Paulot, F, et al.Sensitivity of nitrate aerosols to ammonia emissions and to nitrate chemistry: implications for present and future nitrate optical depth”. Atmos. Chem. Phys. 16 (2016): , 16, 1459–1477. Web. Publisher's VersionAbstract
We update and evaluate the treatment of nitrate aerosols in the Geophysical Fluid Dynamics Laboratory (GFDL) atmospheric model (AM3). Accounting for the radiative effects of nitrate aerosols generally improves the simulated aerosol optical depth, although nitrate concentrations at the surface are biased high. This bias can be reduced by increasing the deposition of nitrate to account for the near-surface volatilization of ammonium nitrate or by neglecting the heterogeneous production of nitric acid to account for the inhibition of N2O5 reactive uptake at high nitrate concentrations. Globally, uncertainties in these processes can impact the simulated nitrate optical depth by up to 25 %, much more than the impact of uncertainties in the seasonality of ammonia emissions (6 %) or in the uptake of nitric acid on dust (13 %). Our best estimate for fine nitrate optical depth at 550 nm in 2010 is 0.006 (0.005–0.008). In wintertime, nitrate aerosols are simulated to account for over 30 % of the aerosol optical depth over western Europe and North America. Simulated nitrate optical depth increases by less than 30 % (0.0061–0.010) in response to projected changes in anthropogenic emissions from 2010 to 2050 (e.g., −40 % for SO2 and +38 % for ammonia). This increase is primarily driven by greater concentrations of nitrate in the free troposphere, while surface nitrate concentrations decrease in the midlatitudes following lower concentrations of nitric acid. With the projected increase of ammonia emissions, we show that better constraints on the vertical distribution of ammonia (e.g., convective transport and biomass burning injection) and on the sources and sinks of nitric acid (e.g., heterogeneous reaction on dust) are needed to improve estimates of future nitrate optical depth.
Lee, H-M, et al.Sources of nitrogen deposition in Federal Class I areas in the US”. Atmos. Chem. Phys. 16 (2016): , 16, 525–540. Web. Publisher's VersionAbstract
It is desired to control excessive reactive nitrogen (Nr) deposition due to its detrimental impact on ecosystems. Using a three-dimensional atmospheric chemical transport model, GEOS-Chem, Nr deposition in the contiguous US and eight selected Class I areas (Voyageurs (VY), Smoky Mountain (SM), Shenandoah (SD), Big Bend (BB), Rocky Mountain (RM), Grand Teton (GT), Joshua Tree (JT), and Sequoia (SQ)) is investigated. First, modeled Nr deposition is compared with National Trends Network (NTN) and Clean Air Status and Trends Network (CASTNET) deposition values. The seasonality of measured species is generally well represented by the model (R2 > 0.6), except in JT. While modeled Nr is generally within the range of seasonal observations, large overestimates are present in sites such as SM and SD in the spring and summer (up to 0.6 kg N ha month−1), likely owing to model high-biases in surface HNO3. The contribution of non-measured species (mostly dry deposition of NH3) to total modeled Nr deposition ranges from 1 to 55 %. The spatial distribution of the origin of Nr deposited in each Class I area and the contributions of individual emission sectors are estimated using the GEOS-Chem adjoint model. We find the largest role of long-range transport for VY, where 50 % (90 %) of annual Nr deposition originates within 670 (1670) km of the park. In contrast, the Nr emission footprint is most localized for SQ, where 50 % (90 %) of the deposition originates from within 130 (370) km. Emissions from California contribute to the Nr deposition in remote areas in the western US (RM, GT). Mobile NOx and livestock NH3 are found to be the major sources of Nr deposition in all sites except BB, where contributions of NOx from lightning and soils to natural levels of Nr deposition are significant (∼ 40 %). The efficiency in terms of Nr deposition per kg emissions of NH3-N, NOx-N, and SO2-S are also estimated. Unique seasonal features are found in JT (opposing efficiency distributions for winter and summer), RM (large fluctuations in the range of effective regions), and SD (upwind NH3 emissions hindering Nr deposition). We also evaluate the contributions of emissions to the total area of Class I regions in critical load exceedance, and to the total magnitude of exceedance. We find that while it is effective to control emissions in the western US to reduce the area of regions in CL exceedance, it can be more effective to control emissions in the eastern US to reduce the magnitude of Nr deposition above the CL. Finally, uncertainty in the nitrogen deposition caused by uncertainty in the NH3 emission inventory is explored by comparing results based on two different NH3 inventories; noticeable differences in the emission inventories and thus sensitivities of up to a factor of four found in individual locations.
Zhao, Y, et al.Atmospheric nitrogen deposition to the northwestern Pacific: seasonal variation and source attribution”. Atmos. Chem. Phys. 15 (2015): , 15, 10905–10924. Web. Publisher's VersionAbstract
Rapid Asian industrialization has led to increased downwind atmospheric nitrogen deposition threatening the marine environment. We present an analysis of the sources and processes controlling atmospheric nitrogen deposition to the northwestern Pacific, using the GEOS-Chem global chemistry model and its adjoint model at 1/2$\,^\circ$ × 2/3$\,^\circ$ horizontal resolution over East Asia and its adjacent oceans. We focus our analyses on the marginal seas: the Yellow Sea and the South China Sea. Asian nitrogen emissions in the model are 28.6 Tg N a−1 as NH3 and 15.7 Tg N a−1 as NOx. China has the largest sources with 12.8 Tg N a−1 as NH3 and 7.9 Tg N a−1 as NOx; the high-NH3 emissions reflect its intensive agricultural activities. We find Asian NH3 emissions are a factor of 3 higher in summer than winter. The model simulation for 2008–2010 is evaluated with NH3 and NO2 column observations from satellite instruments, and wet deposition flux measurements from surface monitoring sites. Simulated atmospheric nitrogen deposition to the northwestern Pacific ranges 0.8–20 kg N ha−1 a−1, decreasing rapidly downwind of the Asian continent. Deposition fluxes average 11.9 kg N ha−1 a−1 (5.0 as reduced nitrogen NHx and 6.9 as oxidized nitrogen NOy) to the Yellow Sea, and 5.6 kg N ha−1 a−1 (2.5 as NHx and 3.1 as NOy) to the South China Sea. Nitrogen sources over the ocean (ship NOx and oceanic NH3) have little contribution to deposition over the Yellow Sea, about 7 % over the South China Sea, and become important (greater than 30 %) further downwind. We find that the seasonality of nitrogen deposition to the northwestern Pacific is determined by variations in meteorology largely controlled by the East Asian monsoon and in nitrogen emissions. The model adjoint further estimates that nitrogen deposition to the Yellow Sea originates from sources over China (92 % contribution) and the Korean peninsula (7 %), and by sectors from fertilizer use (24 %), power plants (22 %), and transportation (18 %). Deposition to the South China Sea shows source contribution from mainland China (66 %), Taiwan (20 %), and the rest (14 %) from the southeast Asian countries and oceanic NH3 emissions. The adjoint analyses also indicate that reducing Asian NH3 emissions would increase NOy dry deposition to the Yellow Sea (28 % offset annually), limiting the effectiveness of NH3 emission controls on reducing nitrogen deposition to the Yellow Sea.
Hu, WW, et al.Characterization of a real-time tracer for isoprene epoxydiols-derived secondary organic aerosol (IEPOX-SOA) from aerosol mass spectrometer measurements”. Atmos. Chem. Phys. 15 (2015): , 15, 11807–11833. Web. Publisher's VersionAbstract
Substantial amounts of secondary organic aerosol (SOA) can be formed from isoprene epoxydiols (IEPOX), which are oxidation products of isoprene mainly under low-NO conditions. Total IEPOX-SOA, which may include SOA formed from other parallel isoprene oxidation pathways, was quantified by applying positive matrix factorization (PMF) to aerosol mass spectrometer (AMS) measurements. The IEPOX-SOA fractions of organic aerosol (OA) in multiple field studies across several continents are summarized here and show consistent patterns with the concentration of gas-phase IEPOX simulated by the GEOS-Chem chemical transport model. During the Southern Oxidant and Aerosol Study (SOAS), 78 % of PMF-resolved IEPOX-SOA is accounted by the measured IEPOX-SOA molecular tracers (2-methyltetrols, C5-Triols, and IEPOX-derived organosulfate and its dimers), making it the highest level of molecular identification of an ambient SOA component to our knowledge. An enhanced signal at C5H6O+ (m/z 82) is found in PMF-resolved IEPOX-SOA spectra. To investigate the suitability of this ion as a tracer for IEPOX-SOA, we examine fC5H6O (fC5H6O= C5H6O+/OA) across multiple field, chamber, and source data sets. A background of   1.7 $\pm$ 0.1 ‰ (‰ = parts per thousand) is observed in studies strongly influenced by urban, biomass-burning, and other anthropogenic primary organic aerosol (POA). Higher background values of 3.1 $\pm$ 0.6 ‰ are found in studies strongly influenced by monoterpene emissions. The average laboratory monoterpene SOA value (5.5 $\pm$ 2.0 ‰) is 4 times lower than the average for IEPOX-SOA (22 $\pm$ 7 ‰), which leaves some room to separate both contributions to OA. Locations strongly influenced by isoprene emissions under low-NO levels had higher fC5H6O (  6.5 $\pm$ 2.2 ‰ on average) than other sites, consistent with the expected IEPOX-SOA formation in those studies. fC5H6O in IEPOX-SOA is always elevated (12–40 ‰) but varies substantially between locations, which is shown to reflect large variations in its detailed molecular composition. The low fC5H6O (< 3 ‰) reported in non-IEPOX-derived isoprene-SOA from chamber studies indicates that this tracer ion is specifically enhanced from IEPOX-SOA, and is not a tracer for all SOA from isoprene. We introduce a graphical diagnostic to study the presence and aging of IEPOX-SOA as a triangle plot of fCO2 vs. fC5H6O. Finally, we develop a simplified method to estimate ambient IEPOX-SOA mass concentrations, which is shown to perform well compared to the full PMF method. The uncertainty of the tracer method is up to a factor of   2, if the fC5H6O of the local IEPOX-SOA is not available. When only unit mass-resolution data are available, as with the aerosol chemical speciation monitor (ACSM), all methods may perform less well because of increased interferences from other ions at m/z 82. This study clarifies the strengths and limitations of the different AMS methods for detection of IEPOX-SOA and will enable improved characterization of this OA component.
Zhu, L, et al.Global evaluation of ammonia bidirectional exchange and livestock diurnal variation schemes”. Atmos. Chem. Phys. 15 (2015): , 15, 12823–12843. Web. Publisher's VersionAbstract
Bidirectional air–surface exchange of ammonia (NH3) has been neglected in many air quality models. In this study, we implement the bidirectional exchange of NH3 in the GEOS-Chem global chemical transport model. We also introduce an updated diurnal variability scheme for NH3 livestock emissions and evaluate the recently developed MASAGE\_NH3 bottom-up inventory. While updated diurnal variability improves comparison of modeled-to-hourly in situ measurements in the southeastern USA, NH3 concentrations decrease throughout the globe, up to 17 ppb in India and southeastern China, with corresponding decreases in aerosol nitrate by up to 7 μg m−3. The ammonium (NH4+) soil pool in the bidirectional exchange model largely extends the NH3 lifetime in the atmosphere. Including bidirectional exchange generally increases NH3 gross emissions (7.1 %) and surface concentrations (up to 3.9 ppb) throughout the globe in July, except in India and southeastern China. In April and October, it decreases NH3 gross emissions in the Northern Hemisphere (e.g., 43.6 % in April in China) and increases NH3 gross emissions in the Southern Hemisphere. Bidirectional exchange does not largely impact NH4+ wet deposition overall. While bidirectional exchange is fundamentally a better representation of NH3 emissions from fertilizers, emissions from primary sources are still underestimated and thus significant model biases remain when compared to in situ measurements in the USA. The adjoint of bidirectional exchange has also been developed for the GEOS-Chem model and is used to investigate the sensitivity of NH3 concentrations with respect to soil pH and fertilizer application rate. This study thus lays the groundwork for future inverse modeling studies to more directly constrain these physical processes rather than tuning bulk unidirectional NH3 emissions.
Paulot, F, et al.Global oceanic emission of ammonia: Constraints from seawater and atmospheric observations”. Global Biogeochem. Cycles (2015): , 2015GB005106. Web. Publisher's VersionAbstract
Current global inventories of ammonia emissions identify the ocean as the largest natural source. This source depends on seawater pH, temperature, and the concentration of total seawater ammonia (NHx(sw)), which reflects a balance between remineralization of organic matter, uptake by plankton, and nitrification. Here we compare [NHx(sw)] from two global ocean biogeochemical models (BEC and COBALT) against extensive ocean observations. Simulated [NHx(sw)] are generally biased high. Improved simulation can be achieved in COBALT by increasing the plankton affinity for NHx within observed ranges. The resulting global ocean emissions is 2.5 TgN a−1, much lower than current literature values (7–23 TgN a−1), including the widely used Global Emissions InitiAtive (GEIA) inventory (8 TgN a−1). Such a weak ocean source implies that continental sources contribute more than half of atmospheric NHx over most of the ocean in the Northern Hemisphere. Ammonia emitted from oceanic sources is insufficient to neutralize sulfate aerosol acidity, consistent with observations. There is evidence over the Equatorial Pacific for a missing source of atmospheric ammonia that could be due to photolysis of marine organic nitrogen at the ocean surface or in the atmosphere. Accommodating this possible missing source yields a global ocean emission of ammonia in the range 2–5 TgN a−1, comparable in magnitude to other natural sources from open fires and soils.
Millet, DB, et al.A large and ubiquitous source of atmospheric formic acid”. Atmos. Chem. Phys. 15 (2015): , 15, 6283–6304. Web. Publisher's VersionAbstract
Formic acid (HCOOH) is one of the most abundant acids in the atmosphere, with an important influence on precipitation chemistry and acidity. Here we employ a chemical transport model (GEOS-Chem CTM) to interpret recent airborne and ground-based measurements over the US Southeast in terms of the constraints they provide on HCOOH sources and sinks. Summertime boundary layer concentrations average several parts-per-billion, 2–3× larger than can be explained based on known production and loss pathways. This indicates one or more large missing HCOOH sources, and suggests either a key gap in current understanding of hydrocarbon oxidation or a large, unidentified, direct flux of HCOOH. Model-measurement comparisons implicate biogenic sources (e.g., isoprene oxidation) as the predominant HCOOH source. Resolving the unexplained boundary layer concentrations based (i) solely on isoprene oxidation would require a 3× increase in the model HCOOH yield, or (ii) solely on direct HCOOH emissions would require approximately a 25× increase in its biogenic flux. However, neither of these can explain the high HCOOH amounts seen in anthropogenic air masses and in the free troposphere. The overall indication is of a large biogenic source combined with ubiquitous chemical production of HCOOH across a range of precursors. Laboratory work is needed to better quantify the rates and mechanisms of carboxylic acid production from isoprene and other prevalent organics. Stabilized Criegee intermediates (SCIs) provide a large model source of HCOOH, while acetaldehyde tautomerization accounts for \textasciitilde 15% of the simulated global burden. Because carboxylic acids also react with SCIs and catalyze the reverse tautomerization reaction, HCOOH buffers against its own production by both of these pathways. Based on recent laboratory results, reaction between CH3O2 and OH could provide a major source of atmospheric HCOOH; however, including this chemistry degrades the model simulation of CH3OOH and NOx : CH3OOH. Developing better constraints on SCI and RO2 + OH chemistry is a high priority for future work. The model neither captures the large diurnal amplitude in HCOOH seen in surface air, nor its inverted vertical gradient at night. This implies a substantial bias in our current representation of deposition as modulated by boundary layer dynamics, and may indicate an HCOOH sink underestimate and thus an even larger missing source. A more robust treatment of surface deposition is a key need for improving simulations of HCOOH and related trace gases, and our understanding of their budgets.
Fu, Tzung-May, et al.Positive but variable sensitivity of August surface ozone to large-scale warming in the southeast United States”. Nature Climate Change 5 (2015): , 5, 454–458. Web. Publisher's VersionAbstract
Surface ozone, a major air pollutant toxic to humans and damaging to ecosystems, is produced by the oxidation of volatile organic compounds in the presence of nitrogen oxides (NOx = NO + NO2) and sunlight. Climate warming may affect future surface ozone levels even in the absence of anthropogenic emission changes, but the direction of ozone change due to climate warming remains uncertain over the southeast US and other polluted forested areas. Here we use observations and simulations to diagnose the sensitivity of August surface ozone to large-scale temperature variations in the southeast US during 1988–2011. We show that the enhanced biogenic emissions and the accelerated photochemical reaction rates associated with warmer temperatures both act to increase surface ozone. However, the sensitivity of surface ozone to large-scale warming is highly variable on interannual and interdecadal timescales owing to variation in regional ozone advection. Our results have important implications for the prediction and management of future ozone air quality.
Nguyen, Tran B, et al.Rapid deposition of oxidized biogenic compounds to a temperate forest”. Proc. Natl. Acad. Sci. U.S.A. 112 (2015): , 112, E392–E401. Web. Publisher's VersionAbstract
We report fluxes and dry deposition velocities for 16 atmospheric compounds above a southeastern United States forest, including: hydrogen peroxide (H2O2), nitric acid (HNO3), hydrogen cyanide (HCN), hydroxymethyl hydroperoxide, peroxyacetic acid, organic hydroxy nitrates, and other multifunctional species derived from the oxidation of isoprene and monoterpenes. The data suggest that dry deposition is the dominant daytime sink for small, saturated oxygenates. Greater than 6 wt %C emitted as isoprene by the forest was returned by dry deposition of its oxidized products. Peroxides account for a large fraction of the oxidant flux, possibly eclipsing ozone in more pristine regions. The measured organic nitrates comprise a sizable portion (15%) of the oxidized nitrogen input into the canopy, with HNO3 making up the balance. We observe that water-soluble compounds (e.g., strong acids and hydroperoxides) deposit with low surface resistance whereas compounds with moderate solubility (e.g., organic nitrates and hydroxycarbonyls) or poor solubility (e.g., HCN) exhibited reduced uptake at the surface of plants. To first order, the relative deposition velocities of water-soluble compounds are constrained by their molecular diffusivity. From resistance modeling, we infer a substantial emission flux of formic acid at the canopy level (∼1 nmol m−2⋅s−1). GEOS−Chem, a widely used atmospheric chemical transport model, currently underestimates dry deposition for most molecules studied in this work. Reconciling GEOS−Chem deposition velocities with observations resulted in up to a 45% decrease in the simulated surface concentration of trace gases.
Fischer, EV, et al.Atmospheric peroxyacetyl nitrate (PAN): a global budget and source attribution”. Atmos. Chem. Phys. 14 (2014): , 14, 2679–2698. Web. Publisher's VersionAbstract
Peroxyacetyl nitrate (PAN) formed in the atmospheric oxidation of non-methane volatile organic compounds (NMVOCs) is the principal tropospheric reservoir for nitrogen oxide radicals (NOx = NO + NO2). PAN enables the transport and release of NOx to the remote troposphere with major implications for the global distributions of ozone and OH, the main tropospheric oxidants. Simulation of PAN is a challenge for global models because of the dependence of PAN on vertical transport as well as complex and uncertain NMVOC sources and chemistry. Here we use an improved representation of NMVOCs in a global 3-D chemical transport model (GEOS-Chem) and show that it can simulate PAN observations from aircraft campaigns worldwide. The immediate carbonyl precursors for PAN formation include acetaldehyde (44% of the global source), methylglyoxal (30%), acetone (7%), and a suite of other isoprene and terpene oxidation products (19%). A diversity of NMVOC emissions is responsible for PAN formation globally including isoprene (37%) and alkanes (14%). Anthropogenic sources are dominant in the extratropical Northern Hemisphere outside the growing season. Open fires appear to play little role except at high northern latitudes in spring, although results are very sensitive to plume chemistry and plume rise. Lightning NOx is the dominant contributor to the observed PAN maximum in the free troposphere over the South Atlantic.
St. Clair, JM, et al.Quantification of hydroxyacetone and glycolaldehyde using chemical ionization mass spectrometry”. Atmos. Chem. Phys. 14 (2014): , 14, 4251–4262. Web. Publisher's VersionAbstract
Chemical ionization mass spectrometry (CIMS) enables online, rapid, in situ detection and quantification of hydroxyacetone and glycolaldehyde. Two different CIMS approaches are demonstrated employing the strengths of single quadrupole mass spectrometry and triple quadrupole (tandem) mass spectrometry. Both methods are generally capable of the measurement of hydroxyacetone, an analyte with known but minimal isobaric interferences. Tandem mass spectrometry provides direct separation of the isobaric compounds glycolaldehyde and acetic acid using distinct, collision-induced dissociation daughter ions. The single quadrupole CIMS measurement of glycolaldehyde was demonstrated during the ARCTAS-CARB (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites - California Air Resources Board) 2008 campaign, while triple quadrupole CIMS measurements of glycolaldehyde and hydroxyacetone were demonstrated during the BEARPEX (Biosphere Effects on Aerosols and Photochemistry Experiment) 2009 campaign. Enhancement ratios of glycolaldehyde in ambient biomass-burning plumes are reported for the ARCTAS-CARB campaign. BEARPEX observations are compared to simple photochemical box model predictions of biogenic volatile organic compound oxidation at the site.
Paulot, F, et al.Ammonia emissions in the United States, European Union, and China derived by high-resolution inversion of ammonium wet deposition data: Interpretation with a new agricultural emissions inventory (MASAGE_NH3)”. J. Geophys. Res. Atmos. 119 (2014): , 119, 4343–4364. Web. Publisher's VersionAbstract

We use the adjoint of a global 3-D chemical transport model ({GEOS}-Chem) to optimize ammonia ({NH}3) emissions in the U.S., European Union, and China by inversion of 2005–2008 network data for {NH}4+ wet deposition fluxes. Optimized emissions are derived on a 2$\,^{\circ}$ × 2.5$\,^{\circ}$ grid for individual months and years. Error characterization in the optimization includes model errors in precipitation. Annual optimized emissions are 2.8 Tg {NH}3−N a−1 for the contiguous U.S., 3.1 Tg {NH}3−N a−1 for the European Union, and 8.4 Tg {NH}3−N a−1 for China. Comparisons to previous inventories for the U.S. and European Union show consistency (∼$\pm$15%) in annual totals but some large spatial and seasonal differences. We develop a new global bottom-up inventory of {NH}3 emissions (Magnitude And Seasonality of Agricultural Emissions model for {NH}3 ({MASAGE}\_NH3)) to interpret the results of the adjoint optimization. {MASAGE}\_NH3 provides information on the magnitude and seasonality of {NH}3 emissions from individual crop and livestock sources on a 0.5$\,^{\circ}$ × 0.5$\,^{\circ}$ grid. We find that U.S. emissions peak in the spring in the Midwest due to corn fertilization and in the summer elsewhere due to manure. The seasonality of European emissions is more homogeneous with a well-defined maximum in spring associated with manure and mineral fertilizer application. There is some evidence for the effect of European regulations of {NH}3 emissions, notably a large fall decrease in northern Europe. Emissions in China peak in summer because of the summertime application of fertilizer for double cropping.

Paulot, Fabien, and Daniel J Jacob. “Hidden Cost of US Agricultural Exports: Particulate Matter from Ammonia Emissions”. Environ. Sci. Technol. 48 (2014): , 48, 903–908. Web. Publisher's VersionAbstract

We use a model of agricultural sources of ammonia ({NH3)} coupled to a chemical transport model to estimate the impact of {U.S.} food export on particulate matter concentrations ({PM2.5).} We find that food export accounts for 11% of total {U.S.} {NH3} emissions (13% of agricultural emissions) and that it increases the population-weighted exposure of the {U.S.} population to {PM2.5} by 0.36 ?g m?3 on average. Our estimate is sensitive to the proper representation of the impact of {NH3} on ammonium nitrate, which reflects the interplay between agricultural ({NH3)} and combustion emissions ({NO}, {SO2).} Eliminating {NH3} emissions from food export would achieve greater health benefits than the reduction of the National Ambient Air Quality Standards for {PM2.5} from 15 to 12 ?g m?3. Valuation of the increased premature mortality associated with {PM2.5} from food export (36 billion {US\$} (2006) per year) amounts to 50% of the gross food export value. Livestock operations in densely populated areas have particularly large health costs. Decreasing {SO2} and {NOx} emissions will indirectly reduce health impact of food export as an ancillary benefit.

Paulot, Fabien, Daniel J Jacob, and Daven K Henze. “Sources and Processes Contributing to Nitrogen Deposition: An Adjoint Model Analysis Applied to Biodiversity Hotspots Worldwide”. Environ. Sci. Technol. 47 (2013): , 47, 3226–3233. Web. Publisher's VersionAbstract
Anthropogenic enrichment of reactive nitrogen (Nr) deposition is an ecological concern. We use the adjoint of a global 3-D chemical transport model ({GEOS-Chem)} to identify the sources and processes that control Nr deposition to an ensemble of biodiversity hotspots worldwide and two {U.S.} national parks (Cuyahoga and Rocky Mountain). We find that anthropogenic sources dominate deposition at all continental sites and are mainly regional (less than 1000 km) in origin. In Hawaii, Nr supply is controlled by oceanic emissions of ammonia (50%) and anthropogenic sources (50%), with important contributions from Asia and North America. Nr deposition is also sensitive in complicated ways to emissions of {SO2}, which affect Nr gas?aerosol partitioning, and of volatile organic compounds ({VOCs)}, which affect oxidant concentrations and produce organic nitrate reservoirs. For example, {VOC} emissions generally inhibit deposition of locally emitted {NOx} but significantly increase Nr deposition downwind. However, in polluted boreal regions, anthropogenic {VOC} emissions can promote Nr deposition in winter. Uncertainties in chemical rate constants for {OH} + {NO2} and {NO2} hydrolysis also complicate the determination of source?receptor relationships for polluted sites in winter. Application of our adjoint sensitivities to the representative concentration pathways ({RCPs)} scenarios for 2010?2050 indicates that future decreases in Nr deposition due to {NOx} emission controls will be offset by concurrent increases in ammonia emissions from agriculture.
Xie, Y, et al.Understanding the impact of recent advances in isoprene photooxidation on simulations of regional air quality”. Atmospheric Chemistry and Physics 13 (2013): , 13, 8439–8455. Web. Publisher's VersionAbstract
The CMAQ (Community Multiscale Air Quality) us model in combination with observations for INTEX-NA/ICARTT (Intercontinental Chemical Transport Experiment–North America/International Consortium for Atmospheric Research on Transport and Transformation) 2004 are used to evaluate recent advances in isoprene oxidation chemistry and provide constraints on isoprene nitrate yields, isoprene nitrate lifetimes, and NOx recycling rates. We incorporate recent advances in isoprene oxidation chemistry into the SAPRC-07 chemical mechanism within the US EPA (United States Environmental Protection Agency) CMAQ model. The results show improved model performance for a range of species compared against aircraft observations from the INTEX-NA/ICARTT 2004 field campaign. We further investigate the key processes in isoprene nitrate chemistry and evaluate the impact of uncertainties in the isoprene nitrate yield, NOx (NOx = NO + NO2) recycling efficiency, dry deposition velocity, and RO2 + HO2 reaction rates. We focus our examination on the southeastern United States, which is impacted by both abundant isoprene emissions and high levels of anthropogenic pollutants. We find that NOx concentrations increase by 4–9% as a result of reduced removal by isoprene nitrate chemistry. O3 increases by 2 ppbv as a result of changes in NOx. OH concentrations increase by 30%, which can be primarily attributed to greater HOx production. We find that the model can capture observed total alkyl and multifunctional nitrates (∑ANs) and their relationship with O3 by assuming either an isoprene nitrate yield of 6% and daytime lifetime of 6 hours or a yield of 12% and lifetime of 4 h. Uncertainties in the isoprene nitrates can impact ozone production by 10% and OH concentrations by 6%. The uncertainties in NOx recycling efficiency appear to have larger effects than uncertainties in isoprene nitrate yield and dry deposition velocity. Further progress depends on improved understanding of isoprene oxidation pathways, the rate of NOx recycling from isoprene nitrates, and the fate of the secondary, tertiary, and further oxidation products of isoprene.
Mao, Jingqiu, et al.Ozone and organic nitrates over the eastern United States: Sensitivity to isoprene chemistry”. J. Geophys. Res. Atmos. 118 (2013): , 118, 11,256–11,268. Web. Publisher's VersionAbstract
We implement a new isoprene oxidation mechanism in a global 3-D chemical transport model ({GEOS-Chem).} Model results are evaluated with observations for ozone, isoprene oxidation products, and related species from the International Consortium for Atmospheric Research on Transport and Transformation aircraft campaign over the eastern United States in summer 2004. The model achieves an unbiased simulation of ozone in the boundary layer and the free troposphere, reflecting canceling effects from recent model updates for isoprene chemistry, bromine chemistry, and {HO2} loss to aerosols. Simulation of the ozone-{CO} correlation is improved relative to previous versions of the model, and this is attributed to a lower and reversible yield of isoprene nitrates, increasing the ozone production efficiency per unit of nitrogen oxides ({NOx} ≡ {NO} + {NO2).} The model successfully reproduces the observed concentrations of organic nitrates ({∑ANs)} and their correlations with {HCHO} and ozone. {∑ANs} in the model is principally composed of secondary isoprene nitrates, including a major contribution from nighttime isoprene oxidation. The correlations of {∑ANs} with {HCHO} and ozone then provide sensitive tests of isoprene chemistry and argue in particular against a fast isomerization channel for isoprene peroxy radicals. {∑ANs} can provide an important reservoir for exporting {NOx} from the {U.S.} boundary layer. We find that the dependence of surface ozone on isoprene emission is positive throughout the {U.S.}, even if {NOx} emissions are reduced by a factor of 4. Previous models showed negative dependences that we attribute to erroneous titration of {OH} by isoprene.
Paulot, F, DK Henze, and PO Wennberg. “Impact of the isoprene photochemical cascade on tropical ozone”. Atmos. Chem. Phys. 12 (2012): , 12, 1307–1325. Web. Publisher's VersionAbstract
Tropical tropospheric ozone affects Earth's radiative forcing and the oxidative capacity of the atmosphere. Considerable work has been devoted to the study of the processes controlling its budget. Yet, large discrepancies between simulated and observed tropical tropospheric ozone remain. Here, we characterize some of the mechanisms by which the photochemistry of isoprene impacts the budget of tropical ozone. At the regional scale, we use forward sensitivity simulation to explore the sensitivity to the representation of isoprene nitrates. We find that isoprene nitrates can account for up to 70% of the local NOx = NO+NO2 sink. The resulting modulation of ozone can be well characterized by their net modulation of NOx. We use adjoint sensitivity simulations to demonstrate that the oxidation of isoprene can affect ozone outside of continental regions through the transport of NOx over near-shore regions (e.g., South Atlantic) and the oxidation of isoprene outside of the boundary layer far from its emissions regions. The latter mechanism is promoted by the simulated low boundary-layer oxidative conditions. In our simulation,  20% of the isoprene is oxidized above the boundary layer in the tropics. Changes in the interplay between regional and global effect are discussed in light of the forecasted increase in anthropogenic emissions in tropical regions.
Kjaergaard, HG, et al.{Atmospheric Fate of Methacrolein. 2. Formation of Lactone and Implications for Organic Aerosol Production}”. J. Phys. Chem. A 116 (2012): , 116, 5763–5768. Web. Publisher's VersionAbstract
We investigate the oxidation of methacryloylperoxy nitrate {(MPAN)} and methacrylicperoxy acid {(MPAA)} by the hydroxyl radical {(OH)} theoretically, using both density functional theory {[B3LYP]} and explicitly correlated coupled cluster theory {[CCSD(T)-F12].} These two compounds are produced following the abstraction of a hydrogen atom from methacrolein {(MACR)} by the {OH} radical. We use a {RRKM} master equation analysis to estimate that the oxidation of {MPAN} leads to formation of hydroxymethyl?methyl-Î$\pm$-lactone {(HMML)} in high yield. {HMML} production follows a low potential energy path from both {MPAN} and {MPAA} following addition of {OH} (via elimination of the {NO3} and {OH} from {MPAN} and {MPAA}, respectively). We suggest that the subsequent heterogeneous phase chemistry of {HMML} may be the route to formation of 2-methylglyceric acid, a common component of organic aerosol produced in the oxidation of methacrolein. Oxidation of acrolein, a photo-oxidation product from 1,3-butadiene, is found to follow a similar route generating hydroxymethyl-Î$\pm$-lactone {(HML).} We investigate the oxidation of methacryloylperoxy nitrate {(MPAN)} and methacrylicperoxy acid {(MPAA)} by the hydroxyl radical {(OH)} theoretically, using both density functional theory {[B3LYP]} and explicitly correlated coupled cluster theory {[CCSD(T)-F12].} These two compounds are produced following the abstraction of a hydrogen atom from methacrolein {(MACR)} by the {OH} radical. We use a {RRKM} master equation analysis to estimate that the oxidation of {MPAN} leads to formation of hydroxymethyl?methyl-Î$\pm$-lactone {(HMML)} in high yield. {HMML} production follows a low potential energy path from both {MPAN} and {MPAA} following addition of {OH} (via elimination of the {NO3} and {OH} from {MPAN} and {MPAA}, respectively). We suggest that the subsequent heterogeneous phase chemistry of {HMML} may be the route to formation of 2-methylglyceric acid, a common component of organic aerosol produced in the oxidation of methacrolein. Oxidation of acrolein, a photo-oxidation product from 1,3-butadiene, is found to follow a similar route generating hydroxymethyl-Î$\pm$-lactone {(HML).}
Crounse, JD, et al.Atmospheric Fate of Methacrolein. 1. Peroxy Radical Isomerization Following Addition of OH and O2”. J. Phys. Chem. A 116 (2012): , 116, 5756–5762. Web. Publisher's VersionAbstract

Peroxy radicals formed by addition of {OH} and O2 to the olefinic carbon atoms in methacrolein react with {NO} to form methacrolein hydroxy nitrate and hydroxyacetone. We observe that the ratio of these two compounds, however, unexpectedly decreases as the lifetime of the peroxy radical increases. We propose that this results from an isomerization involving the 1,4-H-shift of the aldehydic hydrogen atom to the peroxy group. The inferred rate (0.5 $\pm$ 0.3 s?1 at T = 296 K) is consistent with estimates obtained from the potential energy surface determined by high level quantum calculations. The product, a hydroxy hydroperoxy carbonyl radical, decomposes rapidly, producing hydroxyacetone and re-forming {OH.} Simulations using a global chemical transport model suggest that most of the methacrolein hydroxy peroxy radicals formed in the atmosphere undergo isomerization and decomposition. Peroxy radicals formed by addition of {OH} and O2 to the olefinic carbon atoms in methacrolein react with {NO} to form methacrolein hydroxy nitrate and hydroxyacetone. We observe that the ratio of these two compounds, however, unexpectedly decreases as the lifetime of the peroxy radical increases. We propose that this results from an isomerization involving the 1,4-H-shift of the aldehydic hydrogen atom to the peroxy group. The inferred rate (0.5 $\pm$ 0.3 s?1 at T = 296 K) is consistent with estimates obtained from the potential energy surface determined by high level quantum calculations. The product, a hydroxy hydroperoxy carbonyl radical, decomposes rapidly, producing hydroxyacetone and re-forming {OH.} Simulations using a global chemical transport model suggest that most of the methacrolein hydroxy peroxy radicals formed in the atmosphere undergo isomerization and decomposition.

Beaver, MR, et al.Importance of biogenic precursors to the budget of organic nitrates: observations of multifunctional organic nitrates by CIMS and TD-LIF during BEARPEX 2009”. Atmos. Chem. Phys. 12 (2012): , 12, 5773–5785. Web. Publisher's Version
Marais, EA, et al.Isoprene emissions in Africa inferred from OMI observations of formaldehyde columns”. Atmos. Chem. Phys. 12 (2012): , 12, 6219–6235. Web. Publisher's Version
Wolfe, GM, et al.Photolysis, OH reactivity and ozone reactivity of a proxy for isoprene-derived hydroperoxyenals (HPALDs)”. Phys. Chem. Chem. Phys. 14 (2012): , 14, 7276–7286. Web. Publisher's VersionAbstract

The C5-hydroperoxyenals {(C5-HPALDs)} are a newly-recognized class of multi-functional hydrocarbons produced during the hydroxyl radical {(OH)-initiated} oxidation of isoprene. Recent theoretical calculations suggest that fast photolysis of these compounds may be an important {OH} source in high-isoprene, low-{NO} r

Paulot, F, et al.Importance of secondary sources in the atmospheric budgets of formic and acetic acids”. Atmos. Chem. Phys. 11 (2011): , 11, 1989–2013. Web. Publisher's VersionAbstract
We present a detailed budget of formic and acetic acids, two of the most abundant trace gases in the atmosphere. Our bottom-up estimate of the global source of formic and acetic acids are  1200 and  1400 Gmol yr−1, dominated by photochemical oxidation of biogenic volatile organic compounds, in particular isoprene. Their sinks are dominated by wet and dry deposition. We use the GEOS-Chem chemical transport model to evaluate this budget against an extensive suite of measurements from ground, ship and satellite-based Fourier transform spectrometers, as well as from several aircraft campaigns over North America. The model captures the seasonality of formic and acetic acids well but generally underestimates their concentration, particularly in the Northern midlatitudes. We infer that the source of both carboxylic acids may be up to 50% greater than our estimate and report evidence for a long-lived missing secondary source of carboxylic acids that may be associated with the aging of organic aerosols. Vertical profiles of formic acid in the upper troposphere support a negative temperature dependence of the reaction between formic acid and the hydroxyl radical as suggested by several theoretical studies.
Barkley, M  P, et al.Can a "state of the art" chemistry transport model simulate Amazonian tropospheric chemistry?”. J. Geophys. Res. 116 (2011): , 116, D16302. Web. Publisher's VersionAbstract
We present an evaluation of a nested high-resolution Goddard Earth Observing System (GEOS)-Chem chemistry transport model simulation of tropospheric chemistry over tropical South America. The model has been constrained with two isoprene emission inventories: (1) the canopy-scale Model of Emissions of Gases and Aerosols from Nature (MEGAN) and (2) a leaf-scale algorithm coupled to the Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) dynamic vegetation model, and the model has been run using two different chemical mechanisms that contain alternative treatments of isoprene photo-oxidation. Large differences of up to 100 Tg C yr$^{-1}$ exist between the isoprene emissions predicted by each inventory, with MEGAN emissions generally higher. Based on our simulations we estimate that tropical South America (30{\ndash}85{\deg}W, 14{\deg}N{\ndash}25{\deg}S) contributes about 15{\ndash}35% of total global isoprene emissions. We have quantified the model sensitivity to changes in isoprene emissions, chemistry, boundary layer mixing, and soil NO$_{x}$ emissions using ground-based and airborne observations. We find GEOS-Chem has difficulty reproducing several observed chemical species; typically hydroxyl concentrations are underestimated, whilst mixing ratios of isoprene and its oxidation products are overestimated. The magnitude of model formaldehyde (HCHO) columns are most sensitive to the choice of chemical mechanism and isoprene emission inventory. We find GEOS-Chem exhibits a significant positive bias (10{\ndash}100%) when compared with HCHO columns from the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) and Ozone Monitoring Instrument (OMI) for the study year 2006. Simulations that use the more detailed chemical mechanism and/or lowest isoprene emissions provide the best agreement to the satellite data, since they result in lower-HCHO columns.
Crounse, John D, et al.Peroxy radical isomerization in the oxidation of isoprene”. Physical Chemistry Chemical Physics 13 (2011): , 13, 13607–13613. Web. Publisher's VersionAbstract
We report experimental evidence for the formation of C5-hydroperoxyaldehydes (HPALDs) from 1,6-H-shift isomerizations in peroxy radicals formed from the hydroxyl radical (OH) oxidation of 2-methyl-1,3-butadiene (isoprene). At 295 K, the isomerization rate of isoprene peroxy radicals relative to the rate of reaction of is , or k295isom 0.002 s−1. The temperature dependence of this rate was determined through experiments conducted at 295, 310 and 318 K and is well described by . The overall uncertainty in the isomerization rate (relative to ) is estimated to be 50%. Peroxy radicals from the oxidation of the fully deuterated isoprene analog isomerize at a rate 15 times slower than non-deuterated isoprene. The fraction of isoprene peroxy radicals reacting by 1,6-H-shift isomerization is estimated to be 8–11% globally, with values up to 20% in tropical regions.
Paulot, F, et al.Isoprene photooxidation: new insights into the production of acids and organic nitrates”. Atmos. Chem. Phys. 9 (2009): , 9, 1479–1501. Web. Publisher's VersionAbstract
We describe a nearly explicit chemical mechanism for isoprene photooxidation guided by chamber studies that include time-resolved observation of an extensive suite of volatile compounds. We provide new constraints on the chemistry of the poorly-understood isoprene δ-hydroxy channels, which account for more than one third of the total isoprene carbon flux and a larger fraction of the nitrate yields. We show that the cis branch dominates the chemistry of the δ-hydroxy channel with less than 5% of the carbon following the trans branch. The modelled yield of isoprene nitrates is 12$\pm$3% with a large difference between the δ and β branches. The oxidation of these nitrates releases about 50% of the NOx. Methacrolein nitrates (modelled yield  15$\pm$3% from methacrolein) and methylvinylketone nitrates (modelled yield  11$\pm$3% yield from methylvinylketone) are also observed. Propanone nitrate, produced with a yield of 1% from isoprene, appears to be the longest-lived nitrate formed in the total oxidation of isoprene. We find a large molar yield of formic acid and suggest a novel mechanism leading to its formation from the organic nitrates. Finally, the most important features of this mechanism are summarized in a condensed scheme appropriate for use in global chemical transport models.
Garden, Anna L, et al.Calculation of conformationally weighted dipole moments useful in ion–molecule collision rate estimates”. Chemical Physics Letters 474 (2009): , 474, 45–50. Web. Publisher's VersionAbstract
We have calculated relative energies and dipole moments of the stable conformers of nitrous acid, ethanol, ethylene glycol and propanone nitrate using a range of ab initio methods and basis sets. We have used these to calculate conformationally weighted dipole moments that are useful in estimates of collision rates between molecules and ions. We find that the average error in the conformationally weighted dipole moments is less than 5% for CCSD(T) with the aug-cc-pVTZ basis set, less than 10% for B3LYP/6-31G(d) and less than 20% for B3LYP/6-31+G(d) and B3LYP/aug-cc-pVTZ.
Paulot, F, et al.Unexpected Epoxide Formation in the Gas-Phase Photooxidation of Isoprene”. Science 325 (2009): , 325, 730-733. Web. Publisher's VersionAbstract

Emissions of nonmethane hydrocarbon compounds to the atmosphere from the biosphere exceed those from anthropogenic activity. Isoprene, a five-carbon diene, contributes more than 40% of these emissions. Once emitted to the atmosphere, isoprene is rapidly oxidized by the hydroxyl radical OH. We report here that under pristine conditions isoprene is oxidized primarily to hydroxyhydroperoxides. Further oxidation of these hydroxyhydroperoxides by OH leads efficiently to the formation of dihydroxyepoxides and OH reformation. Global simulations show an enormous flux–nearly 100 teragrams of carbon per year–of these epoxides to the atmosphere. The discovery of these highly soluble epoxides provides a missing link tying the gas-phase degradation of isoprene to the observed formation of organic aerosols.