NO2 + M = PYPAN LPL: 9.0E-28(300/T)^8.9 HPL:7.70E-12(300/T)^0.2 Fc: 0.6
PYPAN =PYPO2 +NO2 9.0E-29exp(14000/T)
PYPO2 + NO = CO2+MCO3 +NO2 2.7E-12 exp(350/T)
PYPO2 + HO2 = CO2+MCO3 +OH 7.40E-13 exp(700/T)
PYPAN = 0.300NO3+0.700NO2+MCO3 +CO2 photolysis
PYPAN = NO3 + MCO3 + CO2 photolysis
PP+OH=0.791OH+0.209PO2+0.791RCHO 8.78E-12exp(200/T) PP+OH=0.791OH+0.209PO2+0.791HAC
DIBOO+HO2 = HO2 + OH + 0.52GLYC + 0.52MGLY + 0.48HAC + 0.48GLYX 7.4E-13exp(700/T) DIBOO + HO2 = 0.15HO2 + 0.15OH + 0.078GLYC + 0.078MGLY + 0.072HAC + 0.072GLYX + 0.85R4P 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 assume 15% recycling of OH, rest goes to R4P
MOBAOO + HO2 = 0.5OH + 0.5HO2 + 0.5RCHO + 0.5CO2 + 0.5R4P 7.4E-13exp(700/T) MOBAOO + HO2=0.15OH + 0.15HO2 + 0.15RCHO + 0.15CO2 + 0.85R4P 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5 assume 15% recycling of OH, rest goes to R4P
IEPOXOO + HO2 = 7.4E-13exp(700/T) 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5
MAOPO2 + HO2 = 7.4E-13exp(700/T) 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4
HC5OO + HO2 = 7.4E-13exp(700/T) 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5
ISOPNDO2 + HO2 = 7.4E-13exp(700/T) 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5
ISOPNBO2 + HO2 = 7.4E-13exp(700/T) 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=5
MACRNO2 + HO2 = 7.4E-13exp(700/T) 2.91E-13*EXP(1300/T)[1-EXP(-0.245*n)], n=4

--Bob Y. 13:50, 12 May 2014 (EDT)

Previous issues that have now been resolved

Set ACTA and HCOOH to active in globchem.dat

This issue will be fixed in v11-01h.

Katie Travis reported an error in the globchem.dat file. Both ACTA and HCOOH are set to inactive (I), but they undergo chemistry and should be set to active (A).

NOTE: FlexChem will likely be installed by v11-01h. Therefore, we will make sure that this fix is introduced into the KPP master equation file. FlexChem will remove SMVGEAR (and the globchem.dat file) completely from GEOS-Chem.

--Melissa Sulprizio (talk) 15:26, 5 February 2016 (UTC)
--Bob Yantosca (talk) 14:58, 8 February 2016 (UTC)

Syntax error in globchem.dat file for MOBA reaction rate

This issue will be fixed in v11-01f.

Will Porter wrote:

I wanted to pass on what I believe is a small error in the default GEOS-Chem v9-02 globchem.dat file. The first line of the MOBA + OH —> MOBAOO reaction reads:

    A 999 2.79E-11   0.0E+00    380 0     0.00     0.     0.

However, there is only one space between the “A” and the “999”, resulting in (I believe) an incorrect parsing of the following numerical value, as evidenced in the smv2.log file:

    388 7.9E-12    0.00    380 .00 MOBA  +OH    +      =1.0MOBAOO

My tests seem to show that the impact on surface O3 is minimal, but anyone interested in this particular species (“5C acid from isoprene”), or isoprene chemistry in general, will likely be very interested in having it fixed! Over the US, correcting globchem.dat reduces average MOBA levels by around 2-6%. I’ve attached plots of base surface MOBA using a nested NA run (2010-2011), along with absolute change and percent change using a corrected globchem.dat file.

Will porter.png

--Bob Yantosca (talk) 22:08, 8 January 2016 (UTC)

Bug in reaction ISNOOA + NO2 in globchem.dat

This issue will be fixed in v11-01f.

Mike Long wrote:

I was comparing rate values btw Flex and Classic KPP implementations:
For the reaction ISNOOA + NO2 --> PMN, the rates in FlexChem were consistently a factor of 1E+15(!!) greater than Classic's values.
A typical value at the surface in the tropics for FlexChem is ~7E-12
A typical value at the surface in the tropics for calcrate is ~9E-28 (really small!)
I double checked: The calculation 'seems' straightforward, globchem.dat indicating it should be treated as pressure dependent, and thus controlled by the "DO 165" loop in calcrate.F.
Barron Henderson did a back-of-the-envelope test and wrote, "Odd. I cut the appropriate code out of calcrate and got the flex chem number. I don't know of any special processing (Mat?). Could the read be choking? Is the FCV value reading right?"
Note that the calcrate.F value is about equivalent to the 1st parameter value passed to the routine (9e-28). The oddity is that all the other reactions that use this same bit of calcrate code to calculate pressure dependent rates are just fine.
Follow-up: In globchem.dat, the reaction statement is missing it's requisite "M". Adding it fixed the differences.

To apply this fix change the following lines in globchem.dat

    A  442 9.00E-28  8.9E+00      0 1 P   0.60     0.     0.    
           7.70E-12  0.2E+00      0 0     0.00     0.     0.    
          ISNOOA        +     NO2                               
    =1.000PMN           +                   +                   +
    +                   +                   +                   +
    +                   +                   +                   +
    +                   +                   +                   +

to

    A  442 9.00E-28  8.9E+00      0 1 P   0.60     0.     0.    
           7.70E-12  0.2E+00      0 0     0.00     0.     0.    
          ISNOOA        +     NO2                 M
    =1.000PMN           +                   +                   +
    +                   +                   +                   +
    +                   +                   +                   +
    +                   +                   +                   +

--Melissa Sulprizio (talk) 18:37, 26 January 2016 (UTC)

Remove duplicate GLYX product from RIO2 reaction

This update was validated in the 1-month benchmark simulation v10-01d and approved on 03 Jun 2014.

Ploy Achakulwisut found a typo in this reaction for RIO2 (in file globchem.dat). The product 0.5GLYX was listed twice but should have been listed just once. The fix is as described below.

Old reaction Old rate New reaction New rate Note
RIO2 = 2.0HO2 + 1.0CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.500HAC + 1.0OH 4.07E+08 exp(-7694/T) RIO2 = 2.0HO2 + 1.0CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.500HAC + 1.0OH same To balance carbon

--Bob Y. 13:53, 12 May 2014 (EDT)

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--Bob Y. 13:55, 12 May 2014 (EDT)