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  <front>
    <journal-meta><journal-id journal-id-type="publisher">ACP</journal-id><journal-title-group>
    <journal-title>Atmospheric Chemistry and Physics</journal-title>
    <abbrev-journal-title abbrev-type="publisher">ACP</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Atmos. Chem. Phys.</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">1680-7324</issn><publisher>
    <publisher-name>Copernicus Publications</publisher-name>
    <publisher-loc>Göttingen, Germany</publisher-loc>
  </publisher></journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.5194/acp-20-10889-2020</article-id><title-group><article-title>CRI-HOM: A novel chemical mechanism for simulating highly oxygenated organic molecules (HOMs) in global chemistry–aerosol–climate models</article-title><alt-title>CRI-HOM</alt-title>
      </title-group><?xmltex \runningtitle{CRI-HOM}?><?xmltex \runningauthor{J.~Weber et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Weber</surname><given-names>James</given-names></name>
          <email>jmw240@cam.ac.uk</email>
        <ext-link>https://orcid.org/0000-0003-0643-2026</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Archer-Nicholls</surname><given-names>Scott</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-3311-9003</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff2">
          <name><surname>Griffiths</surname><given-names>Paul</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-1089-340X</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Berndt</surname><given-names>Torsten</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Jenkin</surname><given-names>Michael</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-7669-2985</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>Gordon</surname><given-names>Hamish</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-1822-3224</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff6">
          <name><surname>Knote</surname><given-names>Christoph</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-9105-9179</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff2">
          <name><surname>Archibald</surname><given-names>Alexander T.</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-9302-4180</ext-link></contrib>
        <aff id="aff1"><label>1</label><institution>Centre for Atmospheric Science, Department of Chemistry, University of
Cambridge, Cambridge, CB2 1EW, UK</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>National Centre for Atmospheric Science, Department of Chemistry,
University of Cambridge, CB2 1EW, UK</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Atmospheric Chemistry Department (ACD), Leibniz Institute for
Tropospheric Research (TROPOS), <?xmltex \hack{\break}?>04318 Leipzig, Germany</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>Atmospheric Chemistry Services, Okehampton, Devon, EX20 4BQ, UK</institution>
        </aff>
        <aff id="aff5"><label>5</label><institution>Engineering Research Accelerator and Center for Atmospheric Particle
Studies, <?xmltex \hack{\break}?>Carnegie Mellon University, Pittsburgh, PA 15213, USA</institution>
        </aff>
        <aff id="aff6"><label>6</label><institution>Meteorologisches Institut, Ludwig-Maximilians-Universität
München, 80333 Munich, Germany</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">James Weber (jmw240@cam.ac.uk)</corresp></author-notes><pub-date><day>22</day><month>September</month><year>2020</year></pub-date>
      
      <volume>20</volume>
      <issue>18</issue>
      <fpage>10889</fpage><lpage>10910</lpage>
      <history>
        <date date-type="received"><day>18</day><month>February</month><year>2020</year></date>
           <date date-type="rev-request"><day>3</day><month>March</month><year>2020</year></date>
           <date date-type="rev-recd"><day>1</day><month>July</month><year>2020</year></date>
           <date date-type="accepted"><day>8</day><month>August</month><year>2020</year></date>
      </history>
      <permissions>
        <copyright-statement>Copyright: © 2020 </copyright-statement>
        <copyright-year>2020</copyright-year>
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://acp.copernicus.org/articles/.html">This article is available from https://acp.copernicus.org/articles/.html</self-uri><self-uri xlink:href="https://acp.copernicus.org/articles/.pdf">The full text article is available as a PDF file from https://acp.copernicus.org/articles/.pdf</self-uri>
      <abstract><title>Abstract</title>
    <p id="d1e183">We present here results from a new mechanism, CRI-HOM, which we have developed to simulate the formation of highly oxygenated organic molecules (HOMs) from the gas-phase oxidation of <inline-formula><mml:math id="M1" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene, one of the most widely emitted biogenic volatile organic compounds (BVOCs) by mass. This concise scheme adds 12 species and 66 reactions to the Common Representative Intermediates (CRI) mechanism v2.2 Reduction 5 and enables the representation of semi-explicit HOM treatment suitable for long-term global chemistry–aerosol–climate modelling, within a comprehensive tropospheric chemical mechanism. The key features of the new mechanism are (i) representation of the autoxidation of peroxy radicals from the hydroxyl radical and ozone initiated reactions of <inline-formula><mml:math id="M2" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene, (ii) formation of multiple generations of peroxy radicals, (iii) formation of accretion products (dimers), and (iv) isoprene-driven suppression of accretion product formation, as observed in experiments. The mechanism has been constructed through optimisation against a series of flow tube laboratory experiments. The mechanism predicts a HOM yield of 2 %–4.5 % under conditions of low to moderate <inline-formula><mml:math id="M3" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, in line with experimental observations, and reproduces qualitatively the decline in HOM yield and concentration at higher <inline-formula><mml:math id="M4" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> levels. The mechanism gives a HOM yield that also increases with temperature, in line with observations, and our mechanism compares favourably to some of the limited observations of [HOM] observed in the boreal forest in Finland and in the southeast USA.</p>
    <p id="d1e222">The reproduction of isoprene-driven suppression of HOMs is a key step forward as it enables global climate models to capture the interaction between the major BVOC species, along with the potential climatic feedbacks. This suppression is demonstrated when the mechanism is used to simulate atmospheric profiles over the boreal forest and rainforest; different isoprene concentrations result in different [HOM] distributions, illustrating the importance of BVOC interactions in atmospheric composition and climate. Finally particle nucleation rates calculated from [HOM] in present-day and pre-industrial atmospheres suggest that “sulfuric-acid-free” nucleation can compete effectively with other nucleation pathways in the boreal forest, particularly in the pre-industrial period, with important implications for the aerosol budget and radiative forcing.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<?pagebreak page10890?><sec id="Ch1.S1" sec-type="intro">
  <label>1</label><title>Introduction</title>
      <p id="d1e234">Aerosols play an important role in the Earth system by affecting the Earth's
radiative balance as well as local air quality and thus human health
(Carslaw et al., 2010). Aerosols can interact directly with solar radiation
through scattering or absorption and indirectly by influencing cloud
properties by seeding cloud droplets as well as increasing cloud albedo
(Forster et al., 2007; Twomey, 1974). Thus, aerosols change the balance
between the energy received from the sun and the energy emitted from the
planet at the top of the atmosphere. However, a major uncertainty in climate
change predictions arises from aerosols and aerosol–cloud interactions
(Stocker et al., 2013). This arises in part from a lack of understanding of
pre-industrial (PI) aerosols, and it is the change in aerosol burden from the
PI period to the present day (PD) which determines the effective radiative forcing
(ERF) of aerosols. As PI aerosol sources are almost exclusively natural, an
understanding of natural sources and the associated aerosol formation
processes is essential if better predictions for climate change are to be
made.</p>
      <p id="d1e237">An important formation route for aerosols is oxidation of volatile organic
compounds which form less volatile species that can partition into the
aerosol phase or nucleate new particles (Kirkby et al., 2016; Shrivastava et
al., 2017). Recently it has been established that the oxidation of organic
compounds can lead to the formation of “highly oxygenated organic
molecules” (HOMs; Mentel et al., 2015; Ehn et al., 2014; Kurtén et
al., 2016; Bianchi et al., 2019; also referred to as “highly oxidised
multifunctional organic compounds”; Ehn et al., 2012) which are formed by
multiple intramolecular oxidation steps, termed autoxidation (Crounse et
al., 2013; Bianchi et al., 2019). Autoxidation typically involves the
abstraction by a peroxy radical of a hydrogen atom bonded to a carbon
elsewhere on the molecule resulting in an alkyl radical and hydroperoxide
group. The alkyl radical reacts rapidly with atmospheric oxygen to form a
new peroxy radical, ultimately reducing the species' volatility and enabling
particle formation and condensation. HOMs are defined as closed-shell species
with at least six oxygens formed by initial atmospheric oxidation and
subsequent autoxidation steps (Bianchi et al., 2019). HOM formation has been
observed from anthropogenic species (Berndt et al., 2018b) and biogenic
species such as <inline-formula><mml:math id="M5" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (Molteni et al., 2019; Berndt et al.,
2018a). The semi-explicit mechanism described for the first time in this
paper describes the formation of HOMs from <inline-formula><mml:math id="M6" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene in a form
suitable for global modelling studies. This provides a framework for
incorporating a comprehensive description of pure biogenic nucleation into a
global model and, ultimately, allowing for a more rigorous description of
aerosol formation and the climatic consequences. <inline-formula><mml:math id="M7" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-Pinene is
considered as it is the most widely studied and widely emitted monoterpene
(<inline-formula><mml:math id="M8" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">32</mml:mn></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M9" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Tg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">yr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>; Sindelarova et al., 2014) and, with
measured HOM yields of around 3 %–10 % (Ehn et al., 2014; Jokinen et al.,
2015), has the potential to produce 2–7 <inline-formula><mml:math id="M10" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">Tg</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">HOM</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">yr</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> with the range
arising from uncertainties in emissions, HOM yield, and difference in mass
between the precursor biogenic volatile organic compounds (BVOC) and the HOMs, which will have at least six
additional oxygen atoms but, in some cases, considerably more. HOM yields
from <inline-formula><mml:math id="M11" display="inline"><mml:mi mathvariant="italic">β</mml:mi></mml:math></inline-formula>-pinene (the second most widely emitted monoterpene;
Sindelarova et al., 2014) and isoprene (the most widely emitted BVOC;
Sindelarova et al., 2014) are negligible (Ehn et al., 2014). Limonene has
emissions at around 25 % of <inline-formula><mml:math id="M12" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (Sindelarova et al., 2014) and
is likely to have a higher HOM yield (Ehn et al., 2014; Jokinen et al.,
2015) although a much wider range of values have been reported than for
<inline-formula><mml:math id="M13" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene. Limonene thus may have the potential to produce a similar
mass of HOMs to <inline-formula><mml:math id="M14" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene, and its consideration may be an area of
future work. Emissions of anthropogenic volatile organic compounds (VOCs) account for <inline-formula><mml:math id="M15" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:math></inline-formula> % of total VOC emissions (Guenther et al., 1995), roughly the same
quantity as monoterpene emissions, and, as no species have HOM yields above
2.5 % (Ehn et al., 2014; Jokinen et al., 2015; Kirkby et al., 2016;
Bianchi et al., 2019), the contribution of anthropogenic VOCs to HOMs is
likely to be significantly smaller. Nevertheless, the speciation of
anthropogenic VOCs in the mechanism means that addition of HOMs from these
sources will be possible and, from an urban air quality perspective, very
important.</p>
      <p id="d1e347">Nucleation of new particles from sulfuric acid is an important means of new
particle formation (NPF) in the atmosphere (Kulmala et al., 1998). Sulfuric
acid can also form new particles with oxidised organic species (Riccobono et
al., 2014). However, extremely involatile HOMs can participate in NPF,
without necessarily needing a sulfuric acid seed in a process termed pure
biogenic nucleation (PBN; Kirkby et al., 2016; Gordon et al., 2016).
Despite playing important roles in aerosol formation and growth, the
relatively recent discovery of HOMs and the complexity of their formation
mean that their role in particle formation and contribution to aerosols has
been assessed in only very few global model studies (Gordon et al., 2016;
Zhu et al., 2019). The ability of PBN to change atmospheric aerosol loading
by providing a route to particle formation without sulfuric acid has been
illustrated (Gordon et al., 2016), with this effect particularly important in
the pre-industrial (PI) atmosphere, where lower <inline-formula><mml:math id="M16" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">SO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> emissions resulted
in greater sensitivity of aerosol loading to alternative formation routes
(i.e. including PBN) and a higher simulated aerosol burden than in previous
studies. As a result, Gordon et al. (2016) calculated that the radiative
forcing change from the PI period to PD caused by cloud cover change was 27 %
lower than previous estimates. Meanwhile, Zhu et al. (2019), highlighting the
fact that many chemistry schemes fail to reproduce nucleation rates in low
sulfuric acid concentrations, showed the complex effect PBN has in the PI period
and PD with a more complicated mechanism although it also omitted
autoxidation and accretion product formation. Including PBN in a global
chemistry–aerosol scheme resulted in a much larger increase in the<?pagebreak page10891?> magnitude
of the (negative) aerosol indirect effect (AIE) in the PI period than in the PD. This
has potentially important consequences as it means that the effective
radiative forcing (ERF) of aerosols from the PI period to the PD may be smaller than
previously expected. This in turn would mean that climate sensitivity is
lower than previously thought as aerosols are offsetting a smaller amount of
warming arising from the enhanced concentrations of greenhouse gases than
previously thought, with implications for predictions of future climate
change as well.</p>
      <p id="d1e361">The peroxy radicals produced from <inline-formula><mml:math id="M17" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene oxidation by OH or
<inline-formula><mml:math id="M18" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> have been observed to undergo autoxidation under typical atmospheric
conditions (Ehn et al., 2014; Jokinen et al., 2014; Berndt et al., 2016,
2018a). The autoxidation competes with the bimolecular
reaction of peroxy radicals with NO, <inline-formula><mml:math id="M19" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M20" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and other peroxy
radicals, and its yield is thus dependent on background atmospheric
composition. Therefore, an accurate description of HOMs requires
consideration of <inline-formula><mml:math id="M21" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and oxidant concentrations as well as
autoxidation; indeed, elevated <inline-formula><mml:math id="M22" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> has been observed to suppress HOM
formation (Lehtipalo et al., 2018). The first-order rate constants for
autoxidation can vary over several orders of magnitude (<inline-formula><mml:math id="M23" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">6</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>–10<inline-formula><mml:math id="M24" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M25" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) depending on nearby functional groups
(Otkjær et al., 2018; Bianchi et al., 2019; Crounse et al.,
2013; Xu et al., 2019; Kurtén et al., 2015). Autoxidation rates also exhibit
a significant positive temperature dependence (Jenkin et al., 2019b; Bianchi
et al., 2019), and HOM yield has been observed to be highly temperature
dependent (Quéléver et al., 2019). Thus, the overall
competitiveness of autoxidation is dependent on the background atmospheric
composition and ambient temperature as well as on the molecule undergoing
oxidation.</p>
      <p id="d1e467">In addition to autoxidation, the formation of HOM accretion products (also
called dimers; Kurtén et al., 2016; Bianchi et al., 2019)
by reactions between two peroxy radicals has been observed to be significant
with large peroxy radicals (Kirkby et al., 2016; Berndt et al., 2018a,
b; Jenkin et al., 2019b; Molteni et al., 2019). These
species are predicted to be more involatile than 10-carbon HOMs (also termed
monomers; Kurtén et al., 2016) with important implications
for new particle formation and contribution to secondary organic aerosol (SOA). In established schemes
such as the Master Chemical Mechanism (MCM; Jenkin et al., 1997; Saunders
et al., 2003), the Common Representative Intermediates (CRI; Utembe et al.,
2010; Watson et al., 2008; Jenkin et al., 2008, 2019b), and the
chemistry of the stratosphere and troposphere (StratTrop) used in the
climate model UKCA (United Kingdom Chemistry and Aerosols; Archibald et al.,
2020), formation of accretion products is not included as it was previously
considered negligible or too complex to include. However, experimental work
suggests that accretion product formation is a competitive pathway for
larger peroxy radicals, such as those formed from <inline-formula><mml:math id="M26" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (Berndt
et al., 2018a; Molteni et al., 2019; Simon et al., 2020), and indeed becomes
more favourable with increasing functionality and size; the rate coefficient
for the accretion reaction between two <inline-formula><mml:math id="M27" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene-derived peroxy
radicals was observed to be 16–80 times greater (depending on the extent of
oxidation) than for the analogous reaction between two isoprene-derived
peroxy radicals (Berndt et al., 2018a, b).</p>
      <p id="d1e484">The mechanistic treatment of HOMs in numerical models has varied
considerably from simple steady-state approximations (Gordon et al., 2016),
through basic mechanisms linked to a volatility basis set (Schervish and Donahue,
2020), to more explicit descriptions based on the MCM featuring either a
limited subset of HOMs without accretion product formation or autoxidation
(Zhu et al., 2019) or a near-explicit description involving over 1700
reactions (Roldin et al., 2019). Whilst the addition of PBN represents an
important process-level improvement in models, the approaches discussed
above all have some degree of limitation. As well as omitting accretion
product formation, simpler models (Gordon et al., 2016; Schervish and Donahue,
2020) do not fully capture the influence of oxidant levels, <inline-formula><mml:math id="M28" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> or
temperature, while the more explicit schemes (Zhu et al., 2019; Roldin et
al., 2019) are too computationally expensive for long-term climate studies.
Further, none of the schemes include the relatively novel observation of
suppression via reactive <inline-formula><mml:math id="M29" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> cross reactions (McFiggans et al., 2019),
although this has been identified as an important area for future research
(Zhu et al., 2019; Roldin et al., 2019) and is addressed in this work.</p>
      <p id="d1e509">New experimental evidence suggests that isoprene may suppress the formation
of the most involatile accretion products and thus the smallest aerosol
particles (Berndt et al., 2018a; McFiggans et al., 2019; Heinritzi et al.,
2020), and reproducing the effect of isoprene has been identified as an
important requirement for future mechanisms (Roldin et al., 2019). This
inhibition is driven firstly by isoprene-scavenging OH radicals (Lee et al.,
2016; Kiendler-Scharr et al., 2009; Berndt et al., 2018a), thus reducing the
formation of large peroxy radicals by reaction of <inline-formula><mml:math id="M30" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene with OH.
The second driver is the scavenging of the 10-carbon <inline-formula><mml:math id="M31" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene peroxy
radicals (C10RO2) by isoprene peroxy radicals (C5RO2) and the other
smaller peroxy radicals from species such as CO and <inline-formula><mml:math id="M32" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">CH</mml:mi><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (McFiggans et
al., 2019). C10RO2 could otherwise form 20-carbon accretion products
(Eq. 1) which are predicted to be highly involatile (Kurtén
et al., 2016). The reaction of isoprene peroxy radicals with the <inline-formula><mml:math id="M33" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene radicals produces the 15-carbon accretion product (C15d; Eq. 2) as well as closed-shell species (C10 and C5; Eq. 3) and alkoxy
radicals (C10RO and C5RO; Eq. 4) which isomerise or fragment
(Jenkin et al., 2019b).

              <disp-formula specific-use="gather" content-type="numbered"><mml:math id="M34" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E1"><mml:mtd><mml:mtext>1</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C20d</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E2"><mml:mtd><mml:mtext>2</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mtext>C5</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C15d</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E3"><mml:mtd><mml:mtext>3</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mtext>C5</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C10</mml:mtext><mml:mo>+</mml:mo><mml:mtext>C5</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E4"><mml:mtd><mml:mtext>4</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mtext>C5</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mtext>C5</mml:mtext><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

          This inhibition affects the aerosol size distribution (an important
parameter for the radiative forcing of aerosols; Zhu et al.,<?pagebreak page10892?> 2019) by
favouring the growth of larger existing aerosol particles by promoting the
production of smaller, more volatile species which can partition into
pre-existing aerosols rather than the nucleation of new particles from
larger, less volatile species. This has the potential to have important
consequences for future predictions of SOA and the negative feedback
proposed to exist between biogenic VOC emissions and atmospheric temperature
(Kulmala et al., 2004; Carslaw et al., 2010; Sporre et al., 2019). Such
predictions, based on the modelled increases in isoprene and monoterpene
emissions in a warmer climate (Kulmala et al., 2013; Sporre et al., 2019),
have not considered the potential perturbation to NPF and atmospheric
aerosol loading by isoprene and the changes in radiative forcing which may
result. Reassessing the sign and size of this feedback by coupling the
chemistry scheme described in this work to an aerosol scheme within a global
climate model is a key long-term aim of this work.</p>
      <p id="d1e714">In this study we describe our work developing a new mechanism that is sufficiently
concise for global chemistry climate models and can simulate the process of
autoxidation, the formation of HOMs from <inline-formula><mml:math id="M35" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene and the influence
of isoprene. In Sect. 2 the development of the mechanism from the
principles of gas-phase chemistry is described, and in Sect. 3 we discuss
mechanism optimisation and validation against experimental data and the
parent mechanism, CRI v2.2. In Sect. 4, the mechanism is used to simulate
atmospheric HOM profiles and explore implications for new particle
formation. Finally, in Sect. 5, conclusions for further work are drawn.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><?xmltex \currentcnt{1}?><label>Figure 1</label><caption><p id="d1e726">Schematic of additions to CRI v2.2 to represent autoxidation and
HOM formation via ozonolysis of <inline-formula><mml:math id="M36" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene. HOMs (C10z, C15d, C20d)
can be produced via reaction of O3RO2 with <inline-formula><mml:math id="M37" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M38" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, while
reaction with NO, <inline-formula><mml:math id="M39" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M40" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> can produce alkoxy radicals which
can fragment or isomerise. New species introduced in this scheme are denoted
by normal font; existing species are denoted by italics. The <inline-formula><mml:math id="M41" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> pool is split into
subsections covering big (<inline-formula><mml:math id="M42" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">b</mml:mi></mml:mrow></mml:math></inline-formula>), medium (<inline-formula><mml:math id="M43" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">m</mml:mi></mml:mrow></mml:math></inline-formula>) and small
(<inline-formula><mml:math id="M44" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">s</mml:mi></mml:mrow></mml:math></inline-formula>) peroxy radicals to facilitate addition of accretion product
formation.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f01.png"/>

      </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><?xmltex \currentcnt{2}?><label>Figure 2</label><caption><p id="d1e840">Schematic of additions to CRI v2.2 to represent autoxidation and
HOM formation via OH oxidation. HOMs can be produced via reaction with
<inline-formula><mml:math id="M45" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M46" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, while reaction with NO, <inline-formula><mml:math id="M47" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M48" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> can
produce alkoxy radicals which can fragment or isomerise. The <inline-formula><mml:math id="M49" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> pool
is split into subsections covering big (<inline-formula><mml:math id="M50" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">b</mml:mi></mml:mrow></mml:math></inline-formula>), medium (<inline-formula><mml:math id="M51" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">m</mml:mi></mml:mrow></mml:math></inline-formula>) and
small (<inline-formula><mml:math id="M52" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">s</mml:mi></mml:mrow></mml:math></inline-formula>) peroxy radicals to facilitate addition of accretion
product formation.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f02.png"/>

      </fig>

</sec>
<sec id="Ch1.S2">
  <label>2</label><title>Mechanism development</title>
      <p id="d1e952">Our new mechanism we have developed builds on the Common Representative
Intermediates (CRI) scheme version 2.2 Reduction 5 (Jenkin et al., 2019a; hereafter the “base mechanism”), developed from the fully explicit Master
Chemical Mechanism (MCM) version 3.3.1 (Jenkin et al., 2015) which describes
the degradation of organic compounds in the troposphere. In the CRI
framework, species are lumped together into surrogate molecules whose
behaviour is optimised against the fully explicit MCM. The CRI v2.2 R5
mechanism describes the degradation of <inline-formula><mml:math id="M53" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene, <inline-formula><mml:math id="M54" display="inline"><mml:mi mathvariant="italic">β</mml:mi></mml:math></inline-formula>-pinene,
isoprene and 19 other emitted VOC species.</p>
      <p id="d1e969">The updates we have made to the base mechanism to produce the new
HOM-forming functionality include the addition of autoxidation of <inline-formula><mml:math id="M55" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene oxidation products and a more detailed peroxy radical pool scheme.
These changes enable the formation of 10-carbon, 15-carbon and 20-carbon
HOMs and add 12 species and 66 reactions to the base mechanism. The new
chemical mechanisms for ozonolysis and OH oxidation are shown in Figs. 1
and 2 respectively. We now describe the changes made to the base
mechanism to incorporate HOM chemistry in more detail.</p><?xmltex \hack{\newpage}?>
<sec id="Ch1.S2.SS1">
  <label>2.1</label><title>Ozonolysis</title>
      <?pagebreak page10893?><p id="d1e987">To simulate the autoxidation reactions formed from ozonolysis five new peroxy
radical species were added to the base mechanism. The peroxy radicals formed
from ozonolysis of <inline-formula><mml:math id="M56" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene and subsequent autoxidation steps are
collectively termed O3RO2. In the base mechanism, <inline-formula><mml:math id="M57" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene
reacts with ozone to produce the single lumped peroxy radical RN18AO2 and
acetone. This single mechanistic step represents multiple chemical steps,
with RN18AO2 representing a six or seven carbon species. In addition, TNCARB26
(closed-shell carbonyl species) and RCOOH25 (pinonic acid) arise from
the reaction of Criegee intermediates with water. The yields of
these species, 17.5 % and 2.5 % respectively, remain unchanged from the
CRI v2.2 mechanism and are well supported in the literature (IUPAC, 2020; Atkinson and Arey,
2003; Johnson and Marston, 2008). RN18AO2 goes on to react with
standard peroxy radical reaction partners; <inline-formula><mml:math id="M58" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>-forming hydroperoxides;
NO- and <inline-formula><mml:math id="M59" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>-forming alkoxy radicals; and the peroxy-radical-pool-forming
alkoxy radicals, carbonyls and alcohols, as described in Jenkin et al. (2019b).</p>
      <p id="d1e1026">In our new mechanism, RN18AO2 is replaced with the tracers RN26BO2 and
RTN24O2. RN26BO2 represents the 10-carbon peroxy radicals formed directly
from the cleavage of the ozonide and subsequent addition of atmospheric
oxygen, which can then undergo autoxidation. RTN24O2, a species already in
the CRI mechanism, represents the 9-carbon peroxy radical species (MCM
species C96O2) which is also formed from ozonolysis but does not undergo
autoxidation in this mechanism. RN26BO2 is termed “first generation” as
it has undergone one oxidation step and it can undergo autoxidation to form
the second-, third- and fourth-generation and lumped higher-generation species,
termed RN25BO2O2, RN24BO4O2, RN23BO4O2 and RNxBOyO2 species respectively
(RNxBOyO2 does not undergo further autoxidation but does undergo all the
other reactions). In the base mechanism, the first number featured in a
species' name is an index which refers to the number of NO-to-<inline-formula><mml:math id="M60" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
conversions possible, which depends on the number of C–C and C–H bonds.
During the H-shift step of autoxidation, a C–H bond is usually broken to
produce the alkyl radical which then forms the peroxy radical from
atmospheric oxygen, and so each autoxidation step reduces the index by 1
while the number of oxygens is increased by 2. For example, the autoxidation
of the second-generation O3RO2 to the third generation is expressed by
Eq. (5).
            <disp-formula id="Ch1.E5" content-type="numbered"><label>5</label><mml:math id="M61" display="block"><mml:mrow><mml:mtext>RN25BO2O2</mml:mtext><mml:mo>→</mml:mo><mml:mtext>RN24BO4O2</mml:mtext></mml:mrow></mml:math></disp-formula>
          Each generation of peroxy radicals also undergoes bimolecular reactions.
Reaction with <inline-formula><mml:math id="M62" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> produces a hydroperoxide species; for the second
and later generations, the product is classified as a HOM (C10z) as it fulfils the criteria discussed by Bianchi et al. (2019), while for the
first-generation species the resulting hydroperoxide is RTN26OOH, a
species already present in the CRI (Eq. 6).
            <disp-formula id="Ch1.E6" content-type="numbered"><label>6</label><mml:math id="M63" display="block"><mml:mrow><mml:mtext>RNaBObO2</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>RTN26OOH</mml:mtext><mml:mtext> or </mml:mtext><mml:mtext>C10z</mml:mtext></mml:mrow></mml:math></disp-formula>
          Reaction with NO and <inline-formula><mml:math id="M64" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> yields nitrates or alkoxy radicals, and
accurately representing the behaviour of these products is crucial to
reproducing the effect of <inline-formula><mml:math id="M65" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> on HOM formation. Alkoxy radicals are not
represented explicitly due to their rapid reactions which, typically for
alkoxy radicals formed from larger peroxy radicals, are decomposition or
isomerisation. Decomposition produces two smaller species, one is closed shell
and one is a peroxy radical, while isomerisation produces a more functionalised
peroxy radical via an alkyl radical intermediate with one fewer oxygen than
would have been added via autoxidation. Faced with very limited data and the
fact that the precise fate of an alkoxy radical will depend considerably on
molecular structure and neighbouring groups, a branching ratio of <inline-formula><mml:math id="M66" display="inline"><mml:mrow><mml:mn mathvariant="normal">50</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">50</mml:mn></mml:mrow></mml:math></inline-formula> for
decomposition and isomerisation was adopted. Sensitivity tests perturbing
the branching ratio between <inline-formula><mml:math id="M67" display="inline"><mml:mrow><mml:mn mathvariant="normal">75</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">25</mml:mn></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M68" display="inline"><mml:mrow><mml:mn mathvariant="normal">25</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">75</mml:mn></mml:mrow></mml:math></inline-formula> were performed to probe the
consequences of this uncertainty. These tests suggested the precise value of
this branching ratio within this range did not affect the fitting of rate
coefficients for autoxidation and accretion product formation (Sect. 3.1).
However, these branching-ratio perturbations did lead to changes in HOM yield (Fig. S4b in the Supplement) and are discussed in more detail in Sect. 3.2. The decomposition
products are existing CRI species CARB16 and RN10O2 or RN9O2, and the
isomerisation product is the next-generation peroxy radical as shown in the
example reaction (Eq. 7).
            <disp-formula id="Ch1.E7" content-type="numbered"><label>7</label><mml:math id="M69" display="block"><mml:mtable columnspacing="1em" class="split" rowspacing="0.2ex" displaystyle="true" columnalign="right left"><mml:mtr><mml:mtd><mml:mrow><mml:mtext>RN25BO2O2</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">NO</mml:mi></mml:mrow></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mo>→</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn><mml:mtext>RN24BO4O2</mml:mtext><mml:mo>+</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn><mml:mtext>CARB16</mml:mtext></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn><mml:mtext>RN9O2</mml:mtext></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:math></disp-formula>
          A schematic of the additions made to the CRI for the ozonolysis scheme is
shown in Fig. 1.</p>
</sec>
<?pagebreak page10894?><sec id="Ch1.S2.SS2">
  <label>2.2</label><title>OH oxidation</title>
      <p id="d1e1195">Autoxidation through the OH initiated oxidation pathway resulted in the
addition of six new species, including five new peroxy radicals. The peroxy
radicals formed from OH oxidation of <inline-formula><mml:math id="M70" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene and subsequent
autoxidation steps are termed OHRO2. The single peroxy radical RTN28O2
in the base mechanism is replaced by RTN28AO2, representing the two species
which do not undergo autoxidation (APINAO2 and APINBO2 in the MCM), and
RTN28BO2 (MCM APINCO2) which can undergo autoxidation to form higher-generation peroxy radicals (Xu et al., 2019). The second- and third-generation OHRO2 are represented explicitly (RTN27BO2O2 and RTN26BO4O2), and
all fourth-generation and higher species are lumped together as RTNxBOyO2
for mechanistic simplicity. The chemical treatment of RTN28AO2 is the same
as for the original CRI species RTN28O2, while all other OHRO2 species (except RTNxBOyO2)
can undergo autoxidation (Eq. 8).
            <disp-formula id="Ch1.E8" content-type="numbered"><label>8</label><mml:math id="M71" display="block"><mml:mrow><mml:mtext>RTNaBObO2</mml:mtext><mml:mo>→</mml:mo><mml:mtext>RTN</mml:mtext><mml:mfenced close=")" open="("><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>-</mml:mo><mml:mi>a</mml:mi></mml:mrow></mml:mfenced><mml:mtext>BO</mml:mtext><mml:mfenced open="(" close=")"><mml:mrow><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:mfenced><mml:mtext>O2</mml:mtext></mml:mrow></mml:math></disp-formula>
          Reaction of the first- and second-generation OHRO2 (RTN28BO2 and
RTN27BO2O2) with <inline-formula><mml:math id="M72" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> yields the hydroperoxide RTN28OOH which is not
classified as a HOM due to insufficient oxygens. The HOM produced by all
later-generation OHRO2 species is termed C10x (Eq. 9).
            <disp-formula id="Ch1.E9" content-type="numbered"><label>9</label><mml:math id="M73" display="block"><mml:mrow><mml:mtext>RTNaBObO2</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>RTN28OOH</mml:mtext><mml:mtext> or </mml:mtext><mml:mtext>C10x</mml:mtext></mml:mrow></mml:math></disp-formula>
          Reaction with NO and <inline-formula><mml:math id="M74" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> is treated in the same manner as O3RO2 except
for RTN28BO2 which follows the reaction of the analogous species APINCO2 in
the MCM. A schematic of the additions made to the base mechanism for the OH
oxidation scheme is shown in Fig. 2.</p>
      <p id="d1e1283">The pathway initiated by reaction of <inline-formula><mml:math id="M75" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene with <inline-formula><mml:math id="M76" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> was not
considered in this work but is identified as an area for future work. A
summary of the peroxy radical species in the two pathways is given in Table 1, and a full mechanistic description is provided in the Supplement.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><?xmltex \currentcnt{1}?><label>Table 1</label><caption><p id="d1e1307">Summary of new species added in HOM mechanism. The removal of
species RN18AO2 and RTN28O2 results in a net increase of 12 species.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Species</oasis:entry>
         <oasis:entry colname="col2">Classification</oasis:entry>
         <oasis:entry colname="col3">Origin</oasis:entry>
         <oasis:entry colname="col4">MCM v3.3.1 equivalent</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">RN26BO2</oasis:entry>
         <oasis:entry colname="col2">First-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">C107O2, C109O2</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RN25BO2O2</oasis:entry>
         <oasis:entry colname="col2">Second-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RN24BO4O2</oasis:entry>
         <oasis:entry colname="col2">Third-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RN23BO6O2</oasis:entry>
         <oasis:entry colname="col2">Fourth-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RNxBOyO2</oasis:entry>
         <oasis:entry colname="col2">Lumped fifth- and higher-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RTN28AO2</oasis:entry>
         <oasis:entry colname="col2">First-generation peroxy radical (no autoxidation)</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">APINAO2 and APINBO2</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RTN28BO2</oasis:entry>
         <oasis:entry colname="col2">First-generation peroxy radical (autoxidation possible)</oasis:entry>
         <oasis:entry colname="col3">OH oxidation</oasis:entry>
         <oasis:entry colname="col4">APINCO2</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RTN27BO2O2</oasis:entry>
         <oasis:entry colname="col2">Second-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">OH oxidation</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RTN26BO4O2</oasis:entry>
         <oasis:entry colname="col2">Third-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">OH oxidation</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">RTNxBOyO2</oasis:entry>
         <oasis:entry colname="col2">Lumped fourth- and higher-generation peroxy radical</oasis:entry>
         <oasis:entry colname="col3">OH oxidation</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">C10z</oasis:entry>
         <oasis:entry colname="col2">10-Carbon HOM</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">C10x</oasis:entry>
         <oasis:entry colname="col2">10-Carbon HOM</oasis:entry>
         <oasis:entry colname="col3">OH oxidation</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">C15d</oasis:entry>
         <oasis:entry colname="col2">15-Carbon HOM</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis and OH oxidation</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">C20d</oasis:entry>
         <oasis:entry colname="col2">20-Carbon HOM</oasis:entry>
         <oasis:entry colname="col3">Ozonolysis and OH oxidation</oasis:entry>
         <oasis:entry colname="col4">Not in MCM</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S2.SS3">
  <label>2.3</label><?xmltex \opttitle{Peroxy radical\,$+$\,peroxy radical interactions}?><title>Peroxy radical <inline-formula><mml:math id="M77" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> peroxy radical interactions</title>
      <p id="d1e1573">Reactions between peroxy radicals can result in the formation of two alkoxy
radicals (Eq. 10), a carbonyl and an alcohol (Eq. 11) or accretion
product (Eq. 12; Jenkin et al., 2019b).

                <disp-formula specific-use="gather" content-type="numbered"><mml:math id="M78" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E10"><mml:mtd><mml:mtext>10</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="normal">R</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="normal">R</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E11"><mml:mtd><mml:mtext>11</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtable rowspacing="0.2ex" class="split" columnspacing="1em" displaystyle="true" columnalign="right left"><mml:mtr><mml:mtd><mml:mrow><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="normal">R</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mo>→</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">R</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mi mathvariant="normal">H</mml:mi></mml:mrow></mml:msub><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="normal">R</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mi mathvariant="normal">OH</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd/><mml:mtd><mml:mrow><mml:mtext>or </mml:mtext><mml:mrow class="chem"><mml:msubsup><mml:mi mathvariant="normal">R</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mi mathvariant="normal">H</mml:mi></mml:mrow><mml:mo>′</mml:mo></mml:msubsup><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">ROH</mml:mi></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E12"><mml:mtd><mml:mtext>12</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="normal">R</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mrow class="chem"><mml:msup><mml:mi mathvariant="normal">ROOR</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

            Rather than represent every possible <inline-formula><mml:math id="M79" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>–<inline-formula><mml:math id="M80" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> reaction combination,
the base mechanism uses a peroxy radical pool. Each peroxy radical undergoes
a unimolecular reaction with a first-order rate coefficient determined by
the total peroxy radical concentration and the geometric mean of the
self-reaction rates of the methyl peroxy radical and radical of interest
(Jenkin et al., 2019b).</p>
      <p id="d1e1790">While computationally efficient, such a mechanism fails to represent the
effect of peroxy radical size on the distribution of products. While
negligible for small peroxy radicals, accretion product formation is more
favourable when larger, more functionalised peroxy radicals react (Berndt et
al., 2018a; Schervish and Donahue,
2020). To describe the reactions between the
differently sized peroxy radicals, we have split the single peroxy radical
pool into three pools for small (less than four carbons), medium (four to seven carbons)
and big (more than seven carbons) peroxy radicals. Each big radical reacts
separately with each peroxy radical pool, while, to minimise the total number
of reactions, all small peroxy radicals react with the total pool as
accretion product formation is much less favourable (Jenkin et al., 2019b).
Medium peroxy radicals are discussed below. The use of large and medium
peroxy radical pools allows for improved representation of the competition
between peroxy radicals with different reactivity in our new mechanism and
is a substantial improvement over the base mechanism.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><?xmltex \currentcnt{2}?><label>Table 2</label><caption><p id="d1e1796">Summary of possible products formed for a particular peroxy
radical reacting with the big, medium and small peroxy radical pools.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="justify" colwidth="3.5cm"/>
     <oasis:colspec colnum="3" colname="col3" align="justify" colwidth="3.5cm"/>
     <oasis:colspec colnum="4" colname="col4" align="justify" colwidth="3.5cm"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Size of reacting peroxy radical</oasis:entry>
         <oasis:entry colname="col2">Product of reaction with big pool</oasis:entry>
         <oasis:entry colname="col3">Product of reaction with medium pool</oasis:entry>
         <oasis:entry colname="col4">Product of reaction with small pool</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Big (<inline-formula><mml:math id="M83" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">7</mml:mn></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M84" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, e.g. RN26BO2)</oasis:entry>
         <oasis:entry colname="col2">C20d HOM accretion product</oasis:entry>
         <oasis:entry colname="col3">C15d HOM accretion product</oasis:entry>
         <oasis:entry colname="col4">C10 HOM or existing CRI species*</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">C10 HOM or existing CRI species*</oasis:entry>
         <oasis:entry colname="col3">C10 HOM or existing CRI species*</oasis:entry>
         <oasis:entry colname="col4">Peroxy radical</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">Peroxy radical</oasis:entry>
         <oasis:entry colname="col3">Peroxy radical</oasis:entry>
         <oasis:entry colname="col4"/>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Medium (4–7 <inline-formula><mml:math id="M85" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, e.g. RU14O2)</oasis:entry>
         <oasis:entry namest="col2" nameend="col4" align="center">Closed shell, alkoxy radical </oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Small (<inline-formula><mml:math id="M86" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M87" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C, e.g. CH3O2)</oasis:entry>
         <oasis:entry namest="col2" nameend="col4" align="center">Closed-shell species, alkoxy radical (no change from CRI v2.2 treatment) </oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p id="d1e1799">* The result depends on the extent to which the reacting peroxy radical has
been oxidised prior to the <inline-formula><mml:math id="M81" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>–<inline-formula><mml:math id="M82" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> reaction. A HOM is classified
as a species which has undergone at least one autoxidation step at
atmospherically relevant temperatures and contains at least six oxygen atoms
(Bianchi et al., 2019). Thus, some of the less oxidised peroxy radicals may
not qualify as HOMs and are assigned to the most relevant non-HOM species
already in the CRI.</p></table-wrap-foot></table-wrap>

      <p id="d1e1967">Table 2 summarises the products for a specific peroxy radical reacting with
the different peroxy radical pools. As discussed previously, alkoxy radials
were not simulated explicitly; rather they decomposed into closed-shell
products and peroxy radicals. A full list of the contents of each peroxy
radical pool is given in the Supplement.</p>
      <p id="d1e1970">In practice, the alkoxy radicals formed from the reaction of
isoprene-derived peroxy radicals (which are likely to dominate the medium
size pool) with other peroxy radicals decompose rapidly into the major
products: closed-shell carbonyls methyl vinyl ketone and methacrolein
(UCARB10) and the minor product hydroxy vinyl carbonyl (UCARB12; Jenkin et
al., 2015). The accretion of isoprene-derived peroxy radicals has been
measured to be over an order of magnitude slower than the accretion of
peroxy radicals derived from <inline-formula><mml:math id="M88" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (Berndt et al., 2018a),
supporting the theory that accretion product formation becomes more
favourable with increasing peroxy radical size. Therefore, to limit
complexity, all medium peroxy radicals in the mechanism simply reacted with
the overall peroxy radical pool and their accretion product formation was
ignored.</p>
<sec id="Ch1.S2.SS3.SSS1">
  <label>2.3.1</label><title>Large peroxy radical pool</title>
      <p id="d1e1987">The reaction of a large peroxy radical with the large peroxy radical pool
(<inline-formula><mml:math id="M89" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) can produce an accretion product (Eq. 13), closed species (Eq. 14) or an alkoxy radical (Eq. 15; Jenkin et al., 2019b) which then reacts
as discussed in Sect. 2.1 and 2.2. Note that a single C10RO2 species will
produce half a C20d accretion product for the purposes of mass conservation.

                  <disp-formula specific-use="gather" content-type="numbered"><mml:math id="M90" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E13"><mml:mtd><mml:mtext>13</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn><mml:mtext>C20d</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>:</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E14"><mml:mtd><mml:mtext>14</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C10z</mml:mtext><mml:mo>/</mml:mo><mml:mtext>C10x</mml:mtext><mml:mo>/</mml:mo><mml:mtext>TNCARB</mml:mtext><mml:mn mathvariant="normal">26</mml:mn><mml:mo>:</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">14</mml:mn></mml:msub></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E15"><mml:mtd><mml:mtext>15</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C10RO</mml:mtext><mml:mo>:</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">15</mml:mn></mml:msub></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

              The rate coefficient for C20d formation, <inline-formula><mml:math id="M91" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, increased with<?pagebreak page10895?> the extent
of oxidation of the reacting peroxy radical. This was done to simulate the
observed behaviour that accretion product formation becomes faster as the
reacting peroxy radicals become more functionalised (Berndt et al., 2018a,
b). Thus, the reaction forming C20d from the first-generation peroxy radicals had a lower rate coefficient than the analogous
reactions involving higher-generation <inline-formula><mml:math id="M92" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> species (see reactions 21, 23, 25,
27, 29, 46, 63, 64, 65 and 66 in the Supplement reaction list for full breakdown).
The rate coefficients used, 0.4–<inline-formula><mml:math id="M93" display="inline"><mml:mrow><mml:mn mathvariant="normal">3.6</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M94" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, were derived from fitting against experimental data
(Berndt et al., 2018a) and, as discussed in Sect. 3.1.3, were in line
with the range measured by Berndt et al. (2018a; 0.97–<inline-formula><mml:math id="M95" display="inline"><mml:mrow><mml:mn mathvariant="normal">7.9</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M96" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>). This resulted in Eq. (13) being
more important than Eqs. (14) and (15) which had rate coefficients based on the
literature (Molteni et al., 2019; Roldin et al., 2019) that were up to an order of
magnitude lower.</p>
      <p id="d1e2260">The rate coefficient for the formation of the closed-shell species from
O3RO2, <inline-formula><mml:math id="M97" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">14</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, was taken as the mean of the rate coefficients measured by
Molteni et al. (2019; <inline-formula><mml:math id="M98" display="inline"><mml:mrow><mml:mn mathvariant="normal">1.68</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">12</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M99" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>). The rate coefficient for alkoxy radical formation, <inline-formula><mml:math id="M100" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">15</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, was
assumed to have the same value as <inline-formula><mml:math id="M101" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">14</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (i.e. a <inline-formula><mml:math id="M102" display="inline"><mml:mrow><mml:mn mathvariant="normal">50</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">50</mml:mn></mml:mrow></mml:math></inline-formula> branching ratio
between these pathways). This value is close to the value of a closed-shell : alkoxy radical of <inline-formula><mml:math id="M103" display="inline"><mml:mrow><mml:mn mathvariant="normal">40</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">60</mml:mn></mml:mrow></mml:math></inline-formula> ratio suggested for primary and secondary peroxy
radicals by Jenkin et al. (2019b) but further from the <inline-formula><mml:math id="M104" display="inline"><mml:mrow><mml:mn mathvariant="normal">20</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">80</mml:mn></mml:mrow></mml:math></inline-formula> ratio suggested for
tertiary peroxy radicals. However, sensitivity tests where the mechanism was
run with branching ratios of <inline-formula><mml:math id="M105" display="inline"><mml:mrow><mml:mn mathvariant="normal">40</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">60</mml:mn></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M106" display="inline"><mml:mrow><mml:mn mathvariant="normal">20</mml:mn><mml:mo>:</mml:mo><mml:mn mathvariant="normal">80</mml:mn></mml:mrow></mml:math></inline-formula> revealed that the precise
values of this branching ratio within this range did not affect the fitting
of rate coefficients for autoxidation and accretion product formation
(Sect. 3.1). These branching ratio<?pagebreak page10896?> perturbations led to negligible changes in HOM yield (Sect. 3.2, Simulation C) which were
much smaller than the range in the HOM yield simulated to arise from the
uncertainty in the autoxidation temperature dependence and are therefore
considered to be of minor importance (Table S6 in the Supplement).</p>
      <p id="d1e2406">The rate coefficients for formation of closed-shell species and alkoxy
radicals from OHRO2 with <inline-formula><mml:math id="M107" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">b</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> were taken from Roldin et al. (2019).</p>
</sec>
<sec id="Ch1.S2.SS3.SSS2">
  <label>2.3.2</label><title>Medium and small peroxy radical pools</title>
      <p id="d1e2430">Reaction of a large peroxy radical with the medium peroxy radical pool
(<inline-formula><mml:math id="M108" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">m</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) can produce a 15-carbon accretion product (Eq. 16), closed-shell
species (Eq. 17), or an alkoxy radical (Eq. 18) which is not modelled
explicitly but rather decomposes rapidly into another closed-shell product
and peroxy radical.

                  <disp-formula specific-use="gather" content-type="numbered"><mml:math id="M109" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E16"><mml:mtd><mml:mtext>16</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">m</mml:mi></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mn mathvariant="normal">0.667</mml:mn><mml:mtext>C15d</mml:mtext><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>:</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">16</mml:mn></mml:msub></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E17"><mml:mtd><mml:mtext>17</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">m</mml:mi></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C10z</mml:mtext><mml:mo>/</mml:mo><mml:mtext>C10x</mml:mtext><mml:mo>/</mml:mo><mml:mtext>TNCARB</mml:mtext><mml:mn mathvariant="normal">26</mml:mn><mml:mo>:</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">17</mml:mn></mml:msub></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E18"><mml:mtd><mml:mtext>18</mml:mtext></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">m</mml:mi></mml:msub></mml:mrow><mml:mo>→</mml:mo><mml:mtext>C10</mml:mtext><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi></mml:mrow><mml:mo>:</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">18</mml:mn></mml:msub></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

              In a manner similar to C20d formation, the rate coefficient for C15d
formation, <inline-formula><mml:math id="M110" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">16</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, in the mechanism increases with the extent of oxidation
of the reacting large peroxy radical; the reaction forming C15d from the first-generation peroxy radicals had a lower rate coefficient than the analogous
reactions involving higher-generation <inline-formula><mml:math id="M111" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> species (see Reactions 36,
37, 38, 39, 40, 47, 71, 72, 73 and 74 in the Supplement reaction list for full
breakdown). The fitting of <inline-formula><mml:math id="M112" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">16</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> rate coefficients to experimental data is
discussed in Sect. 3.1.3. The chosen fitted values of 1.8–<inline-formula><mml:math id="M113" display="inline"><mml:mrow><mml:mn mathvariant="normal">7.5</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">12</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M114" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> were lower than the range
measured by Berndt et al. (2018a; 1.2–<inline-formula><mml:math id="M115" display="inline"><mml:mrow><mml:mn mathvariant="normal">3.6</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M116" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>).</p>
      <p id="d1e2717">Reaction of a large peroxy radical with the small peroxy radical pool
(<inline-formula><mml:math id="M117" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">RO</mml:mi><mml:msub><mml:mn mathvariant="normal">2</mml:mn><mml:mi mathvariant="normal">s</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>) produces a closed-shell species or an alkoxy radical, in a
manner analogous to Eqs. (17) and (18).</p>
</sec>
</sec>
<sec id="Ch1.S2.SS4">
  <label>2.4</label><title>HOM loss mechanisms</title>
      <p id="d1e2742">The number of different molecules falling under the C10x, C10z, C15d and
C20d umbrellas is huge, making the treatment of loss processes complex.
Losses will occur via chemical or photolytic degradation as well as to
condensation to aerosols, to the nucleation sink, and dry and wet deposition.
Physical loss is believed to be the major sink for HOMs (Dal Maso et al., 2002;
Petäjä et al., 2009; Tan et al., 2018; Wu et al., 2007; Bianchi et
al., 2019). For simplicity, in the simulations below, we ignore wet and dry
deposition but do include loss to the condensation sink for modelling
simulations C and D (Table 3).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3" specific-use="star"><?xmltex \currentcnt{3}?><label>Table 3</label><caption><p id="d1e2748">Simulations used for developing and testing new mechanism.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="justify" colwidth="3cm"/>
     <oasis:colspec colnum="3" colname="col3" align="justify" colwidth="3cm"/>
     <oasis:colspec colnum="4" colname="col4" align="justify" colwidth="3cm"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Simulation</oasis:entry>
         <oasis:entry colname="col2">Purpose</oasis:entry>
         <oasis:entry colname="col3">Mechanism version(s) used</oasis:entry>
         <oasis:entry colname="col4">Conditions</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">A: flow cell experiment</oasis:entry>
         <oasis:entry colname="col2">Optimise mechanism by fitting autoxidation coefficients and rate coefficients for accretion product formation</oasis:entry>
         <oasis:entry colname="col3">Temperature-independent mechanism</oasis:entry>
         <oasis:entry colname="col4">297 K, <inline-formula><mml:math id="M118" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M119" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">8</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M120" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, dark, <?xmltex \hack{\newline}?> 26 ppb <inline-formula><mml:math id="M121" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, initial <inline-formula><mml:math id="M122" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene concentration varied</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">B: flow cell experiment</oasis:entry>
         <oasis:entry colname="col2">Along with Simulation A, optimise mechanism by fitting autoxidation coefficients and rate coefficients for accretion product formation</oasis:entry>
         <oasis:entry colname="col3">Temperature-independent mechanism</oasis:entry>
         <oasis:entry colname="col4">297 K, <inline-formula><mml:math id="M123" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M124" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">8</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M125" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, dark, <?xmltex \hack{\newline}?> 80 ppb <inline-formula><mml:math id="M126" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, 15.6 ppb <inline-formula><mml:math id="M127" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene concentration, initial isoprene concentration varied</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">C: chamber experiment</oasis:entry>
         <oasis:entry colname="col2">HOM yield calculation</oasis:entry>
         <oasis:entry colname="col3">Temperature-dependent mechanisms with autoxidation activation energies of 6000, 9000 and 12 077 K</oasis:entry>
         <oasis:entry colname="col4">270, 290 or 310 K; <?xmltex \hack{\newline}?> 15 ppb <inline-formula><mml:math id="M128" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene; 40 ppb <inline-formula><mml:math id="M129" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>; <?xmltex \hack{\newline}?> NO and <inline-formula><mml:math id="M130" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> varied from 0.01 to 10 ppb</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">D: tropical boundary layer experiment</oasis:entry>
         <oasis:entry colname="col2">Compare new mechanism with concentrations predicted by CRI v2.2</oasis:entry>
         <oasis:entry colname="col3">Temperature-independent and all temperature-dependent mechanisms</oasis:entry>
         <oasis:entry colname="col4">8 d run with diurnally varying photolysis, temperature (<inline-formula><mml:math id="M131" display="inline"><mml:mrow><mml:mn mathvariant="normal">298</mml:mn><mml:mo>±</mml:mo><mml:mn mathvariant="normal">4</mml:mn></mml:mrow></mml:math></inline-formula> K), <inline-formula><mml:math id="M132" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene and isoprene emissions, <?xmltex \hack{\newline}?> multiple runs performed with scaled NO and <inline-formula><mml:math id="M133" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene emissions <?xmltex \hack{\newline}?> (full details in Supplement)</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p id="d1e3027">Chemical losses of HOMs are highly uncertain. It is suggested that HOMs will
react with OH (Bianchi et al., 2019). In this model, OH reacts with C10x,
C10z, C15d and C20d with the rate coefficient of the large hydroperoxide,
RTN28OOH, to produce the smaller closed-shell CRI species CARB10 and CARB15
as well as UCARB10 (lumped methacrolein and methyl vinyl ketone) for
15-carbon dimers. This rate coefficient was
<inline-formula><mml:math id="M134" display="inline"><mml:mrow><mml:mn mathvariant="normal">2.38</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> cm<inline-formula><mml:math id="M135" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> molec.<inline-formula><mml:math id="M136" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M137" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, and, in light of the suggestion that the rate
coefficient of OH with HOMs could be higher (Bianchi et al., 2019),
sensitivity tests increasing the rate coefficient to <inline-formula><mml:math id="M138" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> cm<inline-formula><mml:math id="M139" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> molec.<inline-formula><mml:math id="M140" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> s<inline-formula><mml:math id="M141" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> were performed, but no material effect was
observed. Photolysis of peroxide and carbonyl linkages produce alkoxy
radicals which behave as previously described. Photolysis frequencies are
taken from the MCM (Jenkin et al., 1997; Saunders et al., 2003). Given the
small concentrations of HOMs we predict that uncertainty in these gas-phase
loss processes is likely to have small impacts on the general features of
tropospheric chemistry (i.e. OH reactivity or ozone production).</p>
      <p id="d1e3134">Physical loss is believed to be the major sink for HOMs (Dal Maso et al.,
2002; Petäjä et al., 2009; Tan et al., 2018; Wu et al., 2007;
Bianchi et al., 2019). Loss to the condensation sink presents a complex
challenge. The saturation vapour pressure will vary considerably (Kurtén et al., 2016) for HOMs, even within the C10 umbrella, affecting
the fraction which partitions into the aerosol phase. Furthermore, some HOMs
are likely to have aldehyde and alcohol moieties which will enhance their
removal via reactive uptake into the aerosol phase, particularly if it is
aqueous. When using our new mechanism in different simulations (Table 3),
condensation sinks have been set to fixed values or values taken from the
literature.</p>
      <p id="d1e3137">Having described the additions and changes made to the base mechanism to
develop our new mechanism, we now discuss the optimisation and validation of
the mechanism.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <label>3</label><title>Mechanism optimisation and validation</title>
      <p id="d1e3149">Here we discuss the optimisation of the new mechanism and its validation. In
total four simulations were performed with the mechanism as detailed in Table 3.</p>
<sec id="Ch1.S3.SS1">
  <label>3.1</label><title>Comparison to experimental data</title>
      <p id="d1e3159">There exist a limited number of experimental data which provide an insight
into the behaviour of the multiple generations of peroxy radicals produced
from ozonolysis and OH oxidation of <inline-formula><mml:math id="M142" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (Berndt et al., 2018a).
Using a flow cell, Berndt et al. (2018a) measured the concentration of <inline-formula><mml:math id="M143" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene-derived peroxy radicals produced by ozonolysis (O3RO2) and OH
oxidation (OHRO2) and 20-carbon (C20d) and 15-carbon (C15d) accretion
products at the end of the flow tube using a chemical ionisation–atmospheric
pressure interface time-of-flight (CI-APi-TOF) mass spectrometer and a
chemical ionisation time-of-flight (CI3-TOF) mass spectrometer. The observed
peroxy radicals spanned several generations of autoxidation, namely the
first to fourth generation for O3RO2 species and first to third
generation<?pagebreak page10897?> for OHRO2. Berndt et al. (2018a) also calculated rate coefficients
for accretion product formation using the observation that accretion product
concentration increased linearly with time with an assumed uncertainty no
greater than a factor of 3. Reagent ions used in the CI-APi-TOF were
<inline-formula><mml:math id="M144" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">C</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">H</mml:mi><mml:mn mathvariant="normal">7</mml:mn></mml:msub><mml:msubsup><mml:mi mathvariant="normal">NH</mml:mi><mml:mn mathvariant="normal">3</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M145" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">CH</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub><mml:msup><mml:mi mathvariant="normal">COO</mml:mi><mml:mo>-</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M146" display="inline"><mml:mrow class="chem"><mml:msubsup><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn><mml:mo>-</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>, and in
the CI3-TOF the reagent ion was <inline-formula><mml:math id="M147" display="inline"><mml:mrow class="chem"><mml:msubsup><mml:mi mathvariant="normal">NH</mml:mi><mml:mn mathvariant="normal">4</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:mrow></mml:math></inline-formula>. The flow tube experiments lasted for 7.9 s, at
which point the flow was sampled by the mass spectrometers. Reactions
proceeded under dark conditions at 1 atm and 297 K under low [<inline-formula><mml:math id="M148" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>]
(<inline-formula><mml:math id="M149" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">8</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M150" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>). The low concentrations of bimolecular
reaction partners <inline-formula><mml:math id="M151" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and NO meant that multiple autoxidation steps
could occur in the reaction time.</p>
      <p id="d1e3291">Flow tubes operating under laminar flow are easily modelled using box models
as there are very few complications to consider in terms of mixing and wall
loss, and no new particle formation was observed. A box model version of the
mechanism was compiled in the BOXMOX framework (Knote et al., 2015). The
experimental data allowed for the autoxidation coefficients of the peroxy
radical species and the rate coefficients of accretion product formation to
be constrained. The concentrations of peroxy radicals and accretion products
in the box model were evaluated at the end of the 7.9 s reaction period and
compared with experiments. A process of iterative adjustment to autoxidation
and accretion product formation rate coefficients in the mechanism was
performed to produce the best reproduction of the experimental data by the
mechanism.</p>
      <p id="d1e3294">Two experiments from Berndt et al. (2018a) were considered. In the first
experiment, flow tube runs were performed with varying initial
concentrations of <inline-formula><mml:math id="M152" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (3–50 ppb) with initial <inline-formula><mml:math id="M153" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> at 26 ppb
(Simulation A). In the second experiment, runs were performed with fixed
initial <inline-formula><mml:math id="M154" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (15.6 ppb) and <inline-formula><mml:math id="M155" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (80 ppb) but with initial
isoprene concentrations varying from 0 to 60 ppb (Simulation B). Comparison with
these experimental data facilitated examination of the model's ability to
reproduce the concentration of HOM precursors and accretion products with
and without isoprene as well as at moderate and high <inline-formula><mml:math id="M156" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> mixing ratios.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T4"><?xmltex \currentcnt{4}?><label>Table 4</label><caption><p id="d1e3348">Autoxidation coefficients for peroxy radicals after fitting to
experimental data (at 297 K) with estimated uncertainty.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="3">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Generation</oasis:entry>
         <oasis:entry colname="col2">O3RO2 (<inline-formula><mml:math id="M158" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col3">OHRO2 (<inline-formula><mml:math id="M159" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>)</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">First</oasis:entry>
         <oasis:entry colname="col2">0.206 (<inline-formula><mml:math id="M160" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">0.025</mml:mn></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math id="M161" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.04</mml:mn></mml:mrow></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col3">2.1<inline-formula><mml:math id="M162" display="inline"><mml:msup><mml:mi/><mml:mo>∗</mml:mo></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Second</oasis:entry>
         <oasis:entry colname="col2">1.7 (<inline-formula><mml:math id="M163" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">1.1</mml:mn></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math id="M164" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.4</mml:mn></mml:mrow></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col3">2.1 (<inline-formula><mml:math id="M165" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">1.6</mml:mn></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math id="M166" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.2</mml:mn></mml:mrow></mml:math></inline-formula>)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Third</oasis:entry>
         <oasis:entry colname="col2">1.7 (<inline-formula><mml:math id="M167" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">1.1</mml:mn></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math id="M168" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.4</mml:mn></mml:mrow></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col3">0.25 (<inline-formula><mml:math id="M169" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">0.3</mml:mn></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math id="M170" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.1</mml:mn></mml:mrow></mml:math></inline-formula>)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Fourth</oasis:entry>
         <oasis:entry colname="col2">1.6 (<inline-formula><mml:math id="M171" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">0.8</mml:mn></mml:mrow></mml:math></inline-formula>/<inline-formula><mml:math id="M172" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn></mml:mrow></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col3">n/a</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p id="d1e3351"><inline-formula><mml:math id="M157" display="inline"><mml:msup><mml:mi/><mml:mo>∗</mml:mo></mml:msup></mml:math></inline-formula> Taken directly from Xu et al. (2019).<?xmltex \hack{\\}?>n/a: not applicable.</p></table-wrap-foot></table-wrap>

      <?pagebreak page10898?><p id="d1e3597">An important parameter in the mechanism was the yield of RN26BO2 from
<inline-formula><mml:math id="M173" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene ozonolysis. This yield is uncertain, and it was found to
affect the autoxidation coefficients required to reproduce the experimental
data for the O3RO2 species. To constrain it, a first-order autoxidation rate
coefficient of 0.206 <inline-formula><mml:math id="M174" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> for RN26BO2 was imposed, based on theoretical
analysis of the <inline-formula><mml:math id="M175" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene ozonolysis system (Kurtén
et al., 2015), and the yield was adjusted until the mechanism was able to
achieve the best possible fit to the data. This resulted in a yield of
50 % for RN26BO2 and 30 % for RTN24O2. However, this remains a source of
uncertainty and warrants further investigation. The low-<inline-formula><mml:math id="M176" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> conditions
meant that the autoxidation coefficients dominated the concentration of
later-generation O3RO2 and OHRO2, and, from this starting point, the
autoxidation rate coefficients for later generations were fitted against
experimental data over multiple rounds of optimisation (Table 4). The
autoxidation coefficient for the first-generation OHRO2, RTN28BO2, was
taken as 2.1 <inline-formula><mml:math id="M177" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> based on Xu et al. (2019). An estimation of the
uncertainty in the autoxidation is also provided in Table 4. These values
were calculated by adjusting the autoxidation rate coefficients one at a
time to determine the maximum and minimum values of an autoxidation rate
coefficient for which the corresponding peroxy radical would fall within the
experimental uncertainty region. This approach neglects any
cross-sensitivities through the joint uncertainty in several rate
coefficients. A full Monte Carlo uncertainty analysis addressing this issue
is beyond the scope of this paper but would make a valuable follow up
for future work in this field. Therefore, the autoxidation rate coefficient
uncertainties are large as the experimental error uncertainties are large.</p>
      <p id="d1e3653">The autoxidation coefficients in Table 4 are higher than those considered in
the theoretical study of Schervish and Donahue (2020) but closer to the values
measured by Zhao et al. (2018) and the values suggested by Roldin et al. (2019). The mechanism used the autoxidation coefficients from Table 4 and
predicted the lumped higher-generation species (fifth generation for
O3RO2, fourth generation for OHRO2) at concentrations higher than those observed
in the work by Berndt et al. (2018a). This suggests there may be additional,
as yet unknown, loss processes for the more highly oxidised peroxy radical
species which are not incorporated into this work. Additional loss processes
would likely reduce the fitted autoxidation coefficients because they would
provide an additional sink for the <inline-formula><mml:math id="M178" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> species which does not lead to
the production of the next-generation <inline-formula><mml:math id="M179" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. Therefore, the autoxidation
coefficients determined in this work are likely to be upper limits, but
further insight into this is not possible with the data currently available.
This is a key area for further study.</p>
      <p id="d1e3678">Unfortunately, the flow tube studies of Berndt et al. (2018a) lack
observations to constrain the full chemical space simulated by the box
model. In particular there were no measurements of OH, <inline-formula><mml:math id="M180" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> or NO. The
effect of the uncertainty in the initial experimental concentrations of NO,
<inline-formula><mml:math id="M181" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and OH on the modelled concentrations of O3RO2, OHRO2 and accretion
products which thus fitted the autoxidation coefficients and accretion
production formation rate coefficients was investigated with a series of
sensitivity tests. Initial conditions of 10<inline-formula><mml:math id="M182" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M183" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> for OH and 4 ppt
for <inline-formula><mml:math id="M184" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> were used. NO and <inline-formula><mml:math id="M185" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> were initialised at 4 ppt, based on
the purity of the flow gas (personal communication with Torsten Berndt). For
<inline-formula><mml:math id="M186" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, NO and <inline-formula><mml:math id="M187" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, sensitivity simulations indicated that increases
of 10 ppt (250 % increase) and decreases of 3 ppt (75 % decrease) did
not lead to deviations in the concentrations of <inline-formula><mml:math id="M188" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> or accretion
products sufficient to warrant a change in the rate coefficients for
autoxidation or accretion product formation. Initial OH concentration had
a negligible effect (<inline-formula><mml:math id="M189" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:math></inline-formula> % change) on O3RO2, OHRO2 and C20d when
varied over 10<inline-formula><mml:math id="M190" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:math></inline-formula>–<inline-formula><mml:math id="M191" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M192" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (90 % decrease,
100 % increase).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><?xmltex \currentcnt{3}?><label>Figure 3</label><caption><p id="d1e3833">Comparison of the HOM-precursors <bold>(a)</bold> O3RO2 and <bold>(b)</bold> OHRO2 produced
by the model and from Berndt et al. (2018a) for experiments performed with
different initial concentrations of <inline-formula><mml:math id="M193" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (Simulation A). The
model reproduces the increase in O3RO2 and second- and third-generation
OHRO2 with initial <inline-formula><mml:math id="M194" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene well. The model struggled to reproduce
concentrations of the first-generation OHRO2 (not shown).  Note that the error
shown is the experimental error from Berndt et al. (2018a) and the error bars
for the third- and fourth-generation O3RO2 species are of a very similar size to the
error bars of the second-generation species but have been omitted for clarity.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f03.png"/>

        </fig>

<sec id="Ch1.S3.SS1.SSS1">
  <label>3.1.1</label><?xmltex \opttitle{Varying $\alpha$-pinene Experiment}?><title>Varying <inline-formula><mml:math id="M195" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene Experiment</title>
      <p id="d1e3878">In Simulation A, the mechanism was used to simulate various experiments with
increasing initial mixing ratios of <inline-formula><mml:math id="M196" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene with a fixed mixing
ratio of 26 ppb of <inline-formula><mml:math id="M197" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. The modelled first- to fourth-generation O3RO2
species (Fig. 3b) agreed well with the observed concentrations, with all
of the model results falling within experimental uncertainty bounds
(although we note these are large).</p>
      <p id="d1e3899">The model was also able to reproduce the second- and third-generation OHRO2
species well (Fig. 3a) but struggled with the first-generation OHRO2
species, overestimating it by a factor of 10, despite reproducing the
general trend of variation with <inline-formula><mml:math id="M198" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene. The experimental
measurements of first-generation OHRO2 concentration from Berndt et al. (2018a) were believed to be underestimated by about a factor of 5 (Fig. S3).
This suggests the model overprediction of the concentration of OHRO2 may be by
about a factor of 2. The cause of the discrepancy between modelled and
measured first-generation OHRO2 remains unclear. The rate coefficient for the
production of the first-generation OHRO2 has undergone extensive evaluation,
and the same coefficient is used in the CRI v2.2 parent mechanism which has
been optimised against the Master Chemical Mechanism (Jenkin et al., 1997, 2015, 2019b;
Saunders et al., 2003).
Sensitivity tests perturbing the branching ratio between RTN28AO2 and
RTN28BO2 revealed that even doubling the fraction of RTN28BO2, a significant
deviation from the literature (Berndt et al., 2016; Pye et al., 2018), had a
negligible effect as did changing initial [OH] by <inline-formula><mml:math id="M199" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">100</mml:mn></mml:mrow></mml:math></inline-formula> % or <inline-formula><mml:math id="M200" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">90</mml:mn></mml:mrow></mml:math></inline-formula> %.
Another explanation is the presence of additional, as yet<?pagebreak page10899?> unknown, loss
processes not currently included in the model, but in the absence of
additional data, no further insights can be made at this time. More
importantly, the first-generation OHRO2 does not form a HOM itself, and so
it is unlikely to have a significant impact on HOM concentration.
Furthermore, the modelled first-generation OHRO2 was dominated by RTN28AO2,
the species which does not autoxidise to form later-generation <inline-formula><mml:math id="M201" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>.
Nevertheless, this remains an important area for future work but one where
more data are needed for additional constraints to be put in place.</p><?xmltex \hack{\newpage}?><?xmltex \floatpos{t}?><fig id="Ch1.F4"><?xmltex \currentcnt{4}?><label>Figure 4</label><caption><p id="d1e3942">Observed and modelled variation for Simulation B of OHRO2 <bold>(a)</bold>,
O3RO2 <bold>(b)</bold>, OH <bold>(c)</bold> and the peroxy radical formed from isoprene oxidation <bold>(d)</bold>
with increasing isoprene (observed data from Berndt et al., 2018a). The
model is able to reproduce the decrease in OHRO2 as well as their
concentrations. The fractional decline in OHRO2 mirrors that observed in the
OH concentration, suggesting the major driver is OH scavenging. The error
shown is the experimental error from Berndt et al. (2018a).</p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f04.png"/>

          </fig>

</sec>
<sec id="Ch1.S3.SS1.SSS2">
  <label>3.1.2</label><title>Varying isoprene experiment</title>
      <p id="d1e3971">In Simulation B, varying initial concentrations of isoprene were employed
under conditions of fixed initial mixing ratios of <inline-formula><mml:math id="M202" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (15.6 ppb) and <inline-formula><mml:math id="M203" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (80 ppb). The model was able to reproduce the observed
decline in the second- and third-generation OHRO2 species (Fig. 4a)
with increasing isoprene while also reproducing the minor decrease in the
O3RO2 species (Fig. 4b). The decline in OHRO2 mirrored the modelled
decrease in OH, providing a strong indication that OH scavenging by isoprene
is playing a major role in the decrease in OHRO2, as suggested by McFiggans et
al. (2019), also highlighting the need for better understanding of
<inline-formula><mml:math id="M204" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> recycling during isoprene oxidation.</p><?xmltex \hack{\newpage}?>
</sec>
<?pagebreak page10900?><sec id="Ch1.S3.SS1.SSS3">
  <label>3.1.3</label><title>Simulation of accretion products</title>
      <p id="d1e4012">The 20-carbon accretion products were measured both in the isoprene-free,
varying-<inline-formula><mml:math id="M205" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene experiment (as in Fig. 3) and, separately, under
conditions of constant <inline-formula><mml:math id="M206" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene and varying isoprene (as in Fig. 4).
The rate coefficients for 20-carbon accretion product formation were fitted
against experimental data (Berndt et al., 2018a) and incorporated the
increase in propensity to form accretion products with <inline-formula><mml:math id="M207" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> oxidation.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5"><?xmltex \currentcnt{5}?><label>Figure 5</label><caption><p id="d1e4042">Variation in Simulation B of observed and modelled
concentrations of C20d <bold>(a)</bold>, C15d <bold>(b)</bold> and total accretion products <bold>(c)</bold> with
isoprene at fixed initial concentrations of <inline-formula><mml:math id="M208" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene (observed data
from Berndt et al., 2018a). The modelled data fall within the experimental
uncertainty shown by the pale red, blue and grey regions. The model
reproduces the observed decrease in C20d accretion products and increase in
C15d accretion products well. Furthermore, the model reproduces qualitatively
the result observed by McFiggans et al. (2019) that addition of isoprene
reduces the total accretion product concentration with potentially
important implications for total aerosol burden and particle size
distribution.</p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f05.png"/>

          </fig>

      <p id="d1e4067">The species with the lowest functionality, the first-generation OHRO2
(RTN28AO2 and RTN28BO2), which contain only three oxygens, had the lowest value
of <inline-formula><mml:math id="M209" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math id="M210" display="inline"><mml:mrow><mml:mn mathvariant="normal">0.4</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M211" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>),
while the first-generation O3RO2 (RN26BO2) with four oxygens had
<inline-formula><mml:math id="M212" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.97</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M213" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, its self-reaction rate coefficient determined by Berndt et al. (2018a). The
most functionalised species for O3RO2 (RNxBOyO2) and OHRO2 (RTNxBOyO2) were
assigned values of <inline-formula><mml:math id="M214" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> of <inline-formula><mml:math id="M215" display="inline"><mml:mrow><mml:mn mathvariant="normal">3.6</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M216" display="inline"><mml:mrow><mml:mn mathvariant="normal">3.5</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M217" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> respectively. The fitted rate coefficients used
were in line with the range of 0.97–<inline-formula><mml:math id="M218" display="inline"><mml:mrow><mml:mn mathvariant="normal">7.9</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M219" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (with an uncertainty no greater than a factor of 3)
measured by Berndt et al. (2018a), and the full list of values is given in the
reaction list in the Supplement. This reproduced, within experimental error, the
total observed C20d concentrations for both experiments (Figs. 5 and S1)
as well as the <inline-formula><mml:math id="M220" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> in simulations A and B. Sensitivity studies which
scaled all <inline-formula><mml:math id="M221" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values by the same factor before rerunning Simulation B and
comparing the output to experimental data suggested that variations in the
C20d formation rate coefficients of <inline-formula><mml:math id="M222" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">100</mml:mn></mml:mrow></mml:math></inline-formula> % and <inline-formula><mml:math id="M223" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">35</mml:mn></mml:mrow></mml:math></inline-formula> % spanned the
experimental uncertainty (Table S6).</p>
      <p id="d1e4358">Using values of <inline-formula><mml:math id="M224" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn mathvariant="normal">0.1</mml:mn></mml:mrow></mml:math></inline-formula>–<inline-formula><mml:math id="M225" display="inline"><mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">12</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M226" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>, as suggested by Roldin et al. (2019) for C20d
formation, produced C20d concentrations lower than those observed (Fig. S1),
while values of 1–<inline-formula><mml:math id="M227" display="inline"><mml:mrow><mml:mn mathvariant="normal">8</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M228" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>
from Molteni et al. (2019) produced values which were higher than
observations.</p>
      <p id="d1e4474">The rate coefficients for 15-carbon accretion product formation, fitted
against experimental data, also increased with the extent of oxidation of
the reacting peroxy radical. Values of <inline-formula><mml:math id="M229" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">16</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> ranging from <inline-formula><mml:math id="M230" display="inline"><mml:mrow><mml:mn mathvariant="normal">1.2</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">12</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M231" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> for the least oxidised <inline-formula><mml:math id="M232" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
to <inline-formula><mml:math id="M233" display="inline"><mml:mrow><mml:mn mathvariant="normal">5</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">12</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M234" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> for the most
oxidised species reproduced observed levels of the C15d accretion product
(Figs. 5 and S2) from the constant <inline-formula><mml:math id="M235" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene and variable
isoprene experiments (as in Fig. 4) and were lower than the values measured
by Berndt et al. (2018a) (1.3–<inline-formula><mml:math id="M236" display="inline"><mml:mrow><mml:mn mathvariant="normal">2.3</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">11</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M237" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">molec</mml:mi><mml:msup><mml:mo>.</mml:mo><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>
with an uncertainty no greater than a factor of 3). Sensitivity studies
which scaled all <inline-formula><mml:math id="M238" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">13</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values by the same factor before rerunning Simulation B
and comparing the output to experimental data suggested that variations in
the C15d formation rate coefficients of <inline-formula><mml:math id="M239" display="inline"><mml:mrow><mml:mo>±</mml:mo><mml:mn mathvariant="normal">50</mml:mn></mml:mrow></mml:math></inline-formula> % spanned the
experimental uncertainty (Table S6).</p>
      <p id="d1e4675">Figure 5 shows that the decrease in 20-carbon accretion products with
increasing isoprene far outweighs the increase in 15-carbon accretion
products. The mechanism reproduces the general trend of suppression of total
accretion product concentration with increasing initial isoprene
concentration. This finding is in good agreement with McFiggans et al. (2019)
and highlights a key component of the new mechanism which simple mechanisms
(e.g. Gordon et al., 2016) will miss. In the model this net decrease in
accretion product concentrations is driven in part by OH scavenging (and
the subsequent reduction in OHRO2; Fig. 4). In this work this was the major
driver of C20d decrease. However, suppression was also observed due to
scavenging of C10RO2 by isoprene-derived <inline-formula><mml:math id="M240" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> as observed by McFiggans et al. (2019). The influence of smaller peroxy radicals such as that from methane
on accretion product formation (McFiggans et al., 2019) will be an area of
future investigation.</p>
</sec>
</sec>
<?pagebreak page10901?><sec id="Ch1.S3.SS2">
  <label>3.2</label><?xmltex \opttitle{HOM yield variation with temperature and {$\protect\chem{NO_{{\mathit{x}}}}$}}?><title>HOM yield variation with temperature and <inline-formula><mml:math id="M241" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula></title>
      <p id="d1e4709">Autoxidation reactions have significant positive temperature dependencies
(Praske et al., 2018; Bianchi et al., 2019; Jenkin et al., 2019b).
Accordingly, HOM yields are expected to be highly temperature sensitive.
Quéléver et al. (2019) recorded a 50-fold increase in HOM yield at
293 K relative to 273 K. This temperature variation cannot be attributed to
the temperature dependence of the initial oxidation of <inline-formula><mml:math id="M242" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene as
the rate coefficient of ozonolysis increases only 17 % between 273 and
293 K while the reactions with OH and <inline-formula><mml:math id="M243" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> exhibit negative temperature
dependencies. Frege et al. (2018) measured a decrease in <inline-formula><mml:math id="M244" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">O</mml:mi><mml:mo>:</mml:mo><mml:mi mathvariant="normal">C</mml:mi></mml:mrow></mml:math></inline-formula> ratio values in
HOMs with reducing temperatures, attributing this to a reduction in
autoxidation.</p>
      <p id="d1e4742">Variation in peroxy radical structure and functionality will result in
different-generation peroxy radicals having different barriers to
autoxidation (Bianchi et al., 2019). A few modelling studies have considered
the temperature dependencies of the autoxidation rate coefficient in peroxy
radicals from <inline-formula><mml:math id="M245" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene derivatives. Schervish and Donahue
(2020) considered
a simple approach where all generations of peroxy radicals from <inline-formula><mml:math id="M246" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene ozonolysis had a fixed activation energy of 62.4 or 66.5 <inline-formula><mml:math id="M247" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">KJ</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">mol</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math id="M248" display="inline"><mml:mrow><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">7500</mml:mn></mml:mrow></mml:math></inline-formula>–8000 K, where the rate coefficient is expressed as
<inline-formula><mml:math id="M249" display="inline"><mml:mrow><mml:mi>k</mml:mi><mml:mo>=</mml:mo><mml:mi>A</mml:mi><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>/</mml:mo><mml:mi>T</mml:mi></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>), while noting that a reduction in barriers
to autoxidation with increasing functionality is plausible but so far
unproven. By contrast, Roldin et al. (2019) considered a higher activation
energy of 100.4 <inline-formula><mml:math id="M250" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">KJ</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">mol</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> (<inline-formula><mml:math id="M251" display="inline"><mml:mrow><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">12</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mn mathvariant="normal">077</mml:mn></mml:mrow></mml:math></inline-formula> K) based on the
theoretical work of Kurtén et al. (2015) which identified activation
energies of 90–120 <inline-formula><mml:math id="M252" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">KJ</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">mol</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> for <inline-formula><mml:math id="M253" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene.</p>
      <p id="d1e4869">Given the lack of additional literature in this area, three versions of the new
mechanism were created to probe the effects of temperature and activation
energy on HOM yield and subsequent evolution. In each mechanism all
autoxidation reactions (for O3RO2 and OHRO2) had the same activation energy
while all other rate coefficients were the same across mechanisms (Table S2 in the Supplement). Activation barriers of <inline-formula><mml:math id="M254" display="inline"><mml:mrow><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">6000</mml:mn></mml:mrow></mml:math></inline-formula> K, <inline-formula><mml:math id="M255" display="inline"><mml:mrow><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">9000</mml:mn></mml:mrow></mml:math></inline-formula> K and
<inline-formula><mml:math id="M256" display="inline"><mml:mrow><mml:mi mathvariant="italic">θ</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">12</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mn mathvariant="normal">077</mml:mn></mml:mrow></mml:math></inline-formula> K were chosen as they included the range suggested by
Roldin et al. (2019) and Schervish and Donahue
(2020), and the mechanism versions were
termed HOM<inline-formula><mml:math id="M257" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">6000</mml:mn></mml:msub></mml:math></inline-formula>, HOM<inline-formula><mml:math id="M258" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">9000</mml:mn></mml:msub></mml:math></inline-formula> and HOM<inline-formula><mml:math id="M259" display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mn mathvariant="normal">12</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mn mathvariant="normal">077</mml:mn></mml:mrow></mml:msub></mml:math></inline-formula> respectively. For the
temperature-dependent versions, the pre-exponential factor of the
autoxidation coefficient (Table S5) was adjusted so that the autoxidation
coefficients were the same at 297 K as those derived from the comparison to
experimental data from Berndt et al. (2018a). It is recognised that the
autoxidation steps are likely to have different activation energies, but
this analysis provides a first approximation of the influence of activation
energy on HOM formation.</p>
      <p id="d1e4944">In a simulation modelling an instantaneous injection of <inline-formula><mml:math id="M260" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene
(Simulation C), the HOM yield for the 10-carbon species, individually and in
total (defined in the Supplement), was calculated with the three different
temperature dependencies (HOM<inline-formula><mml:math id="M261" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">6000</mml:mn></mml:msub></mml:math></inline-formula>, HOM<inline-formula><mml:math id="M262" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">9000</mml:mn></mml:msub></mml:math></inline-formula> and HOM<inline-formula><mml:math id="M263" display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mn mathvariant="normal">12</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mn mathvariant="normal">077</mml:mn></mml:mrow></mml:msub></mml:math></inline-formula>) at
temperatures of 270, 290 and 310 K for initials conditions of <inline-formula><mml:math id="M264" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene at 15 ppb, <inline-formula><mml:math id="M265" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> at 40 ppb, OH at 10<inline-formula><mml:math id="M266" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M267" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> and a
temperature-independent condensation sink of <inline-formula><mml:math id="M268" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M269" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><?xmltex \currentcnt{6}?><label>Figure 6</label><caption><p id="d1e5061"><bold>(a)</bold> Maximum modelled HOM yields (C10x and C10z) exhibiting
significant decline under high-<inline-formula><mml:math id="M270" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> conditions (Simulation C). The
spread in the modelled yield between HOM mechanisms (HOM<inline-formula><mml:math id="M271" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">6000</mml:mn></mml:msub></mml:math></inline-formula>,
HOM<inline-formula><mml:math id="M272" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">9000</mml:mn></mml:msub></mml:math></inline-formula> and HOM<inline-formula><mml:math id="M273" display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mn mathvariant="normal">12</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mn mathvariant="normal">077</mml:mn></mml:mrow></mml:msub></mml:math></inline-formula>), shown by the shaded regions, indicates the
lower sensitivity to autoxidation activation energy at temperatures above
<inline-formula><mml:math id="M274" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">290</mml:mn></mml:mrow></mml:math></inline-formula> K. <bold>(b)</bold> Observed HOM concentrations from 8 d tropical
planetary boundary layer (PBL) run (Simulation D) showing decrease in concentration for all HOM species
with <inline-formula><mml:math id="M275" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. Under tropical PBL conditions, a negligible difference was
observed between HOM mechanisms due to daytime temperatures exceeding 300 K.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f06.png"/>

        </fig>

      <p id="d1e5139">Figure 6a shows the results from the simulations performed with initial
concentrations of NO and <inline-formula><mml:math id="M276" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> of 0.01–10 ppb. These simulations showed
that the 10-carbon HOM yield tends to increase slightly from very low (0.02 ppb) to moderate (2 ppb) <inline-formula><mml:math id="M277" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, before starting to decrease with
increasing <inline-formula><mml:math id="M278" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> thereafter. This behaviour is likely to be due to the
inclusion in the mechanism of the isomerisation pathway via reaction with NO
which yields the next-generation peroxy radical. This pathway has been
suggested as an important route for forming more highly oxidised derivatives
of <inline-formula><mml:math id="M279" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene due to the potential rapid ring-opening mechanism
involving alkoxy radicals and the cyclobutyl ring found in <inline-formula><mml:math id="M280" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene
ozonolysis products (Rissanen et al., 2015). Figure 6a indicates that the
absolute yield is also sensitive to temperature, with the highest yields
simulated at the highest temperatures. At low temperatures (blue data), the
uncertainty in autoxidation temperature dependence has the greatest effect,
while at high temperatures this feature is muted. The increase in yield with
temperature is in qualitative agreement with observation (Quéléver
et al., 2019; Simon et al., 2020).</p>
      <p id="d1e5189">The model predicted total HOM yields at 290 K of <inline-formula><mml:math id="M281" display="inline"><mml:mrow><mml:mn mathvariant="normal">1.9</mml:mn><mml:mo>±</mml:mo><mml:mn mathvariant="normal">0.2</mml:mn></mml:mrow></mml:math></inline-formula> % (0.01 ppb NO) to <inline-formula><mml:math id="M282" display="inline"><mml:mrow><mml:mn mathvariant="normal">3.9</mml:mn><mml:mo>±</mml:mo><mml:mn mathvariant="normal">0.5</mml:mn></mml:mrow></mml:math></inline-formula> % (1 ppb NO), with the quoted range resulting
from the range of temperature dependencies considered. This is within the
ranges previously suggested by Jokinen et al. (2015; 1.7 %–6.8 %) and close
to the values from Ehn et al. (2014; 3.5 %–10.5 %) and Sarnela et al. (2018; 3.5 %–6.5 %), while lower than Roldin et al. (2019; <inline-formula><mml:math id="M283" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">7</mml:mn></mml:mrow></mml:math></inline-formula> %). In addition, the HOM yield at 270 K of <inline-formula><mml:math id="M284" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">0.6</mml:mn></mml:mrow></mml:math></inline-formula> %–1.9 %
compared favourably with the yield of <inline-formula><mml:math id="M285" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> % determined by
Roldin et al. (2019). This suggests that the mechanism is doing a good job of
simulating HOM yield. The slight low bias may be in part due to the values of
<inline-formula><mml:math id="M286" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">14</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M287" display="inline"><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mn mathvariant="normal">15</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> which were shown to influence the HOM yield relatively strongly.
Sensitivity tests involving doubling and halving of the rate coefficients
produced HOM yield changes of around <inline-formula><mml:math id="M288" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">65</mml:mn></mml:mrow></mml:math></inline-formula> % and <inline-formula><mml:math id="M289" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">40</mml:mn></mml:mrow></mml:math></inline-formula> % respectively while preserving the general dependencies on <inline-formula><mml:math id="M290" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and
temperature (Fig. S4a; Table S6). This area of uncertainty will be the
focus of future work.</p>
      <p id="d1e5300">The HOM yield showed negligible sensitivity to the alkoxy radical
decomposition–isomerisation branching ratio below 200 ppt of <inline-formula><mml:math id="M291" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and
around <inline-formula><mml:math id="M292" display="inline"><mml:mrow><mml:mo>±</mml:mo><mml:mn mathvariant="normal">0.7</mml:mn></mml:mrow></mml:math></inline-formula> percentage points (<inline-formula><mml:math id="M293" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">20</mml:mn></mml:mrow></mml:math></inline-formula> %) at 2 ppb
<inline-formula><mml:math id="M294" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. However, this range was encompassed by the range arising from
autoxidation temperature dependence uncertainty. Above 2 ppb <inline-formula><mml:math id="M295" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, this
ratio had greater influence as NO reactions with <inline-formula><mml:math id="M296" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> started to compete
more efficiently with autoxidation, but this coincided with the sharp drop in
HOM yield (Fig. S4b). Therefore, while further work is needed to develop
the isomerisation–decomposition branching ratio description, it is unlikely
to have a significant influence in the low-<inline-formula><mml:math id="M297" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> conditions where HOMs are
predicted to be most prevalent, and in these<?pagebreak page10902?> conditions the uncertainty in
temperature dependence of autoxidation is predicted to have a larger effect.</p>
</sec>
<sec id="Ch1.S3.SS3">
  <label>3.3</label><title>Comparison to CRI v2.2</title>
      <p id="d1e5387">The ability of the new mechanism to reproduce the concentrations of key
atmospheric species from CRI v2.2 under different emissions of <inline-formula><mml:math id="M298" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>
and <inline-formula><mml:math id="M299" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene was assessed using an 8 d box-modelling run
(Simulation D). Over the majority of emissions space, <inline-formula><mml:math id="M300" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> differed by
less than 0.05 ppb (0.1 %), OH by less than 0.4 % and NO by less than
2.5 ppt (0.4 %; Figs. S6–S8) with similar (or better) agreement for other
important species (Figs. S9–S17). Acetone was routinely underpredicted (Fig. S18) by between a factor of <inline-formula><mml:math id="M301" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">14</mml:mn></mml:mrow></mml:math></inline-formula> at 50 ppt <inline-formula><mml:math id="M302" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math id="M303" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">20</mml:mn></mml:mrow></mml:math></inline-formula> % at 2–10 ppb of <inline-formula><mml:math id="M304" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, but this did not result in
significant deviation between the base mechanism and new mechanism for
<inline-formula><mml:math id="M305" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> or OH. This indicates that the basic features of atmospheric
chemistry, such as <inline-formula><mml:math id="M306" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> recycling processes added in CRI v2.2, which
have been shown to have important consequences for atmospheric composition
(Jenkin et al., 2019a), are preserved in the new mechanism.</p>
<sec id="Ch1.S3.SS3.SSS1">
  <label>3.3.1</label><title>Peroxy radicals and HOMs</title>
      <p id="d1e5491">As our model simulations indicate, and as has previously been observed
(Lehtipalo et al., 2018), at higher concentrations of <inline-formula><mml:math id="M307" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> there is
inhibition of HOM formation with the principle driver being the reaction of
NO with peroxy radicals occurring at a rate outcompeting autoxidation. While
reaction with NO can in part aid HOM formation by increasing the
isomerisation pathway, the fragmentation pathway (forming smaller species)
and formation of non-HOM nitrates leads to a reduction in total HOMs.
Accordingly, all these mechanisms predict a decrease in HOM concentration
with increasing <inline-formula><mml:math id="M308" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> (Fig. 6b). Furthermore, very little difference is
observed between the different HOM mechanisms, suggesting that uncertainty
in the activation energy may not be too great an impediment to understanding
general HOM behaviour, at least at the temperatures considered.</p>
      <p id="d1e5516">However, it should be remembered that, at present, the HOM tracers in the
mechanism represent a range of species with varying levels of oxidation. For example, C10z corresponds to HOMs formed from the second to fifth generations of O3RO2, and C10x corresponds to HOMs formed from the third and fourth generations of OHRO2. The
predicted concentrations of different generations of O3RO2 (Fig. S19) and
OHRO2 (Fig. S20) were also observed to decrease with <inline-formula><mml:math id="M309" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> with little
difference between different HOM mechanisms. Furthermore, the most abundant
peroxy radicals for both pathways were the lumped highest-generation
species, highlighting the potential issue of lack of loss processes for the
most highly oxidised <inline-formula><mml:math id="M310" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">RO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> species, as was encountered when fitting
parameters to flow cell data.</p>
</sec>
<sec id="Ch1.S3.SS3.SSS2">
  <label>3.3.2</label><title>Closed-shell and non-HOM species</title>
      <?pagebreak page10903?><p id="d1e5549">In the base mechanism, <inline-formula><mml:math id="M311" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene oxidation predominantly leads to the
formation of the closed-shell species CARB16 and TNCARB26 (carbonyls) and
RN18NO3 and RTN28NO3 (nitrates). Whilst the base mechanism has been
optimised against the MCM, these pathways have not themselves been tuned
extensively to reproduce concentrations observed in experimental systems.
These species are still present in the new mechanism, but the concentrations
of RTN28NO3 and TNCARB26 are predicted to be slightly lower than in the base
mechanism (Fig. S21), while CARB16 is simulated as being much lower in
concentration than in the base mechanism in low-<inline-formula><mml:math id="M312" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> conditions with the difference
attributed to the added competition from the autoxidation pathways.</p>
      <p id="d1e5570">The nitrate species formed from RN18AO2 in the base mechanism, RN18NO3, is
significantly lower in the HOM mechanism. Nitrate yield is a complicated
topic, not least because the MCM predicts that the peroxy radicals C107O2
and C109O2, which are used to represent the first-generation O3RO2 in part
(RN26BO2), do not form nitrate upon reaction with NO or <inline-formula><mml:math id="M313" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>.
Importantly this does not affect the <inline-formula><mml:math id="M314" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and OH concentrations, but this
should be an area that future work addresses.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S4">
  <label>4</label><title>Simulation of HOM vertical profiles</title>
      <p id="d1e5605">Given the success of the mechanism in simulating the laboratory flow tube
experiments and its ability to capture the sensitivity of HOMs to changes in
the reactivity of the peroxy radical pool, we focus now on using the scheme
to simulate tropospheric conditions to investigate, to first order, how the
scheme would predict ambient HOM concentrations. Here we focus on using our
new mechanism to simulate the surface [HOMs] and the vertical profile of
[HOMs]. We also look at the effect of the simulated HOMs on nucleation rates
in the lower troposphere.</p>
      <p id="d1e5608">The vertical profiles of HOMs over the boreal forest near Hyytiälä in
Finland (61<inline-formula><mml:math id="M315" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>9<inline-formula><mml:math id="M316" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> N, 23<inline-formula><mml:math id="M317" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>4<inline-formula><mml:math id="M318" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> E) and near Manaus in the Amazon
rainforest (<inline-formula><mml:math id="M319" display="inline"><mml:mn mathvariant="normal">2</mml:mn></mml:math></inline-formula><inline-formula><mml:math id="M320" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>35<inline-formula><mml:math id="M321" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> S, 60<inline-formula><mml:math id="M322" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>12<inline-formula><mml:math id="M323" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> W) were investigated along with
surface concentrations representative of Brent, Alabama (32<inline-formula><mml:math id="M324" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>54<inline-formula><mml:math id="M325" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> N, 87<inline-formula><mml:math id="M326" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>15<inline-formula><mml:math id="M327" display="inline"><mml:msup><mml:mi/><mml:mo>′</mml:mo></mml:msup></mml:math></inline-formula> W). For each altitude level, the sensitivity
simulations were performed with three different activation energies for the
autoxidation steps (HOM<inline-formula><mml:math id="M328" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">6000</mml:mn></mml:msub></mml:math></inline-formula>, HOM<inline-formula><mml:math id="M329" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">9000</mml:mn></mml:msub></mml:math></inline-formula> and HOM<inline-formula><mml:math id="M330" display="inline"><mml:msub><mml:mi/><mml:mrow><mml:mn mathvariant="normal">12</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mn mathvariant="normal">077</mml:mn></mml:mrow></mml:msub></mml:math></inline-formula>). Vertical
transport was neglected – a different box model was run at each vertical
level with the inputs being the output of a simulation with the UKCA model
(Archibald et al., 2019) sampled at 14:00 LT (photolysis frequencies were
adjusted to account for the solar zenith angle but not for altitude
variation). Hourly concentration data from UKCA were provided for <inline-formula><mml:math id="M331" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>,
OH, isoprene, <inline-formula><mml:math id="M332" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene, <inline-formula><mml:math id="M333" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, NO, <inline-formula><mml:math id="M334" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M335" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>,
<inline-formula><mml:math id="M336" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">N</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">5</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, temperature and pressure for 16 June averaged over
2010–2014, from the grid boxes in UKCA corresponding to the respective
locations discussed above, and were supplemented with monthly mean concentrations
of a further 23 species (Table S3) with the concentration of certain species
adjusted to observations (Kuhn et al., 2007; Lee et al., 2016) and scaled
vertically to account for biases in the UKCA output. The scaled values of
isoprene and <inline-formula><mml:math id="M337" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene showed reasonable agreement with observations
taken at up to 80 m in altitude at the Amazon Tall Tower Observatory (ATTO) facility (Yáñez-Serrano et
al., 2015). Modelled isoprene fell within 0.5 ppb of observations taken at 14:00 LT in June, while modelled monoterpene was within 0.1 ppb of observations,
well within the observational standard deviation in both cases (Fig. S22).
HOM condensation sinks (CSs; equal for all HOM species) discussed in Lee et
al. (2016; Table S4) were used at the surface and scaled using the modelled
vertical profile of aerosol surface area density. Sensitivity studies
revealed that the output of the 1D box modelling shows significant
sensitivity of [HOMs] to the magnitude and profile of the CS (Fig. S22).
Therefore, we can suggest that our simulated vertical profiles be regarded
as illustrative and that more work is required to identify if the condensation
sink should be species dependent.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T5" specific-use="star"><?xmltex \currentcnt{5}?><label>Table 5</label><caption><p id="d1e5836">Observed and modelled concentrations after adjustment of model
input. The model performs well in comparison to observed [HOMs] at Hyytiälä.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="justify" colwidth="3cm"/>
     <oasis:colspec colnum="4" colname="col4" align="justify" colwidth="3cm"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Location</oasis:entry>
         <oasis:entry colname="col2">Species adjusted to observations</oasis:entry>
         <oasis:entry colname="col3">Mean observed concentrations at relevant time of day (ppt)<inline-formula><mml:math id="M346" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">c</mml:mi></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col4">Model concentrations with input adjusted to observations (ppt)<inline-formula><mml:math id="M347" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">e</mml:mi></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Hyytiälä<inline-formula><mml:math id="M348" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col2">Monoterpene</oasis:entry>
         <oasis:entry colname="col3">10-carbon HOM:  0.2–0.8 (mean 0.4)</oasis:entry>
         <oasis:entry colname="col4">10-carbon HOM: 0.75–0.85</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3">20-carbon accretion product: 0.04–0.16 (mean 0.08)</oasis:entry>
         <oasis:entry colname="col4">20-carbon accretion product: 0.28–0.30</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Alabama<inline-formula><mml:math id="M349" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">b</mml:mi></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col2">Monoterpene, isoprene, OH, <inline-formula><mml:math id="M350" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col3">C9 &amp; C10<inline-formula><mml:math id="M351" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">d</mml:mi></mml:msup></mml:math></inline-formula>: 30</oasis:entry>
         <oasis:entry colname="col4">C10<inline-formula><mml:math id="M352" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">f</mml:mi></mml:msup></mml:math></inline-formula>: 4.5–13.3</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p id="d1e5839"><inline-formula><mml:math id="M338" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">a</mml:mi></mml:msup></mml:math></inline-formula> Roldin et al. (2019). <inline-formula><mml:math id="M339" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">b</mml:mi></mml:msup></mml:math></inline-formula> Lee et al. (2016). <inline-formula><mml:math id="M340" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">c</mml:mi></mml:msup></mml:math></inline-formula> Ranges given account for an uncertainty of a factor of 2 in observed concentrations. <inline-formula><mml:math id="M341" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">d</mml:mi></mml:msup></mml:math></inline-formula> Includes concentrations from C9 species (<inline-formula><mml:math id="M342" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">C</mml:mi><mml:mn mathvariant="normal">9</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">H</mml:mi><mml:mrow><mml:mn mathvariant="normal">14</mml:mn><mml:mo>-</mml:mo><mml:mn mathvariant="normal">20</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mrow><mml:mn mathvariant="normal">4</mml:mn><mml:mo>-</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>) and C10 species (<inline-formula><mml:math id="M343" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">C</mml:mi><mml:mn mathvariant="normal">10</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">H</mml:mi><mml:mrow><mml:mn mathvariant="normal">16</mml:mn><mml:mo>-</mml:mo><mml:mn mathvariant="normal">22</mml:mn></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mrow><mml:mn mathvariant="normal">4</mml:mn><mml:mo>-</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>). <inline-formula><mml:math id="M344" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">e</mml:mi></mml:msup></mml:math></inline-formula> Model was run with surface conditions in May for comparison to data from Roldin et al. (2019). <inline-formula><mml:math id="M345" display="inline"><mml:msup><mml:mi/><mml:mi mathvariant="normal">f</mml:mi></mml:msup></mml:math></inline-formula> Range arises from model runs using range of CS values suggested in Lee et al. (2016).</p></table-wrap-foot></table-wrap>

      <p id="d1e6097">Table 5 summarises the comparison of our model simulations of near surface
[HOMs] compared to observations. In the boreal forest in Hyytiälä, the range
of predicted 10-carbon [HOMs] falls at the higher end of the mean
observational range and well below the maximum observed concentrations
(1–1.5 ppt; Roldin et al., 2019). The predicted 20-carbon accretion product
concentration is around double the mean observational range and well
below the maximum observed values (0.6–0.7 ppt). In Alabama, the model
produces a reasonable value given that the observation dataset includes
9-carbon species not considered in the model at present. The model results
in Table 5 provide strong support that when implemented in a global
chemistry climate model, our new scheme should perform well if the
underlying emissions of BVOCs and <inline-formula><mml:math id="M353" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and the CS are well simulated.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7"><?xmltex \currentcnt{7}?><label>Figure 7</label><caption><p id="d1e6113">HOM profiles in June (14:00 LT) above <bold>(a)</bold> Hyytiälä and <bold>(b)</bold> the
Amazon near Manaus. Despite higher [<inline-formula><mml:math id="M354" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene], the significantly
higher CS in the Amazon results in lower [HOM]. The temperature dependence
(shown by the shading) is more significant at low altitude with Hyytiälä's
cooler temperatures. The Amazon's higher isoprene <inline-formula><mml:math id="M355" display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> <inline-formula><mml:math id="M356" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene ratio
(<inline-formula><mml:math id="M357" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">20</mml:mn></mml:mrow></mml:math></inline-formula>) results in greater suppression of the 20-carbon
accretion product than at Hyytiälä.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f07.png"/>

      </fig>

      <?pagebreak page10904?><p id="d1e6160">Figure 7 shows the concentrations of the different HOMs from the box model
version as a function of altitude above Hyytiälä and over the Amazon
rainforest near Manaus. In both locations, the 10-carbon HOM profiles
roughly mirror <inline-formula><mml:math id="M358" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene with roughly equal abundance of the species
from ozonolysis and OH oxidation. HOMs from OH showed a significantly greater
sensitivity to temperature, diverging from the HOM from <inline-formula><mml:math id="M359" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> at around 5 km in Hyytiälä and 8 km in the Amazon due to the elevated temperature
profile. This was attributed to the requirement for first-generation
OHRO2 to undergo two autoxidation steps before HOMs can be formed (Sect. 2.2), while first-generation O3RO2 species only need to undergo one autoxidation
step and thus have a weaker temperature dependence. This effect only becomes
noticeable at temperatures below <inline-formula><mml:math id="M360" display="inline"><mml:mrow><mml:mo>∼</mml:mo><mml:mn mathvariant="normal">250</mml:mn></mml:mrow></mml:math></inline-formula> K when autoxidation
ceases to compete effectively with bimolecular reactions. In spite of higher
[BVOCs], the considerably higher CS in the Amazon region (Lee et al., 2016)
resulted in lower [HOMs] within the boundary layer than at Hyytiälä, while
the warmer temperatures also resulted in a negligible dependence on the
activation energy in the lowest 4 km (i.e. the shaded areas are smaller in
Fig. 7b than in Fig. 7a).</p>
      <p id="d1e6191">Hyytiälä and the Amazon represent very different chemical environments with
the isoprene <inline-formula><mml:math id="M361" display="inline"><mml:mo>/</mml:mo></mml:math></inline-formula> <inline-formula><mml:math id="M362" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene ratio (<inline-formula><mml:math id="M363" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">I</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">AP</mml:mi></mml:mrow></mml:math></inline-formula>) playing an important role in the
accretion product distribution; 15-carbon accretion products are simulated
as being more abundant than 20-carbon accretion products in the Amazon with
the biggest difference predicted at low altitude where <inline-formula><mml:math id="M364" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">I</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">AP</mml:mi></mml:mrow></mml:math></inline-formula> is greatest. By
contrast, in Hyytiälä where <inline-formula><mml:math id="M365" display="inline"><mml:mrow class="chem"><mml:mi mathvariant="normal">I</mml:mi><mml:mo>/</mml:mo><mml:mi mathvariant="normal">AP</mml:mi></mml:mrow></mml:math></inline-formula> is smaller, 20-carbon accretion products
are more abundant.</p>
      <p id="d1e6244">Figure 7 highlights strong vertical profiles for the simulated [HOMs]. The
simulations over the Amazon suggest a significant secondary peak in [HOMs]
at around 4–5 km in altitude, in part linked to an increase in the [BVOCs]
at this height. In our simulations each vertical level is represented by a
different box model simulation, so there is no simulation of the advection of
HOMs. It will be interesting to see how future fully coupled model
simulations simulate the vertical profile of [HOMs] and how this affects
processes like aerosol formation and climate.</p>
<sec id="Ch1.S4.SSx1" specific-use="unnumbered">
  <title>Nucleation rates</title>
      <p id="d1e6253">Given the important role Gordon et al. (2016) identified for HOMs in NPF, we
extend our 1D calculations to investigate the implications of the predicted
HOM profiles on nucleation rates using monthly mean climate model data from
the PD and PI period. Nucleation rates from two different nucleation mechanisms
were studied: (i) neutral and ion-induced pure biogenic nucleation (PBN; Kirkby et al., 2016) and (ii) activation of sulfuric acid (SA<inline-formula><mml:math id="M366" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula>; Kulmala et al., 2006; Sihto et al., 2006) suitable for the boundary layer.
All HOMs were treated as being equally proficient at nucleating new
particles, in agreement with the approach and nucleation rates used by Kirkby et
al. (2016) and Gordon et al. (2017). Recent work by Heinritzi et al. (2020)
suggests that 20-carbon accretion products may be better at nucleating new
particles, and therefore the results presented are likely to be an upper
bound although nevertheless informative. Representing the different
nucleation efficiencies of different HOM species will be investigated in
future work. The results of the calculations of nucleation rates using these
schemes are summarised in Fig. 8. (The nucleation rate expressions are
given in the Supplement.)</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8"><?xmltex \currentcnt{8}?><label>Figure 8</label><caption><p id="d1e6267">PD and PI modelled nucleation rates averaged over June for <bold>(a)</bold> summed (neutral <inline-formula><mml:math id="M367" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> ion-induced) pure biogenic nucleation (assumes
altitude-independent ion production rate – IPR – of 2 <inline-formula><mml:math id="M368" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>; Hirsiko et al., 2011; shading shows IPR variation of 0.5–5 <inline-formula><mml:math id="M369" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) and <bold>(b)</bold> nucleation from sulfuric acid only (SA<inline-formula><mml:math id="M370" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula>). Both
mechanisms are predicted to produce greater nucleation rates in the PD due
to greater concentrations of precursor species. Importantly however, PBN at
low altitude at Hyytiälä is predicted to be comparable to SA nucleation in
the PI period due to the greater modelled ion concentration arising from a lower
condensation sink and reduction in rates from SA<inline-formula><mml:math id="M371" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula> due to lower
sulfuric acid concentrations. This leads to a larger increase in the total
nucleation rate in the PI period than in the PD with potential implications for PI
aerosol burden and climate.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://acp.copernicus.org/articles/20/10889/2020/acp-20-10889-2020-f08.png"/>

        </fig>

      <p id="d1e6354">There exist few observational data on nucleation solely from PBN
mechanisms, making model validation hard. Modelled surface sulfuric acid
concentrations at Hyytiälä (2–<inline-formula><mml:math id="M372" display="inline"><mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M373" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) fall within the range of
observations (<inline-formula><mml:math id="M374" display="inline"><mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula>–<inline-formula><mml:math id="M375" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">7</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M376" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>; Boy et al., 2005;
Petäjä et al., 2009). Modelled concentrations in the Amazon
(<inline-formula><mml:math id="M377" display="inline"><mml:mrow><mml:mn mathvariant="normal">3</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">4</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M378" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>) were lower than observations (10<inline-formula><mml:math id="M379" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:math></inline-formula>–10<inline-formula><mml:math id="M380" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">6</mml:mn></mml:msup></mml:math></inline-formula> <inline-formula><mml:math id="M381" display="inline"><mml:mrow class="unit"><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>; Wimmer et al., 2018) although the observations were taken in a
pasture site downwind of Manaus surrounded by the rainforest and not in the
rainforest itself and are therefore likely to be higher than in<?pagebreak page10905?> situ
rainforest values. Thus, the nucleation rates we have calculated for
SA<inline-formula><mml:math id="M382" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula> are likely to be a reasonable estimate in Hyytiälä and low biased
in the Amazon.</p>
      <p id="d1e6501">Figure 8 shows predicted nucleation rates in the PI period and PD in the Amazon and
Hyytiälä derived from our simulated [HOMs] vertical profile in the boundary
layer and low free troposphere using June monthly mean data from a United Kingdom Earth System Model (UKESM)
historical run taken from the PI period (June average 1851–1856) and PD (June
average 2009–2014). In all cases, the PBN rates decline rapidly
with height above the boundary layer. In the boreal forest, the nucleation
rate from PBN at very low altitudes is calculated to be around 20 %–25 % of
that from SA<inline-formula><mml:math id="M383" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula> in the PD. However, in the PI period it is comparable to the
SA<inline-formula><mml:math id="M384" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula> rate, contributing 40 %–80 % of the total nucleation rate in the
lowest 500 m (Fig. S23). The greater relative importance of PBN in the PI period,
despite lower predicted [HOMs], was attributed to two factors. Firstly,
predicted steady-state ion concentrations were higher in the PI period in Finland
than in the PD due to the PI period's lower ion CS. This increased the rate of the
ion-induced PBN pathway. Secondly, the considerably lower modelled
concentrations of sulfuric acid in the PI period (around <inline-formula><mml:math id="M385" display="inline"><mml:mrow><mml:mn mathvariant="normal">10</mml:mn><mml:mo>×</mml:mo></mml:mrow></mml:math></inline-formula> lower than in the PD)
reduced the importance of SA<inline-formula><mml:math id="M386" display="inline"><mml:msub><mml:mi/><mml:mi mathvariant="normal">act</mml:mi></mml:msub></mml:math></inline-formula>. By contrast, the lower concentrations
of predicted [HOMs] in the Amazon led to PBN having a much smaller
contribution to the total nucleation rate (<inline-formula><mml:math id="M387" display="inline"><mml:mrow><mml:mo>&lt;</mml:mo><mml:mn mathvariant="normal">5</mml:mn></mml:mrow></mml:math></inline-formula> % in the PD and a
negligible impact in the PI period). This is in agreement with multiple sources
(Andreae et al., 2015; Wimmer et al., 2018; Varanda Rizzo et al., 2018). The
importance of PBN in the PI atmosphere in certain locations, qualitatively
in agreement with Gordon et al. (2016), illustrates the potential importance
including PBN in climate models could have on aerosol burden and the
associated radiative effects.</p>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <label>5</label><title>Summary and conclusions</title>
      <p id="d1e6561">We present a novel chemical mechanism, CRI-HOM, for simulating HOM formation
based on the latest version of the Common Representative Intermediates scheme
(CRI v2.2). Focusing on the most important natural source of HOMs, <inline-formula><mml:math id="M388" display="inline"><mml:mi mathvariant="italic">α</mml:mi></mml:math></inline-formula>-pinene, the CRI-HOM mechanism is one of the first HOM mechanisms ready for
incorporation into existing chemistry–aerosol climate models. The scheme is
much more complex than previous steady-state approximations (Gordon et al.,
2016) and so enables non-linear interactions and feedbacks with the chemical
environment to be represented, but it is far more concise than other mechanisms
that have been developed which treat the complex structural characteristics
of the formation of HOMs (Roldin et al., 2019). The addition of 12 new
species and 66 reactions means that this scheme can be used for long-term
global chemistry–aerosol–climate studies.</p>
      <p id="d1e6571">Firstly, the mechanism was optimised against flow cell data and validated by
comparison to observed HOM yields. A key result was the ability of the
mechanism to reproduce observations of isoprene driving a decline in HOM
peroxy radical precursors and 20-carbon accretion products (and total
accretion product concentration; McFiggans et al., 2019). The need for
further research into the loss processes of the highly oxidised peroxy
radicals was identified to reconcile the disparity between modelled and
observed concentrations. The effect of other peroxy radicals, such as those
from smaller more abundant organic species, on accretion product formation
is also an area for future investigation.</p>
      <?pagebreak page10906?><p id="d1e6574">After optimisation, the CRI-HOM was compared to the base mechanism (CRI
v2.2), and very good agreement was observed for a wide range of atmospheric
gases including <inline-formula><mml:math id="M389" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and OH and its precursors. This indicated that
the important features of <inline-formula><mml:math id="M390" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">HO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> recycling and accurate <inline-formula><mml:math id="M391" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>
representation, developed in CRI v2.2, had been preserved in CRI-HOM.</p>
      <p id="d1e6610">In further tests of CRI-HOM, HOM yields and concentrations were predicted to
decrease with increasing <inline-formula><mml:math id="M392" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and increase with temperature, in
agreement with previous theoretical and observational studies. The
temperature dependence of autoxidation was investigated using activation
energies spanning the range of values suggested in the literature (Roldin et
al., 2019; Schervish and Donahue,
2020). Temperature dependence was predicted to
have a significant effect on HOM yield at 270 K but a much smaller effect at
290 and 310 K.</p>
      <p id="d1e6625">In a final experiment, vertical profiles of HOMs were simulated using a
pseudo 1D box model for Finland, Alabama and the Amazon using chemistry
climate model data as inputs. The model performed well relative to
observations in Finland and Alabama. The influence of the condensation sink
(CS) value on [HOM] was shown to be significant with [HOM] predicted to be
significantly lower in the Amazon, despite higher [BVOC], due to the higher
CS. Improving the description of the CS within the mechanism has been
identified as an important area of future work. The profiles also
illustrated the dependence of HOMs on the chemical environment, driven
chiefly by the interaction of isoprene and monoterpenes. The higher
concentrations of isoprene in the Amazon resulted in lower concentrations of
the most involatile species, the 20-carbon accretion product. Simulated
[HOMs] were also used to probe the importance of various particle nucleation
mechanisms. In Finland, a pure-biogenic-nucleation mechanism (i.e. nucleation
without sulfuric acid) at low altitude was predicted to be responsible for
around 60 % of new particle formation in the lowest 500 m in the
pre-industrial atmosphere and around 20 % in the present day, indicating
the importance of HOMs, particularly in the pre-industrial era, with
implications for aerosol burden and climate. PBN was predicted to be less
important in the Amazon given the lower simulated [HOM].</p>
      <p id="d1e6628">CRI-HOM can provide a framework for simulating HOMs in global
chemistry–aerosol–climate studies and simulating the effects of
isoprene-driven suppression of involatile biogenic-derived species and the
consequences for SOA and NPF while also providing a state-of-the-art
description of atmospheric chemistry. Such an effect, and the influence on
the proposed “BVOC negative feedback”, is likely to be important in a
warming climate with enhanced emissions of BVOCs and in determining the size
and sign of the feedback. Once incorporated into a global
chemistry–aerosol–climate model, assessing the effect of HOMs on
pre-industrial, present-day and future climate will be a key area of future
work.</p>
</sec>

      
      </body>
    <back><notes notes-type="dataavailability"><title>Data availability</title>

      <p id="d1e6635">All modelled data are available upon request from James Weber, and all
experimental data are available upon request from Torsten Berndt. The KPP files for the CRI-HOM
mechanism have been deposited in the University of Cambridge data repository
and can be viewed at <ext-link xlink:href="https://doi.org/10.17863/CAM.54546" ext-link-type="DOI">10.17863/CAM.54546</ext-link> (Weber et al., 2020).</p>
  </notes><app-group>
        <supplementary-material position="anchor"><p id="d1e6641">The supplement related to this article is available online at: <inline-supplementary-material xlink:href="https://doi.org/10.5194/acp-20-10889-2020-supplement" xlink:title="pdf">https://doi.org/10.5194/acp-20-10889-2020-supplement</inline-supplementary-material>.</p></supplementary-material>
        </app-group><notes notes-type="authorcontribution"><title>Author contributions</title>

      <p id="d1e6650">Mechanism development was carried out by JW, ATA, MJ and SAN; modelling experiments
were designed and executed by JW, ATA, PG, HG and CK, and flow cell data were
compiled and interpreted by TB. JW and ATA wrote the paper. All co-authors
discussed the results and commented on the paper.</p>
  </notes><notes notes-type="competinginterests"><title>Competing interests</title>

      <p id="d1e6656">The authors declare that they have no conflict of interest.</p>
  </notes><ack><title>Acknowledgements</title><p id="d1e6662">We would like to thank the Cambridge-LMU Strategic Partnership for supporting
collaborations with the BOXMOX model. We would like to thank NERC, through
NCAS, and the Met Office for the support of the JWCRP UKCA project.</p></ack><notes notes-type="financialsupport"><title>Financial support</title>

      <p id="d1e6667">James Weber has been funded by a Vice-Chancellor's Award from the Cambridge Trust. Scott Archer-Nicholls and
Alexander T. Archibald have been funded by NERC PROMOTE (grant no. NE/P016383/1). Hamish Gordon is supported by the
NASA ROSES Atmospheric Composition Modeling and Analysis Program (grant
no. 80NSSC19K0949).</p>
  </notes><notes notes-type="reviewstatement"><title>Review statement</title>

      <p id="d1e6673">This paper was edited by Astrid Kiendler-Scharr and reviewed by two anonymous referees.</p>
  </notes><ref-list>
    <title>References</title>

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    <!--<article-title-html>CRI-HOM: A novel chemical mechanism for simulating highly oxygenated organic molecules (HOMs) in global chemistry–aerosol–climate models</article-title-html>
<abstract-html><p>We present here results from a new mechanism, CRI-HOM, which we have developed to simulate the formation of highly oxygenated organic molecules (HOMs) from the gas-phase oxidation of <i>α</i>-pinene, one of the most widely emitted biogenic volatile organic compounds (BVOCs) by mass. This concise scheme adds 12 species and 66 reactions to the Common Representative Intermediates (CRI) mechanism v2.2 Reduction 5 and enables the representation of semi-explicit HOM treatment suitable for long-term global chemistry–aerosol–climate modelling, within a comprehensive tropospheric chemical mechanism. The key features of the new mechanism are (i) representation of the autoxidation of peroxy radicals from the hydroxyl radical and ozone initiated reactions of <i>α</i>-pinene, (ii) formation of multiple generations of peroxy radicals, (iii) formation of accretion products (dimers), and (iv) isoprene-driven suppression of accretion product formation, as observed in experiments. The mechanism has been constructed through optimisation against a series of flow tube laboratory experiments. The mechanism predicts a HOM yield of 2&thinsp;%–4.5&thinsp;% under conditions of low to moderate NO<sub><i>x</i></sub>, in line with experimental observations, and reproduces qualitatively the decline in HOM yield and concentration at higher NO<sub><i>x</i></sub> levels. The mechanism gives a HOM yield that also increases with temperature, in line with observations, and our mechanism compares favourably to some of the limited observations of [HOM] observed in the boreal forest in Finland and in the southeast USA.</p><p>The reproduction of isoprene-driven suppression of HOMs is a key step forward as it enables global climate models to capture the interaction between the major BVOC species, along with the potential climatic feedbacks. This suppression is demonstrated when the mechanism is used to simulate atmospheric profiles over the boreal forest and rainforest; different isoprene concentrations result in different [HOM] distributions, illustrating the importance of BVOC interactions in atmospheric composition and climate. Finally particle nucleation rates calculated from [HOM] in present-day and pre-industrial atmospheres suggest that <q>sulfuric-acid-free</q> nucleation can compete effectively with other nucleation pathways in the boreal forest, particularly in the pre-industrial period, with important implications for the aerosol budget and radiative forcing.</p></abstract-html>
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