Isoprene (2-methyl-1,3-butadiene) makes up 70 % of all non-methane biogenic volatile organic compound (BVOC) emissions, with annual average emissions of 594±34 TgCyr-1 over the period 1980–2010 (Sindelarova et al., 2014). Isoprene's rapid chemical oxidation in the atmosphere by OH, O3, and NO3 directly affects the tropospheric oxidizing capacity, ozone burden, and the processing of other trace gases like methane (e.g. Archibald et al., 2011; Khan et al., 2020), while also serving as an important source of secondary organic aerosol (SOA) (e.g. Scott et al., 2014; Kelly et al., 2018; Claeys and Maenhaut, 2021). Thus, isoprene has substantial effects on the radiative balance of the atmosphere, both directly via production of SOA and ozone and indirectly via its changes to the oxidizing capacity of the atmosphere, influencing methane lifetime and production of other aerosol species, such as from oxidation of monoterpenes and SO2 (Unger et al., 2014; Makonnen et al., 2012; Sporre et al., 2020). An accurate representation of isoprene chemistry in climate models is essential to understanding the feedbacks between the biosphere and the rest of the Earth system and thus capturing isoprene's climatic impact.

However, the treatment of isoprene in the chemistry schemes of many climate models is outdated or oversimplified (e.g. Squire et al., 2015). The last decade has seen significant advances in our understanding of the isoprene oxidation pathway, principally the concept of rapid, intramolecular hydrogen shifts (H-shifts), also termed isomerization reactions, in the isoprene hydroxy peroxy radicals (frequently termed ISOPOO). Predictions from theoretical work (Peeters et al., 2009; Peeters et al., 2014) and observations (Crounse et al., 2011; Teng et al., 2017; Wennberg et al., 2018) have established this pathway to be competitive with the traditional bimolecular reactions of the peroxy radical with NO, NO3, HO2, and RO2 in certain conditions such as low NOx(=NO+NO2) environments. These H-shift reactions lead to the production of HOx(=OH+HO2) either directly or indirectly following the degradation of the isomerization products (e.g. Archibald et al., 2011; Jenkin et al., 2015; Wennberg et al., 2018).

This process, termed HOx recycling, has been shown to be important for low-NOx, high-isoprene regions of the atmosphere (Butler et al., 2008; Lelieveld et al., 2008). By adding a simple, fixed-yield OH production pathway from ISOPOO to represent OH production from hydroperoxy aldehydes (HPALDs), Archibald et al. (2011) simulated an 8 %–18 % increase in tropospheric O3 burden, while the tropospheric OH burden increased by 17 % in the present day (PD) and by 50 % in a pre-industrial (PI) atmosphere featuring 1860 emissions of key chemical species such as NOx, CO, and isoprene. Consequently, the lifetime of methane was predicted to decrease by between 11 % (in a future climate scenario) and 35 % (in the PI). This illustrated the significant impact that such a process could have on our understanding of the PI atmosphere (and the radiatively active components therein) and thus the PD–PI change and climate sensitivity. While the greatest change to the chemistry was simulated in the boundary layer (BL), convection of isoprene and its oxidation products into the free troposphere resulted in this added chemistry having global impacts.

The effect on oxidants from HOx recycling influences the lifetimes of isoprene and other BVOCs such as monoterpenes and thus the extent of their dispersion and the location of the subsequent SOA formation. Karset et al. (2018) found that when lower oxidant fields were applied to the PI atmosphere, isoprene, monoterpenes, SO2, and other key aerosol precursors were more dispersed from their sources, reaching higher altitudes and enhancing particle number concentration in the remote free troposphere. The radiative impact of the resulting aerosols was greater due to their enhanced lifetime (from slower deposition) and the highly non-linear relationship between aerosol number and cloud forcing, where the addition of a given concentration of aerosol has a much greater impact in remote regions where the background concentration of aerosol is smaller (Chen et al., 2016). The importance of oxidants to BVOCs and aerosol was also shown in Sporre et al. (2020) where models with an interactive oxidant scheme simulated a BVOC-driven depletion of oxidants and attendant greater dispersion of BVOCs and their oxidation products (including SOA precursors). In contrast, a prescribed oxidant approach saw BVOC oxidation confined far more to source regions, reducing dispersion.

Changes in oxidant fields also perturb the oxidation pathways of SO2. In the United Kingdom Chemistry and Aerosols (UKCA) model, SO2 can be oxidized in the gas phase by OH (to yield H2SO4) or in the aqueous phase by O3 or H2O2 (Mulcahy et al., 2020). This has consequences for the aerosol mass and number distributions because only H2SO4 can nucleate new particles in UKCA; therefore, amplifying the gas-phase pathway over the aqueous pathways leads to a greater number of smaller aerosols. Thus, uneven changes to these pathways can alter the size and number distribution of the aerosol population, affecting the radiative properties of aerosols and clouds. Decreases in OH in other UKCA studies (Weber et al., 2020a; O'Connor et al., 2021) have resulted in simulated reductions in particle number concentration and cloud droplet number concentration. The resulting negative cloud radiative forcing is smaller in magnitude, as the lower cloud droplet number concentration (CDNC) makes the clouds less “bright” (Twomey, 1974). The impact of different oxidant schemes on the burden and lifetime of dimethylsulfide (DMS), an important SO2 precursor, and the impact on sulfate aerosol transport are both highlighted by Mulcahy et al. (2020).

While Archibald et al. (2011) used a relatively simple approach to simulate HOx recycling, further advances in the chemical understanding have led to a near-explicit representation of HOx recycling being incorporated into comprehensive mechanisms, including the Master Chemical Mechanism (MCM v3.3.1) (Jenkin et al., 2015) and the CalTech isoprene scheme (Wennberg et al., 2018). However, such mechanisms are far too large for use in global chemistry–climate models.

There exist a few reduced mechanisms featuring this state-of-the-art isoprene chemistry suitable for use in chemistry–climate models, including the CalTech reduced isoprene scheme (Bates et al., 2019), the MAGRITTE v1.1 model (Müller et al., 2019), the Mainz Organic Mechanism (Sander et al., 2019), the updated ECHAM-MESSy (Novelli et al., 2020), and the Common Representative Intermediates mechanism v2.2 (CRI v2.2) (Jenkin et al., 2019a), the latter of which is the focus of this work. The CRI v2.2 is an update to the Common Representative Intermediate v2.1 mechanism (Jenkin et al., 2008; Utembe et al., 2010; Watson et al., 2008) and was 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 reactivity is optimized against the fully explicit MCM. A description of CRI v2.2 is given in Jenkin et al. (2019a). The CRI v2.1, along with the corresponding stratospheric chemistry, has already been incorporated into UKCA as CRI-Start (CS) (Archer-Nicholls et al., 2021) as an alternative to the simpler but more widely used STRAT-TROP (ST) chemistry scheme (Archibald et al., 2020a), the scheme used for UKESM's contributions to CMIP6 (e.g. Sellar et al., 2020; Thornhill et al., 2021).

Using the reduced Caltech Isoprene Mechanism, which includes H-shifts of ISOPOO in GEOS-CHEM, Bates et al. (2019) simulated significant increases in OH (>100 %) and HO2 (up to 50 %) over the Amazon and other forested tropical regions as a result of the HOx recycling. After implementing updated rate constants for isoprene H-shifts in GEOS-CHEM, Møller et al. (2019) also found that globally around 30 % of all isoprene peroxy radicals undergo at least one H-shift reaction, resulting in an OH yield of 47 % per isoprene molecule, and that adding all isoprene H-shift reactions increased boundary layer OH by up to a factor of 3 in the Amazon. Using CESM and CAM-CHEM and the MOZART-TS2 mechanism, Schwantes et al. (2020) showed reasonable agreement for some isoprene oxidation products over the southeastern USA.

Jenkin et al. (2019a), using CRI v2.2 in the STOCHEM Lagrangian chemistry transport model, showed the significant influence of HOx recycling in CRI v2.2 simulating a 6.4 % increase in the tropospheric OH burden relative to the CRI v2.1 and increases in surface OH of 20 %–50 % over much of the forested tropical regions. Khan et al. (2020), using the same setup, also simulated enhanced surface OH and attendant decreases in methane lifetime (0.5 years) and isoprene burden (17 %).

However, while the reduced mechanisms featuring HOx-recycling chemistry have been tested in chemistry–climate models, less work has been done in terms of multi-species comparison to observations and detailed analysis of the effect to global atmospheric composition. This study introduces the CS2, based on CRIv2.2 and expanded with stratospheric chemistry, as a mechanism in UKCA, evaluates its performance against observational data, and compares its output and key processes to the related CS mechanism and the well-established ST mechanism. By providing a wide-ranging comparison to observations and a detailed description of the changes CS2 causes in global and regional atmospheric chemistry, this current work builds on the existing literature to further develop our understanding of the consequences of HOx recycling.

It is important to note that the CRI v2.2 mechanism, like the CRI v2.1 mechanism, is strictly a tropospheric chemistry scheme. In developing the whole atmosphere mechanism CS, Archer-Nicholls et al. (2021) merged the CRI v2.1 mechanism with the stratospheric chemistry scheme (Morgenstern et al., 2009) in UKCA (Table 1) to allow this scheme to be used within UKESM1 (Sellar et al., 2019). The same approach was taken in this work with the stratospheric scheme unchanged and tropospheric scheme switched from CRI v2.1 to CRI v2.2. Therefore, to differentiate the “CRI v2.2” mechanism used in UKCA in this work from the solely tropospheric CRI v2.2 mechanism described on the CRI v2.2 website (http://cri.york.ac.uk/, last access: 10 July 2021), the UKCA mechanism will henceforth be referred to as CRI-Strat 2 (CS2) (Table 1). A full description of the changes made to CS to update it to CS2 is given Sect. 1.1 in the Supplement, and a summary of the changes will now be discussed.

CS2 features a significant update to isoprene oxidation chemistry relative to CS with the incorporation of 1,6 and 1,4 H-shift reactions of isoprene peroxy radicals and an update to the organonitrate scheme (as detailed in Jenkin et al., 2019a). To the best of our understanding, CS2 also features updates to multiple reaction rate constants (which were out of date in CS, Archer-Nicholls et al., 2021), as documented in the IUPAC Task Group on Atmospheric Chemical Kinetic Data Evaluation (http://iupac.pole-ether.fr/, last access: 9 April 2021). Changes were implemented to the rate constants of the reactions of O(1D) with H2O, O2, and N2; rate constants of multiple inorganic nitrogen reactions such as those forming species with the peroxy acyl nitrate moiety, termed PAN-type, and HONO2; and the HO2+NO reaction and the rate constants of organic peroxy radicals (RO2) with NO and NO3. These updates ensure consistency between the CS2 mechanism incorporated in UKCA and that described on the CRI v2.2 website (http://cri.york.ac.uk/, last access: 10 July 2021). The photolysis of glyoxal, formaldehyde, and propionaldehyde was also updated (see Sect. S6 in the Supplement).

CS2 has 9 more species than CS (Tables 1, 2) as well as 46 additional bimolecular reactions, 12 additional photolysis reactions, and 8 additional unimolecular and termolecular reactions (Table 1). This leads to a modest increase in runtime (6 %) compared with CS, whose runtime was already ∼75 % greater than ST. Incorporation of CS2 into UKCA involved extensive use of the UM-UKCA virtual machine environment (Abraham et al., 2018).

The main update to the isoprene chemistry is the inclusion of 1,6 and 1,4 H-shift reactions of the isoprene peroxy radical (termed RU14O2 in CRI nomenclature). The 1,6 H-shift process is well studied (Peeters et al., 2009; Crounse et al., 2011; Teng et al., 2017; Wennberg et al., 2018) and follows the kbulk1,6H rate coefficient described in Jenkin et al. (2019a), capturing the dependence of isomerization on both temperature and the rates of reaction of RU14O2 with the standard bimolecular partners (NO, NO3, HO2, and RO2). This pathway yields hydroperoxy aldehydes (HPALDs, termed HPUCARB12 in CS2) and dihydroperoxy carbonyls peroxy radicals (DHPR12O2). The photolysis of the highly photolabile HPALD (HPUCARB12) and its product HUCARB9 (unsaturated hydroxy carbonyl) are key routes for HOx regeneration.

The production of the isoprene epoxy diol (IEPOX) from the isoprene hydroperoxide (RU14OOH) and the hydroxymethyl-methyl-a-lactone (HMML) also represent important updates (Jenkin et al., 2019a). IEPOX and HMML are known SOA precursors (Nguyen et al., 2014, 2017; Allan et al., 2014), and thus their addition may enable a more explicit representation of SOA formation within the CRI framework, as opposed to the current framework whereby SOA formation is represented by the condensation on existing aerosol of a single inert tracer, Sec_Org, which is made from monoterpene oxidation (Mann et al., 2010; Mulcahy et al., 2020). This is beyond the scope of this paper but will be a focus of future work.

The introduction of HPUCARB12 and HUCARB9 necessitates a careful update to the FASTJX photolysis scheme used by UKCA (Telford et al., 2013). The cross-sectional dependence of wavelength for HPALDs is assumed to be the same as methacrolein (Peeters et al., 2009; Wennberg et al., 2018; Schwantes et al., 2020) but with a significantly larger quantum yield (QY). Prather (2015) recommends a QY of 0.003 for methacrolein, and Liu et al. (2017) recommends a QY of 0.55 for HPALDs (both used by Wennberg et al., 2018). To implement the photolysis of these new species, the photolysis frequency of HPUCARB12 was taken to be the photolysis frequency for methacrolein scaled by the ratio of the QY of HPALDs to the QY of methacrolein, the same approach used by Schwantes et al. (2020) for δ-HPALDs. A scaling of 0.5 was applied to the photolysis frequency of HUCARB9 in agreement with the MCM v3.3.1.

In addition to the updates to isoprene chemistry, CRIv2.2 has had the rate coefficients for many organic and inorganic reactions updated to bring the mechanism into agreement with the MCM v3.3.1 and IUPAC. These affect the overall chemistry in three major ways. The first involves the major reactions of the excited oxygen radical, O(1D). The rate constants of O(1D) with H2O, O2, and N2 changed by -3 %, -1 %, and +20 %, respectively, to bring them into agreement with the current IUPAC values (http://iupac.pole-ether.fr, last access: 9 April 2021). This also means the rate constant of O(1D) with N2 became much closer (within ±1.5 %) to that used in ST (Archibald et al., 2020a) and that rate constants for the reactions with O2 and H2O also move closer to those used by ST. The result of this is a reduction in the fraction of O(1D) reacting with H2O by 10 %–15 %, thus lowering OH production while also reducing Ox loss via this pathway.

The second involves multiple inorganic reactions of nitrated species. The formation rate constants for PAN-type species (species with peroxyacyl nitrate functionality), HONO2, HO2NO2, and N2O5 changed by around -45 %, -15 %, -45 %, and +50 %–75 % in the troposphere, respectively. The change for PAN brought its formation rate constant much closer to that used in ST (within ±7 %), and this was also the case for HONO2 and HO2NO2 formation. The rate constant of HO2+NO, the single biggest production source of Ox, decreased by 4 %.

Finally, the rate constants for most RO2+NO and RO2+NO3 reactions have been changed by +12.5 % and -8 %, respectively, while maintaining the same temperature dependence. This is likely to have a smaller impact than the other chemistry changes but at the margins will make reactions with NO more competitive with the isomerization reactions of the ISOPOO.

The implementation of CRI v2.2 by Khan et al. (2020) in the STOCHEM model, while including the updates to isoprene chemistry and the RO2+NO and RO2+NO3 reactions, did not feature updates to the rate constants for O(1D) with H2O, O2, and N2 or the inorganic nitrogen reactions. Therefore, even in low-altitude terrestrial conditions where isoprene HOx recycling tends to dominate the change in OH, comparison between Khan et al. (2020) and the results of this work must be caveated with the changes to the inorganic chemistry.

In addition to the chemistry changes, updates are made to the photolysis of several species. Two additional photolysis reactions of glyoxal (CARB3 in the CRI mechanisms) were added in addition to updates to the photolysis parameters for HCHO and EtCHO (propionaldehyde). The wavelength bins of the product of the cross section and quantum yield used by FAST-JX (Telford et al., 2013) were updated to the v7.3 values from Prather (2015) for HCHO and EtCHO. The photolysis of CARB3, which had previously been estimated in CS by a scaling of HCHO photolysis (Archer-Nicholls et al., 2021), is replaced with the glyoxal photolysis for 999 hPa from v7.3 of Prather (2015). This reaction does exhibit a modest pressure dependence, but this has not been incorporated into FAST-JX at the current time.

In addition to the changes to the chemistry and photolysis, updates to the wet deposition scheme were implemented to both CS and CS2 schemes. The previous approach of applying parameters for a standard surrogate for other species with the same functional groups (e.g. EtOOH was used for most hydroperoxides), as described in Archer-Nicholls et al. (2021), was updated to use either data for the precise species (taken from Schwantes et al., 2020) or a more closely related surrogate. The changes to the wet deposition parameters are detailed in Table S1 in the Supplement. As they were applied to both CS and CS2 mechanisms, they are unlikely to have a significant influence on the inter-mechanism difference. No changes were made to the dry deposition scheme in this work.

All model runs were performed using the United Kingdom Chemistry and Aerosols Model (UKCA), run at a horizontal resolution of 1.25∘×1.875∘ with 85 vertical levels up to 85 km (Walters et al., 2019), and the GLOMAP-mode aerosol scheme, which simulates sulfate, sea salt, BC, organic matter, and dust but does not simulate currently nitrate aerosol (Mulcahy et al., 2020). In this setup, the inert chemical tracer Sec_Org, which condenses irreversibly onto existing aerosol, was produced at a 26 % yield solely from reactions of α-pinene and β-pinene with O3, OH, and NO3 with the enhanced yield applied to account for a lack of SOA formation from isoprene or anthropogenic species (Mulcahy et al., 2020).

The runs in this work fell into two distinct categories. Firstly, short runs (generally 1–2 months, Table 3) with higher-frequency (hourly) output using the ST, CS, and CS2 chemical mechanisms were performed to evaluate each mechanism's performance against the observational data. Secondly, longer runs (2–5 years, Table 4) with monthly output using the CS and CS2 chemical mechanisms (or variants of CS2 for sensitivity tests) were conducted to facilitate a rigorous comparison of the global chemical composition (Table 4).

Temperature and horizontal wind fields were nudged (Telford et al., 2013) in all model runs to atmospheric reanalyses from ECMWF (Dee et al., 2011) to constrain the simulations to consistent meteorology, thus preventing diverging meteorology from adding to the differences resulting from the chemical mechanisms and replicating the atmospheric conditions experienced when the observations were recorded as closely as possible. Nudging only occurred above ∼1200 m in altitude, and thus the majority of the planetary boundary layer was not nudged. The model runs were atmosphere-only runs with prescribed sea surface temperatures (SSTs). CO2 is not emitted but set to a constant field, while methane, CFCs, and N2O are prescribed with constant lower boundary conditions, all at 2014 levels (Archibald et al., 2020a).

The emissions used in this study are the same as those from Archer-Nicholls et al. (2021) and are those developed for the Coupled-Model Intercomparison Project 6 (CMIP6) (Collins et al., 2017). Anthropogenic and biomass burning emissions data for CMIP6 are from the Community Emissions Data System (CEDS), as described by Hoesly et al. (2018). For the short runs, time series anthropogenic and biomass burning emissions were used for all ST runs and all CRI runs up to 2015. For the runs done for the purpose of comparison to the observational date recorded at the ZF2 site near Manaus in 2016 (see Tables 3, 5), time slice 2014 emissions were used due to a lack of post-2015 CRI emissions, but the impact of the difference is expected to be minimal.

All longer runs used time slice 2014 emissions for anthropogenic and biomass burning emissions. Oceanic emissions were from the POET 1990 data set (Olivier et al., 2003), and all biogenic emissions except isoprene and monoterpenes (see Sect. 3.3) were based on 2001–2010 climatologies from Model of Emissions of Gases and Aerosols from Nature under the Monitoring Atmospheric Composition and Climate project (MEGAN-MACC) (MEGAN) version 2.1 (Guenther et al., 2012) and are discussed further in Sect. 3.3. A full description of the emission sources for each emitted species is given in Table S2 in the Supplement.

All mechanisms used the same raw emissions data. However, the additional emitted species required by CS and CS2 means the total mass of emitted organic compounds is greater in CS and CS2, and the lumping of species for emissions is also different. The approach and consequences are discussed in Archer-Nicholls et al. (2021).

The shorter UKCA models runs listed in Table 3 were used to evaluate mechanism performance against six high frequency observational data sets (three surface or near-surface data sets and three aircraft campaigns) from the Amazon, Borneo, and the southeastern USA, all important regions for BVOC production. In addition, satellite-derived isoprene columns (Wells et al., 2020) were compared to model output (Isoprene Column, Table 3). Monthly mean data from the longer CS and CS2 runs (Table 4) for O3, CO, and HONO2 were also compared to a range of observational data. A summary of the observation data sets is given in Table 5, and locations of the surface and airborne campaigns are shown in Fig. S3 in the Supplement.

Diel profiles for multiple species were calculated from the three surface and near-surface sites, and the vertical profiles were calculated from the ATTO site.

The three flight campaigns considered were the October 2005 Amazon GABRIEL campaign (Butler et al., 2008), the July 2008 Borneo Facility for Airborne Atmospheric Measurements (FAAM) (Hewitt et al., 2010), and the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) flight campaign over the southeastern USA in August–September 2013 (Toon et al., 2016). Hourly model output corresponding to the days and times of the flights was used for the mechanism–observation comparison for each campaign. Model and observational data were binned into 250 m/500 m altitude bins and median values for the variables of interest across the whole region for a given altitude bin were considered. For the SEAC4RS comparison, observational data were also filtered to exclude urban plumes (NO2>4 ppb), fire plumes (acetonitrile >0.2 ppb), and stratospheric air (O3/CO>1.25), while missing data were not used, and data flagged as a lower limit of detection were set to zero as previously done in Schwantes et al. (2020). Estimated limits of detection are shown for relevant species for the GABRIEL and FAAM campaigns.

The performance of each mechanism is now described for the key species, e.g. O3, HOx, isoprene, certain isoprene oxidation products, and monoterpenes. A brief commentary about other species including HONO2, CO, PAN, HCHO, MeCHO, EtCHO, and acetone is given in the Supplement.

The performance of the CS mechanism compared to the simpler ST mechanism was discussed in detail in Archer-Nicholls et al. (2021). Here we describe chemical composition of the atmosphere simulated by CS2 relative to that from CS using the longer model runs summarized in Table 2. Particular attention is paid to O3 and its production and loss fluxes, HOx, isoprene and monoterpenes, the isoprene oxidation productions IEPOX and HPALDs, nitrated species (NOy), and the potential impacts to aerosols. Changes to CO and HCHO are discussed in Sect. S5 in the Supplement.

The key changes between CS and CS2, driven by the multiple chemistry changes, can be summarized as follows.

Ox production increases marginally in CS2, but a larger decrease in Ox destruction, driven by a significant reduction in the O(1D)+H2O flux, leads to a greater O3 tropospheric burden and mixing ratios.

The radiative impact of isoprene, via its influence on atmospheric chemical composition and organic aerosol, means an accurate description of its chemistry is crucial for advancing our understanding of pre-industrial, present-day and future atmospheres. In this study we describe the incorporation of the Common Representative Intermediates chemistry scheme version 2.2 (CRI v2.2), along with accompanying stratospheric chemistry, into the global chemistry–climate model UKCA to create the mechanism CRI-Strat 2 (CS2). The introduction of CS2 into UKCA facilitates a semi-explicit description of HOx-recycling chemistry during isoprene oxidation via the isomerization of isoprene peroxy radicals to produce HPALDs that yield HOx upon photolysis. This is a key process for reconciling the model low bias of HOx in low-NOx, BVOC-rich regions. In addition, CS2 also features updates to the rate constants of the reactions of O(1D), inorganic nitrogen, and organic peroxy radicals with NO and NO3, bringing the mechanism into agreement with the most recent IUPAC values. CS2 is one of the first mechanisms with this functionality suitable for long-term climate integrations.

A rigorous comparison using UKCA with CS2 and two other chemical mechanisms, STRAT-TROP (ST) (the standard chemistry mechanism used in UKESM1's contributions to CMIP6 experiments) and CRI-STRAT (CS) (which has tropospheric chemistry from an earlier version of the CRI, CRI v2.1), is performed against high-frequency surface and airborne observational data from BVOC-rich regions for multiple chemical species, including O3, OH, HO2, and isoprene, and monoterpene and isoprene oxidation production. The HOx recycling in CS2 results in significantly enhanced surface diel OH (up to 50 % higher than CS at midday) in the Amazon and Borneo (improving model low bias), leading to improved modelling of diel and vertical isoprene profiles and reducing the mean 24 h bias by 50 %–60 % and 20 %–40 % relative to ST and CS, respectively, across the locations considered. However, CRI-Strat 2 exacerbates the existing isoprene model low bias away from the surface, suggesting potential issues with model vertical convection. CS and CS2 yield smaller isoprene column biases compared to observations than ST, in line with the surface and free troposphere observational comparisons, while also illustrating the significant influence the chemical mechanism has on modelled column. This comparison also highlights the significant influence that the different chemistry schemes have on the simulated isoprene column and thus the considerable challenges of determining isoprene emissions via back-calculation.

The low-altitude high biases for O3 in CS increase modestly (1–2 ppb) in CS2. Simulated monoterpene concentrations are biased high at the surface at most of the locations considered, with CS2 returning the smallest bias. As with isoprene, simulated monoterpenes display sharp morning and evening peaks that are believed to be due to boundary layer height issues. Modelled high bias of IEPOX and the low bias of HPALDs suggest further investigation of the key processes of loss to aerosol for IEPOX and HPALD photolysis frequency are needed.

In addition to observational comparisons, a detailed comparison of UKCA model output using CS2 is performed, complementing the earlier comparison of ST and CS (Archer-Nicholls et al., 2021). Sensitivity tests are also performed to help isolate the drivers of the differences between CS and CS2. CS2 simulates an 8 % increase in tropospheric O3 burden this is primarily driven by reduced Ox loss as the changes to rate constants of O(1D) with H2O, O2, and N2 mean that a smaller fraction of O(1D) reacts with H2O to produce OH. Low-altitude O3 increases by 2–4 ppb over much of the globe, driven predominantly by changes to the O(1D) and inorganic nitrogen reactions. More broadly, the widespread influence of the changes to the rate constants of O(1D) and multiple inorganic nitrogen species highlights the importance of having accurate information for these parameters.

Relative to CS, low-altitude OH increases over terrestrial regions, exceeding 50 % in some tropical forested regions, primarily due to the influence of HOx recycling from isoprene. However, OH decreases over the oceans and in much of the free troposphere, driven by updates to the rate constants of the reaction of O(1D) with H2O, O2, and N2. As a result, methane lifetime increases by 1.9 %, which is in stark contrast to previous studies using CRI v2.2 in the STOCHEM model that did not make changes to O(1D) and inorganic nitrogen reactions. When the changes to isoprene chemistry are isolated, methane lifetime decreases by 2.2 %, which is qualitatively in line with previous studies. The addition of isomerization pathways in the updated isoprene scheme reduces the methyl (7 %) and non-methyl peroxy (36 %) radical burdens.

The distribution of nitrated species (NOy) in CS2 is closer to that simulated in ST than CS is with a significant reduction (20 %) in the burden of PANs thatis driven by a reduction in the precursor RO2. The NOx burden increases by 4 %.

The increase in low-altitude OH reduced the burdens of isoprene (25 %) and monoterpenes (11 %–18 %) and the extent of their dispersion: more oxidation takes place in the boundary layer, where loss of oxidation products such as the lumped SOA precursor Sec_Org to existing aerosol is likely to be greater. Enhanced SO2 oxidation in the boundary layer is also simulated. These changes are likely to have implications for SOA and sulfate aerosol, particularly as CS has already been shown to have a more highly oxidizing boundary layer than ST. Therefore, the difference between CS2 and ST (the mechanism used to explore chemical–aerosol coupling in UKESM1 in CMIP6 experiments) is likely to be significant and will be the subject of future work.

The addition of CS2 also lays the groundwork for the incorporation of a novel chemistry scheme that describes the formation of the highly oxidized organic molecules (HOMs) derived from biogenic species such as α-pinene (e.g. CRI-HOM, Weber et al., 2020b). HOMs are crucial for new particle formation without sulfuric acid (Kirkby et al., 2016; Simon et al., 2020), a process which is an important source of new particles in the Amazonian free troposphere (Zhao et al., 2020) and has been simulated to have consequences for our understanding of pre-industrial aerosol burden (Gordon et al., 2016). The influence of isoprene in HOM production (Kiendler-Schaar et al., 2009; McFiggans et al., 2019; Heinritzi et al., 2020) can also be captured by the addition of CRI-HOM, making UKCA one of the very first global chemistry–climate models to feature a semi-explicit representation of HOMs and enabling further investigation into the climatic impact of the interaction between BVOCs. The addition of long-chain terpenes to CS2 is also planned, including sesquiterpenes, which may reduce the surface ozone high bias, form HOMs, and make improvements to the uptake of oxidized species to plant surfaces.

While certain elements of the CRI-STRAT 2 mechanism in UKCA such as the ozone high bias remain problematic, its incorporation represents a major step forward in our ability to simulate isoprene chemistry in low-NOx environments. The simulated changes to oxidants in CRI-Strat 2 will affect the atmosphere's radiative balance by perturbing certain greenhouse gases and aerosols, and investigating the impact of this will be a major topic of future work. In particular, the feedback between the biosphere and climate, mediated by BVOCs, will be evaluated using multiple mechanisms to assess their influence. CRI-Strat 2 can be taken up for use, alongside other mechanisms, to further our understanding of the wide-ranging impact BVOCs have on climate.