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Atmos. Chem. Phys., 9, 7753–7767, 2009
www.atmos-chem-phys.net/9/7753/2009/
© Author(s) 2009. This work is distributed under
the Creative Commons Attribution 3.0 License.

Atmospheric
Chemistry
and Physics

Rapid formation of isoprene photo-oxidation products
observed in Amazonia

T. Karl1, A. Guenther1, A. Turnipseed1, G. Tyndall1, P. Artaxo2, and S. Martin3
1National Center for Atmospheric Research, 1850 Table Mesa Dr, Boulder, 80301, CO, USA
2Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo, Brazil
3School of Engineering and Applied Sciences & Department of Earth and Planetary Sciences, Harvard University,
Cambridge, MA, USA

Received: 20 May 2009 – Published in Atmos. Chem. Phys. Discuss.: 22 June 2009
Revised: 26 August 2009 – Accepted: 28 September 2009 – Published: 19 October 2009

Abstract. Isoprene represents the single most important re-
active hydrocarbon for atmospheric chemistry in the tropical
atmosphere. It plays a central role in global and regional at-
mospheric chemistry and possible climate feedbacks. Photo-
oxidation of primary hydrocarbons (e.g. isoprene) leads to
the formation of oxygenated VOCs (OVOCs). The evolu-
tion of these intermediates affects the oxidative capacity of
the atmosphere (by reacting with OH) and can contribute to
secondary aerosol formation, a poorly understood process.
An accurate and quantitative understanding of VOC oxida-
tion processes is needed for model simulations of regional
air quality and global climate. Based on field measurements
conducted during the Amazonian Aerosol Characterization
Experiment (AMAZE-08) we show that the production of
certain OVOCs (e.g. hydroxyacetone) from isoprene photo-
oxidation in the lower atmosphere is significantly underpre-
dicted by standard chemistry schemes. Recently reported
fast secondary production could explain 50% of the observed
discrepancy with the remaining part possibly produced via
a novel primary production channel, which has been pro-
posed theoretically. The observations of OVOCs are also
used to test a recently proposed HOx recycling mechanism
via degradation of isoprene peroxy radicals. If generalized
our observations suggest that prompt photochemical forma-
tion of OVOCs and other uncertainties in VOC oxidation
schemes could result in uncertainties of modelled OH re-
activity, potentially explaining a fraction of the missing OH
sink over forests which has previously been largely attributed
to a missing source of primary biogenic VOCs.

Correspondence to: T. Karl
(tomkarl@ucar.edu)

1

Introduction

Volatile organic compounds (VOCs) critically influence the
composition of the Earth’s atmosphere by fueling tropo-
spheric chemistry (Atkinson, 2000), and providing con-
densable oxidation products for organic aerosol formation
(Kanakidou et al., 2005). On a global scale the emission
strength of biogenic VOCs dominates the annual VOC bud-
get (∼1000–2000 Tg/y). A large fraction of this reduced car-
bon flux enters the atmosphere in form of isoprene, which
could exceed global methane emissions (Guenther et al.,
2006). VOCs are emitted from many terrestrial plants at high
rates, in particular in tropical ecoregions, and some species
are known to re-emit up to 10% of their assimilated carbon
in form of isoprene (Kesselmeier et al., 2002). Isoprene is
also highly reactive and its photochemical evolution there-
fore plays a central role in atmospheric chemistry.

Detailed chemical schemes are needed in global atmo-
spheric chemistry models (e.g. Brasseur et al., 1998; Bey
et al., 2001; Kuhlmann et al., 2003) to simulate the tropi-
cal photo-reactor and assess how the oxidizing capacity of
the remote tropical atmosphere is modulated by this com-
pound. Isoprene chemistry schemes (Fan and Zhang, 2004;
Carter and Atkinson, 1996; Pinho et al., 2005) are typi-
cally condensed so they can be incorporated in global and
regional chemistry models. Most current lumped chemistry
schemes include near explicit representation of the first and
second generation oxidation products of isoprene (Emmons
et al., 2009; Taraborelli et al., 2008; Emmerson and Evans,
2009). Some of these schemes have been applied in field
studies conducted in the tropics (e.g. Warneke et al., 2001;
Ganzeveld et al., 2008). Recent theoretical and laboratory
evidence suggested that some of the basic steps of isoprene

Published by Copernicus Publications on behalf of the European Geosciences Union.

7754

T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia

peroxy radical cycling are still poorly understood (Dibble,
2004; Park et al., 2003; Peeters et al., 2009; Paulot et al.,
2009a) and ramifications for HOx cycling have been dis-
cussed (Lelieveld et al., 2008; Hofzumahaus et al., 2009;
Paulot et al., 2009a). Here we use field measurements of iso-
prene and its oxidation products methyl vinyl ketone (MVK),
methacrolein (MAC) and hydroxyacetone to assess their pho-
tochemical evolution and test existing kinetic schemes at a
remote field site approx. 60 km NNW of Manaus in the cen-
tral Amazon basin during the wet season in 2008.

2 Methods

2.1 Measurement site

Measurements were conducted as part of the Amazonian
Aerosol Characterization Experiment (AMAZE-08) from 9
to 28 February 2008. The site (02◦35.6570 S, 60◦12.5570 W)
located in the Reserva Biologica do Cuieiras and managed by
the Instituto Nacional de Pesquisas da Amazonia (INPA) and
the Large-Scale Biosphere-Atmosphere Experiment in Ama-
zonia (LBA). The vegetation cover consists of primary trop-
ical rainforest (approx. leaf area index of 5–6 m2/m2) with
an average canopy height of ∼30 m surrounding the ∼40 m
measurement tower.

2.2 VOC measurement and data analysis

A Proton-Transfer-Reaction Mass Spectrometer was used
for gradient measurements of selected VOCs. The instru-
ment is based on soft chemical ionization using protonated
water ions (H3O+).
It combines the advantage of online
analysis while maintaining linearity and low detection lim-
its (Ionicon, Austria) (Lindinger et al. 1998; Hansel et al.,
1998). The instrument was operated at 2.3 mbar drift pres-
sure and 540 V drift voltage and calibrated using two mul-
ticomponent ppmv VOC standards: VOC standard 1 con-
tained a mixture of methanol, acetonitrile, acetaldehyde,
acetone, isoprene, methyl vinyl ketone, methyl ethyl ke-
tone, benzene, toluene, m,o,p xylenes and camphene; VOC
standard 2 contained a mixture of benzene, toluene, m,o,p
xylenes + ethylbenzene, chlorobenzene, trimethylbenzenes,
dichlorobenzenes and trichlorobenzenes. Ultrapure hydrox-
yacetone (SigmaUltra, Sigma Aldrich, CAS 116-09-6, Mil-
waukee, WI) was injected into the instrument to determine
the instrument specific response for this compound. The in-
strument sequentially sampled of six independent 1
inch
4
Teflon (PFA) sampling lines mounted at 2, 10.9, 16.7, 23.9,
30.3, and 39.8 m on the tower. A valve switching system
changed sampling lines every 5 min and cycled through the
entire gradient over a 30 min period. Gradients were calcu-
lated from the 5 min averages. High flow rates through the
sampling lines resulted in delay times of less than 8–12 s,
measured by spiking a VOC pulse at each sampling inlet.

00

Isoprene and the sum of MVK and MAC were mea-
sured at ion channels m/z 69 and m/z 71 respectively. The
specificity of the PTRMS to monitor isoprene and the sum
of MVK+MAC has been demonstrated previously (e.g. de
Gouw and Warneke, 2007). Hydroxyacetone was moni-
tored on ion channel m/z 75 and was identified as a ma-
jor VOC observed by PTRMS in tropical ecosystems in the
past (Williams et al., 2001). The detection limits for iso-
prene, MVK+MAC and hydroxyacetone for a 5 s integra-
tion time were 10, 5 and 5 pptv respectively. Particular sen-
sitivities corresponded to proton-transfer reaction rate con-
stants of 2e-9, 3e-9 and 3.5e-9 cm3/s respectively. PTRMS
hydroxyacetone concentration data from earlier field cam-
paigns (Williams et al., 2001; Holzinger et al., 2007; Stroud
et al., 2005) were corrected by the relative difference of the
rate constants between hydroxyacetone and isoprene. Poten-
tial interferences on m/z 75 due to butanol can be excluded as
butanol completely dehydrates and is observed exclusively
on m/z 57 under operating conditions used here. Propionic
acid also dehydrates partially into m/z 57. Our dataset shows
no significant correlation between signals observed on m/z 57
and m/z 75, which is indicative that propionic acid did not
contribute to m/z 75. The most likely candidate for m/z 75
is therefore a compound originating from isoprene oxida-
tion. We can further exclude other interferences such as di-
ethylether and methyl acetate from GC samples. We con-
clude that the PTRMS mass channel m/z 75 was specific for
the measurement of hydroxyacetone in this high isoprene en-
vironment and confirm conclusions drawn from earlier stud-
ies (Williams et al., 2001).

GC-MS air samples were collected on carbotrap and tenax
cartridges that were stored at approximately 0◦C until anal-
ysis at NCAR Boulder laboratory, except during transit from
Brazil to USA, when they were at ambient temperature for
approximately 1 day. The cartridges were desorbed ther-
mally using an NCAR-made system (Greenberg et al., 1994)
and analyzed by gas chromatography with mass spectromet-
ric detection (Hapsite Smart, Inficon, East Syracuse NY) us-
ing a 30 m×0.3 mm ID 1 mm film DB-1 column, temperature
programmed from 40 to 200◦C at 3◦C per min after an ini-
tial 2 min hold. VOC were quantified with respect to NIST
traceable standards as described by Greenberg et al. (1994).
Ozone (O3), and nitric oxide (NO) concentrations were
also measured via the 6-level sampling manifold. Ozone was
measured by UV absorbance (2B Technologies, Model 205)
every 10 s and then averaged over the entire 5 min sampling
time on each level, excluding only the first 15 s to insure ad-
equate flushing of the connecting gas lines. The ozone ana-
lyzer was compared with laboratory instruments both prior
to and following the experiment and found to agree with
±5% with a detection limit of 2 ppbv.
It was zeroed pe-
riodically by placing an ozone scrubber on the 1.5 m in-
let. NO was measured by ozone-induced chemiluminescence
(Ecophysics, Model 88Y) at a sample rate of 1 s. Mea-
surements were averaged over the first 2 min of sampling

Atmos. Chem. Phys., 9, 7753–7767, 2009

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T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia

7755

Fig. 1. Integrated flux and concentration profiles through 30 m canopy. Left panel: Integrated flux profiles of Isoprene (C5H8), MVK+MAC
(C4H6O) and Hydroxyacetone (C3H6O2). Right panel: Ozone concentration profile.

on a given level (excluding initial 15 s). During the other
3 min, the air was either passed through a photolytic con-
verter (Droplet Technology, BLC-100) to convert NO2 to NO
or through a molybdenum catalyst which reduces oxidized
nitrogen to NO which was subsequently detected by chemi-
luminescence. The NO analyzer was zeroed automatically
every hour by diverting the sample flow through a pre-reactor
and adding a large excess of ozone which consumed the NO.
It was calibrated periodically during the campaign by stan-
dard addition of a known NO concentration to the 2m inlet.
The detection limit was ∼50 pptv. Laboratory tests indicated
no measurable loss of either ozone, NO or NO2 within any of
the PFA inlet lines. Wind velocities at 40 m were measured
by a 3-dimensional sonic anemometer (Applied Technolo-
gies, SATI-K) mounted on a boom extending 2 m from the
tower and sampled at 20 Hz.

2.3 VOC gradient fluxes

Ecosystemscale fluxes of VOCs were calculated based on
concentration gradients throughout the canopy and applying
an Inverse Lagrangian Transport Model (Raupach, 1989, Ne-
mitz et al., 2000, and Karl et al., 2004). The VOC fluxes were
→
→
C −Cref =
S , where C is the
computed according to
VOC concentration (µg/m3) vector for each level, Cref is the
VOC concentration (µg/m3) at reference height (e.g. 14 m),
D (m) represents a dispersion matrix and S (mg/m2/h/m)
the resulting VOC source/sink vector. D can be expressed
as a function of Lagrangian timescale (Tl) and profiles of

↔
D ·

the standard deviation of the vertical wind speed (σw) di-
vided by the friction velocity (u∗). The calculation was per-
formed using a 10×4 dispersion matrix.
Integration over
all source and sink terms (S) yielded the canopy scale VOC
flux (mg/m2/h). Fluxes were calculated for 30 min intervals.
The parameterization of D was based on turbulence measure-
ments inside and above the canopy and calculated using the
far- and near-field approach described by Raupach (1989).
The Lagrangian timescale was parameterized according to
Raupach (1989).

3 Results and discussion

3.1 Biosphere-Atmosphere

exchange
MVK+MAC and Hydroxyacetone

of

isoprene,

Figure 1 (left panel) shows the exchange of VOCs at the
atmosphere-biosphere interface and depicts the mean inte-
grated vertical source/sink distribution of isoprene, MVK,
MAC and hydroxyacetone measured by PTR-MS during
daytime (11:00–17:00 local time (LT)). The source/sink dis-
tribution was inferred from in-canopy concentration mea-
surements using an inverse Lagrangian transport model. Av-
erage midday ozone mixing ratios (Fig. 1, right panel) were
∼8 ppbv decreasing to <3 ppbv near the ground. Isoprene was mostly emitted in the upper part of the canopy as ex- pected because of the light environment and the distribu- tion of sun and shade leaves throughout the canopy. The oxidation products MVK, MAC and hydroxyacetone were www.atmos-chem-phys.net/9/7753/2009/ Atmos. Chem. Phys., 9, 7753–7767, 2009 36 36 Figures: 808 Figure 1 809 810 Figure 2 811 812 7756 T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia deposited to the canopy with maximum deposition occurring near the top. The calculated source/sink distribution inte- grated over the entire canopy for these VOCs suggests that the primary source was located above the forest. The analy- sis shows that primary biological emissions of MVK, MAC and hydroxyacetone were negligible during this study. Observed OVOC mixing ratios are determined by the bal- ance of their combined loss and production rates. While their production rates are dominated by photochemistry, their loss rates are influenced by photochemical destruction, dry deposition and vertical mixing (such as entrainment of air from the free troposphere). In order to estimate the relative importance of these three loss terms we assume a 1000 m deep well-mixed planetary boundary layer (PBL) (Karl et al., 2007). The lifetime due to dry deposition equals the mixed layer concentration times the PBL height divided by the de- position flux (Fig. 1). Taking mixing ratios of 3 and 1.5 ppbv for MVK+MAC and hydroxyacetone, the lifetime due to dry deposition is on the order of 25 and 22 h respectively. Sim- ilarly the influence of entrainment can be estimated. Mix- ing ratios in the free troposphere (FT) are typically an order of magnitude lower (Karl et al., 2007; Kuhn et al., 2007). The concentration jump of a VOC between the PBL and FT can then be approximated by the mixed layer concentration. For the measured entrainment velocities obtained during an earlier study (e.g. Karl et al., 2007; 8–10 cm/s) the dilution timescale of vertical mixing is 3–4 h. These physical loss processes can be compared to the chemical destruction rate for a daytime OH densitiy of 5e6 molecules/cm3 (Ganzeveld et al., 2008). The corre- sponding chemical lifetimes for isoprene, MVK+MAC and hydroxyacetone are 0.5, 2 and 18 h respectively. Since day- time concentrations of isoprene, MVK, MAC and hydroxy- acetone in the FT are typically much lower than in the PBL the effect of vertical dilution has minimal influence on VOC correlations observed in the PBL, because all VOCs are di- luted at the similar rates. When investigating correlations of OVOCs (e.g. MVK and MAC) with respect to isoprene, the additional sink due to OVOC dry deposition would result in systematically lower OVOC mixing ratios than would be cal- culated from photochemical destruction alone. 3.2 Photochemical production of MVK, MAC and hydroxyacetone The first steps of the photo oxidation of isoprene via the hy- droxyl radical (OH) can be summarized as: C5H8 + OH O2−→ C5H9O3 C5H9O3 + NO−→carbonyls C5H9O3 + HO2−→peroxides (R1a) (R1b) (R1c) Measured NO mixing ratios were sufficiently high (100– 300 pptv, lifetime τ of ∼30 s) in the surface layer to dominate over the reaction with HO2 radical estimates (10–20 pptv; τ ∼300 s) according to results from a photochemical box model based on the Mozart Chemistry Mechanism v4 (Em- mons et al., 2009). Consequently peroxy radical reac- tions with NO (τ ∼30 s) led to significant production of the carbonyls methyl vinyl ketone (MVK) and methacrolein (MAC). For VOCs discussed here Reaction (R1) can there- fore be simplified to the following kinetic reaction model, where Y is the branching ratio for each channel. C5H8 + OH Y=0.32−→ MVK C5H8 + OH Y=0.32−→ MAC MAC + OH Y=0.42−→ Hydroxyacetone MVK + OH −→ Products (R2a) (R2b) (R2c) (R2d) Uncertainties for yields are typically on the order of 20% (Atkinson et al., 1997). While the focus in this section is on the observed mixing ratios of isoprene, MVK, MAC and hydroxyacetone a more detailed representation of the atmo- spheric production of OVOCs from isoprene is discussed in Sect. 3.3. During daytime the evolution of isoprene chem- istry in the PBL is conceptually different than many en- vironmental chamber experiments in that there is continu- ous supply of isoprene. As a result the production of com- pounds originating directly from first generation isoprene peroxy radicals is relatively more prominent in the real at- mosphere. For example the ratio of (MVK+MAC)/isoprene will approach infinity in batch-mode environmental cham- bers, while there is a steady-state upper limit of ∼2.4 in the PBL (assuming yields according to reaction R2 and OH reac- tion rate constants of 1e–10 cm3/s, 1.9e–11 cm3/s and 3.4e– 11 cm3/s for isoprene, MVK and MAC respectively). How- ever, due to the time-dependent isoprene supply and the slower OH reactions of the products, steady state conditions are rarely reached. During AMAZE-08 a daytime (11:00– 17:00 LT) ratio of 0.44±0.05 was observed (Fig. 2, left panel). Similar ratios were observed in previous field studies (e.g. Warneke et al., 2001; Kuhn et al., 2007; Eerdekens et al., 2008; Karl et al., 2007). The major source of hydroxyacetone is oxidation of MAC (e.g. Carter and Atkinson, 1996). Figure 2 (right panel) shows a correlation plot between hydroxyacetone and the sum of the first generation oxidation products MVK and MAC. For a given MVK+MAC to isoprene ratio of 0.44 we calculate a slope of 0.03 between hydroxyacetone and MVK+MAC according to Reaction (R2) (assuming constant isoprene emissions). This is ∼10 times smaller than the observed ratio (0.30±0.08) and implies that an additional source of hydroxyacetone, which is highly correlated with the oxidation products MVK and MAC (R2=0.79) and iso- prene (R2=0.70), is missing. The high degree of correlation suggests that the missing source of hydroxyacetone comes Atmos. Chem. Phys., 9, 7753–7767, 2009 www.atmos-chem-phys.net/9/7753/2009/ T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia 7757 Fig. 2. Left panel: Correlation between MVK+MAC and isoprene. Right panel: Correlation between hydroxyacetone and MVK+MAC. Regressions based on a robust fitting procedure are indicated by solid red lines (Holland et al., 1977). The dashed red lines indicate steady state limits. The modelled hydroxyacetone/(MVK+MAC) slope is depicted by the blue dashed line. from within the isoprene oxidation chain, but has to be faster than the production from MAC, which is thought to be the major contributor to the secondary formation of hydroxyace- tone. Other possible chemical sources of hydroxyacetone in- clude oxidation of peroxides originating from propene and production from acetone oxidation (e.g. acetonyl peroxy rad- icals reacting with methyl peroxy radicals). However, both of these are expected to be slow due to the low concentrations of propene and subsequent peroxides or the need for radical- radical reactions in the case of acetone oxidation. Since iso- prene mixing ratios (e.g. up to 8 ppbv) dominate the tropical environment these processes must compete with the domi- nant production path via MAC. Although anticipated to be small in the wet season of the central Amazon Basin, an- other possible source of hydroxyacetone is biomass burning (Yokelson et al., 2007). We investigated this using acetoni- trile as specific gas phase marker. Periods of elevated ace- tonitrile (∼10% of the entire dataset) were excluded from the analysis. A further argument against a significant biomass burning source is the good correlation observed between hy- droxyacetone and MVK+MAC as well as with isoprene. In order to check whether the observed ratios between iso- prene, MVK+MAC and hydroxyacetone are comparable to previous datasets we have re-analyzed data reported in the lit- erature. The triangular plot shown in Fig. 3 summarizes find- ings from five field campaigns, including the present study, conducted near isoprene emission sources (Williams et al., 2001; Holzinger et al., 2007; Stroud et al., 2005; Spauld- ing et al., 2003). Concentrations from these datasets, which are representative for typical local noontime conditions, were normalized by the sum of isoprene, MVK, MAC and hydrox- yacetone in order to quantitatively compare their relative ra- tios. The color coded triangular symbols represent a chem- ical trajectory along which the relative ratios would evolve according to Reaction (R2). The color coding indicates pho- tochemical age (time exposure to OH). Due to a constant sup- ply of isoprene the theoretical trajectory ends at the steady state limit, typically reached after 107 molecules cm−3 days of OH exposure for the reaction sequence discussed here. Measured distributions from all field observations, in partic- ular the AMAZE-08 dataset discussed here, show that hy- droxyacetone mixing ratios are significantly higher than what would be expected from the reaction model described by Re- action (R2) when only production from MAC is assumed. The discrepancy becomes larger for data collected closer to the source corresponding to a recent supply of isoprene. Reconciliation with such fast production of hydroxyace- tone requires additional production paths from isoprene (e.g. through isoprene alkenoxy radicals). We extended the set of reactions listed in Reaction (R2) by including direct production from isoprene plus OH and obtained an optimal yield (Yiso) based on a non-linear least square regression procedure (Seber et al., 1989) of the coupled set of differen- tial reactions (R2). The color coded circles in Fig. 3 depicts www.atmos-chem-phys.net/9/7753/2009/ Atmos. Chem. Phys., 9, 7753–7767, 2009 36 36 Figures: 808 Figure 1 809 810 Figure 2 811 812 7758 T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia Fig. 3. Triangular correlation plot for the measured and modelled mixing ratios of isoprene, MVK+MAC and hydroxyacetone. Mixing ratios are normalized by the sum of the concentrations of isoprene, MVK, MAC and hydroxyacetone. Modelled concentrations are color coded by photochemical age. Field datasets are depicted by symbols as following: red circle (AMAZE, 2008; this study), blue diamond (LBA-Claire, 1999; Williams et al., 2001), green triangle (CELTIC 2003; Stroud et al., 2005), magenta triangle (ICARTT, 2004; Holzinger et al., 2007) and black square (Blodgett Forest, 2003; Spaulding et al., 2003). Triangles represent the standard model (i.e. no fast production). Circles show the model case that includes fast production based on non-linear regression. The chemical trajectories of the models terminate at the steady state limit, typically reached after 107 molecules cm−3 days of OH exposure. a curve based on direct production with a fitted Yiso of 8.3 (±2.2) %, which would be sufficient to explain the observed distribution of hydroxyacetone in isoprene dominated envi- ronments. Several studies have proposed primary (Dibble et al., 2004) and fast secondary production of hydroxyacetone (Paulot et al., 2009b). Dibble et al. (2004) recently conducted a theoretical study on the decomposition of certain isoprene – alkenoxy radicals and hypothesized a direct channel which would lead to the formation of products typically associated with secondary and tertiary chemistry (e.g. hydroxyacetone and glyoxal). Paulot et al. (2009b) reported very fast produc- tion of hydroxyacetone from isoprene nitrates and hydroxy- carbonyls after initial reaction with OH. In order to investigate the sensitivity of the proposed ad- ditional production paths for hydroxyacetone, we compared four reaction mechanisms. We implemented (1) the Mozart mechanism (Emmons et al., 2009), (2) a recently developed isoprene oxidation scheme proposed by Paulot et al. (2009b), which was extended for low NOx conditions (Paulot et al., 2009a), (3) a simple sequential reaction model (SRM) sum- marized in Table 2 (Appendix), which was extended to in- clude fast production of hydroxyacetone, and (4) a novel reaction mechanism for isoprene proposed by Peeters et al. (2009) (Table 3, Appendix). Figure 4 shows the results for these model runs, for the conditions encountered during the AMAZE-08 study (viz. constant isoprene emissions and NO mixing ratios of 100 pptv). The top panel in Fig. 4 shows the evolution of the ratio of MVK+MAC to isoprene. Obser- vations during AMAZE-08 (Fig. 2) correspond to a ratio of 0.44, which is shown on the left side of Fig. 4. The SRM, Mozart and Paulot mechanisms yield systemati- cally higher ratios than does the Peeters mechanism. In order to further investigate the reason for this discrepancy we show the MVK to MAC ratios in the middle panel of Fig. 4. Dur- ing AMAZE-08, GC-MS measurements suggested a ratio of 1.34±0.10 which is similar to earlier studies in the Amazon (Kuhn et al., 2007) and comparable to other isoprene domi- nated environments (Apel et al., 2002; Stroud et al., 2001). The SRM, Mozart und Paulot mechanisms reproduce the ob- served MVK/MAC ratios well. The mechanism by Peeters et al. (2009), would predict a ratio of ∼10 for an observed (MVK+MAC) to isoprene ratio of 0.44 (see red vertical line in Fig. 4). Possible reasons for such a large discrepancy are explored in the next section. The modelled to (MVK+MAC) ratios are plotted in the lower panel of hydroxyacetone observed and Atmos. Chem. Phys., 9, 7753–7767, 2009 www.atmos-chem-phys.net/9/7753/2009/ 37 37 Figure 3 813 814 Figure 4 815 T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia 7759 Fig. 4. Observed (left edge) and modelled (main figure) ratios of OVOC to isoprene for four different models (Peeters et al., 2009; Paulot et al., 2009a and b; SRM, a sequential reaction model according to Table A2; Mozart, Emmons et al., 2009). Top: MVK+MAC/isoprene. Middle: MVK/MAC. Bottom: Hydroxyacetone/(MVK+MAC). The dashed black horizontal line corresponds to the (MVK+MAC)/isoprene ratio of 0.44 measured during AMAZE-08, and the dashed black vertical line shows the value of the corresponding photochemical age obtained by the predictions from three models (Paulot, SRM, Mozart). The vertical red line corresponds to the photochemical age by the mechanism of Peeters et al. (2009). Fig. 4. For a given (MVK+MAC) to isoprene ratio of 0.44 (e.g. vertical black line), the modelled hydroxyacetone to (MVK+MAC) ratio obtained from the Paulot mechanism is closest to the observed ratio (e.g. within 50%), which was used to derive the modelled SRM curve. This suggests that fast secondary production of hydroxyactone could explain about 50% of the observed hydroxacetone to (MVK+MAC) ratio during AMAZE-08. The remaining 50% could be related to primary production mechanisms similar to those proposed by Dibble et al. (2004). 3.3 Implications for atmospheric chemistry 3.3.1 HOx recycling In the last section OVOC ratios were compared to different photochemical oxidation mechanism. While three of these oxidation schemes could reproduce the observed MVK and MAC mixing ratios, the mechanism presented by Peeters et al. (2009) suffered from unrealistically high MVK/MAC ratios and underestimated the sum of MVK and MAC rel- ative to isoprene. This mechanism is proposed as a novel HOx recycling scheme which could potentially explain large missing HOx sources in isoprene dominated environments reported by Lelieveld et al. (2008) and Hofzumahaus et al. (2009). The mechanism is summarized in the Table 3 in the Appendix. Briefly, after initial addition of OH to one of the four unsat- urated C-atoms of isoprene, O2 addition leads to the forma- tion of three isoprene peroxyradicals, which are considered in thermodynamic equilibrium. The two major adducts (1- OH-isoprene and 4-OH-isoprene) account for 90% of the iso- prene oxidation channels and are considered here. The Z-1- OH-4-OO* and Z-4-OH-1-OO* peroxyradicals are proposed to undergo a fast 1,6-H-shift (HO2 regenerating channels) that competes with conventional reaction channels through HO2, RO2 and NO. Similarly, the 1-OH-2-OO* and 4-OH-3- OO* peroxyradicals would undergo a 1,5-H-shift (OH regen- erating channels) competing with reaction via HO2, RO2 and NO. These proposed radicals would then decompose in a sin- gle concerted reaction to generate HO2, OH, a hydroperox- ymethylbutenal, MVK and MAC. The decomposition rates for the 1,6-H-shift reactions are highly dependent on energy barriers and are proposed to be on the order of 1 s−1 and 8 s−1. For comparison the reaction rates via the conven- tional NO channel would correspond to 0.01–0.03 s−1 for conditions of AMAZE-08. Thus one reason for the differ- ent MVK, MAC and hydroxyacetone ratios discussed earlier can be found in these fast decomposition rates. www.atmos-chem-phys.net/9/7753/2009/ Atmos. Chem. Phys., 9, 7753–7767, 2009 38 38 816 Figure 5 817 818 Figure 6 819 7760 T. Karl et al.: Rapid formation of isoprene photo-oxidation products observed in Amazonia Fig. 5. Analysis of the sensitivity of the OVOCs for increasing photochemical age for the mechanism of Peeters et al. (2009). Top: MVK. Middle: MAC. Lower: Hydroxyacetone. The sensitivity (dln(u)/dln(p): change of variable u (e.g. concentration) vs change of parameter p (e.g. rate constant)) of each OVOC is shown with respect to three specific reaction rates of the mechanism (see Table A3). Figure 5 shows the sensitivity of MVK, MAC and hydrox- yacetone with respect to the 1,5-H-shift, 1,6-H-shift and re- verse reaction rates of the Z-1-OH-4-OO* and Z-4-OH-1- OO* peroxyradicals. For example, a change in the reverse reaction rate (kr (Z-1-OH-4) – green dashed line in upper panel) of 100% leads to a change in the MVK concentra- tion of 62% in steady state (e.g. >1e5 molecules cm−3 days).
Similarly, a change of the rate constant of the 1,6-H-shift of
the Z-1-OH-4 reaction (blue line) by 100% shifts the MVK
concentration by −59%. By changing the rate of the 1,6-
H-shift for the Z-4-OH-1-peroxy radical by a factor of 10
(e.g. 0.8 s−1 vs 8 s−1), the MAC concentration would in-
crease by a factor of 5 and the hydroxyacetone concentration
would increase between a factor of 8 at low photochemical
age (<5e4 molecules cm−3 days) and 5 at high photochem- ical age (>1e6 molecules cm−3 days), where the production
of hydroxyacetone is dominated by secondary production via
MAC.

Reconciliation of the mechanism of Peeters et al. (2009)
with our observed OVOC ratios would require that the 1,5-
H and 1,6-H-shift decomposition reactions be as fast as the
conventional reaction channels via NO and the reverse re-
action rates of the Z-1-OH-4-OO* and Z-4-OH-1-OO* per-
oxyradicals be reduced. The implication is that the thermo-
dynamic stability of these radicals would have to increase.
Independent experimental evidence was recently presented
by Paulot et al. (2009a), who tentatively concluded that

much smaller yields for the (2Z)-hydroperoxymethylbutenal
(e.g. <10%) than would be predicted via the 1,6-H shifts were needed to explain their observations. One consequence of these independent experimental results is that they suggest a lower HOx recycling efficiency. For the standard mecha- nism proposed by Peeters et al. (2009)