Difference between revisions of "Caltech isoprene scheme"
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− | ''' | + | <div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>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 [[GEOS-Chem_v9-02_benchmark_history#v9-02g|v9-02g]] and approved on 24 Mar 2013.</p><p>Previous page of description can be found here [[New isoprene scheme prelim]].</p><p>— Bob Yantosca, 28 May 2014</p>'''</div> |
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== Implementation of the Paulot isoprene scheme == | == Implementation of the Paulot isoprene scheme == |
Revision as of 19:05, 28 May 2014
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.
Previous page of description can be found here New isoprene scheme prelim.
— Bob Yantosca, 28 May 2014
Contents
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:
- Isomerization of RIO2 base on Peeters et al. (2009, 2010) an Crounse et al. (2011).
- Isomerization of MRO2 base on Crounse et al. (2012).
- Nighttime isoprene oxidation based on Rollins et al. (2009) and Xie et al. (2012).
- 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.
- First, a few recent papers show potential high gamma(NO3) on all types of aerosols.
- 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.
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:
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)
Updates to be implemented
The following updates have not yet been added to GEOS-Chem as of this writing (May 2013):
Remove duplicate GLYX product from RIO2 reaction
This update is slated to be added into GEOS-Chem v10-01d.
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)
References
- Butkovskaya, N. I., Pouvesle, N., Kukui, A., and Le Bra, G.: Mechanism of the OH-initiated oxidation of glycolaldehyde over the temperature range 233-296 K, J. Phys. Chem. A, 110, 13492-13499, 10.1021/jp064993k, 2006a.
- Butkovskaya, N. I., Pouvesle, N., Kukui, A., Mu, Y. J., and Le Bras, G.: Mechanism of the OH-initiated oxidation of hydroxyacetone over the temperature range 236-298 K, J. Phys. Chem. A, 110, 6833-6843, 10.1021/jp056345r, 2006b.
- Chuong, B., and Stevens, P.: Measurements of the kinetics of the OH-initiated oxidation of methyl vinyl ketone and methacrolein, Int. J. Chem. Kinet., 36, 12-25, 2004.
- Crounse, J. D., Paulot, F., Kjaergaard, H. G., and Wennberg, P. O.: Peroxy radical isomerization in the oxidation of isoprene, Phys. Chem. Chem. Phys., 13, 13607-13613, 10.1039/C1CP21330J 2011.
- Crounse, J. D., Knap, H. C., Ørnsø, K. B., Jørgensen, S., Paulot, F., Kjaergaard, H. G., and Wennberg, P. O.: Atmospheric Fate of Methacrolein. 1. Peroxy Radical Isomerization Following Addition of OH and O2, The Journal of Physical Chemistry A, 116, 5756-5762, 10.1021/jp211560u, 2012.
- Dillon, T. J., and Crowley, J. N.: Direct detection of OH formation in the reactions of HO2 with CH3C(O)O-2 and other substituted peroxy radicals, Atmos. Chem. Phys., 8, 4877-4889, 2008.
- Ito, A., Sillman, S., and Penner, J. E.: Effects of additional nonmethane volatile organic compounds, organic nitrates, and direct emissions of oxygenated organic species on global tropospheric chemistry, J. Geophys. Res.-Atmos., 112, 10.1029/2005jd006556, 2007.
- Jenkin, M. E., Saunders, S. M., and Pilling, M. J.: The tropospheric degradation of volatile organic compounds: a protocol for mechanism development, Atmos. Environ., 31, 81-104, http://dx.doi.org/10.1016/S1352-2310(96)00105-7, 1997.
- Kwok, E. S. C., and Atkinson, R.: Estimation of hydroxyl radical reaction-rate constants for gas-phase organic-compounds using a structure-reactivity relationship - an update, Atmos. Environ., 29, 1685-1695, 10.1016/1352-2310(95)00069-b, 1995.
- Lockwood, A. L., Shepson, P. B., Fiddler, M. N., and Alaghmand, M.: Isoprene nitrates: preparation, separation, identification, yields, and atmospheric chemistry, Atmos. Chem. Phys., 10, 6169-6178, 10.5194/acp-10-6169-2010, 2010.
- Lurmann, F. W., Lloyd, A. C., and Atkinson, R.: A chemical mechanism for use in long-range transport acid deposition computer modeling, J. Geophys. Res.-Atmos., 91, 905-936, 1986.
- Madronich, S., and Calvert, J. G.: Permutation reactions of organic peroxy radicals in the troposphere, Journal of Geophysical Research: Atmospheres, 95, 5697-5715, 10.1029/JD095iD05p05697, 1990.
- Mao, J., F. Paulot, D.J. Jacpb, R.C. Cohen, J.D. Crounse, P.O. Wennberg, C.A. Keller, R.C. Hudman, M.P. Barkley, and L.W. Horowitz, Ozone and organic nitrates over the eastern United States: sensitivity to isoprene chemistry, Journal of Geophysical Research: Atmospheres, 118, doi:10.1002/jgrd.50817, 2013, http://dx.doi.org/10.1002/jgrd.50817.
- Marais, E. A., Jacob, D. J., Kurosu, T. P., Chance, K., Murphy, J. G., Reeves, C., Mills, G., Casadio, S., Millet, D. B., Barkley, M. P., Paulot, F., and Mao, J.: Isoprene emissions in Africa inferred from OMI observations of formaldehyde columns, Atmos. Chem. Phys., 12, 6219-6235, 10.5194/acp-12-6219-2012, 2012.
- Master Chemical Mechanism, MCM v3.2 (Jenkin et al., Atmos. Environ., 31, 81, 1997; Saunders et al., Atmos. Chem. Phys., 3, 161, 2003), via website: http://mcm.leeds.ac.uk/MCM.
- Orlando, J. J., Tyndall, G. S., Bertman, S. B., Chen, W., and Burkholder, J. B.: Rate coefficient for the reaction of OH with CH2C(CH3)C(O)OONO2 (MPAN), Atmos. Environ., 36, 1895-1900, http://dx.doi.org/10.1016/S1352-2310(02)00090-0, 2002.
- Paulot, F., Crounse, J. D., Kjaergaard, H. G., Kroll, J. H., Seinfeld, J. H., and Wennberg, P. O.: Isoprene photooxidation: new insights into the production of acids and organic nitrates, Atmos. Chem. Phys., 9, 1479-1501, 2009a.
- Paulot, F., Crounse, J. D., Kjaergaard, H. G., Kurten, A., St Clair, J. M., Seinfeld, J. H., and Wennberg, P. O.: Unexpected Epoxide Formation in the Gas-Phase Photooxidation of Isoprene, Science, 325, 730-733, 10.1126/science.1172910, 2009b.
- Peeters, J., Nguyen, T. L., and Vereecken, L.: HOx radical regeneration in the oxidation of isoprene, Phys. Chem. Chem. Phys., 11, 5935-5939, 10.1039/b908511d, 2009.
- Peeters, J., and Müller, J. F.: HOx radical regeneration in isoprene oxidation via peroxy radical isomerisations. II: experimental evidence and global impact, Phys. Chem. Chem. Phys., 12, 14227-14235, 10.1039/c0cp00811g, 2010.
- Rollins, A. W., Kiendler-Scharr, A., Fry, J. L., Brauers, T., Brown, S. S., Dorn, H. P., Dubé, W. P., Fuchs, H., Mensah, A., Mentel, T. F., Rohrer, F., Tillmann, R., Wegener, R., Wooldridge, P. J., and Cohen, R. C.: Isoprene oxidation by nitrate radical: alkyl nitrate and secondary organic aerosol yields, Atmos. Chem. Phys., 9, 6685-6703, 10.5194/acp-9-6685-2009, 2009.
- Saunders, S. M., Jenkin, M. E., Derwent, R. G., and Pilling, M. J.: Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds, Atmos. Chem. Phys., 3, 161-180, 2003.
- Sander, S. P., J. Abbatt, J. R. Barker, J. B. Burkholder, R. R. Friedl, D. M. Golden, R. E. Huie, C. E. Kolb, M. J. Kurylo, G. K. Moortgat, V. L. Orkin and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 17," JPL Publication 10-6, Jet Propulsion Laboratory, Pasadena, 2011 http://jpldataeval.jpl.nasa.gov.
- Stavrakou, T., Peeters, J., and Muller, J. F.: Improved global modelling of HOx recycling in isoprene oxidation: evaluation against the GABRIEL and INTEX-A aircraft campaign measurements, Atmos. Chem. Phys., 10, 9863-9878, 10.5194/acp-10-9863-2010, 2010.
- Tyndall, G. S., Cox, R. A., Granier, C., Lesclaux, R., Moortgat, G. K., Pilling, M. J., Ravishankara, A. R., and Wallington, T. J.: Atmospheric chemistry of small organic peroxy radicals, Journal of Geophysical Research: Atmospheres, 106, 12157-12182, 10.1029/2000jd900746, 2001.
- Vaghjiani, G. L., and Ravishankara, A. R.: Kinetics and mechanism of hydroxyl radical reaction with methyl hydroperoxide, The Journal of Physical Chemistry, 93, 1948-1959, 10.1021/j100342a050, 1989.
- Xie, Y., Paulot, F., Carter, W. P. L., Nolte, C. G., Luecken, D. J., Hutzell, W. T., Wennberg, P. O., Cohen, R. C., and Pinder, R. W.: Understanding the impact of recent advances in isoprene photooxidation on simulations of regional air quality, Atmos. Chem. Phys. Discuss., 12, 27173-27218, 10.5194/acpd-12-27173-2012, 2012.
--Bob Y. 13:55, 12 May 2014 (EDT)