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Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA), but the mechanism and yields are uncertain. Aerosol is prevailingly aqueous under the humid conditions typical of isoprene-emitting regions. Here we develop an aqueous-phase mechanism for isoprene SOA formation coupled to a detailed gas-phase isoprene oxidation scheme. The mechanism is based on aerosol reactive uptake coefficients (γ) for water-soluble isoprene oxidation products, including sensitivity to aerosol acidity and nucleophile concentrations. We apply this mechanism to simulation of aircraft (SEAC(4)RS) and ground-based (SOAS) observations over the Southeast US in summer 2013 using the GEOS-Chem chemical transport model. Emissions of nitrogen oxides (NO(x) ≡ NO + NO(2)) over the Southeast US are such that the peroxy radicals produced from isoprene oxidation (ISOPO(2)) react significantly with both NO (high-NO(x) pathway) and HO(2) (low-NO(x) pathway), leading to different suites of isoprene SOA precursors. We find a mean SOA mass yield of 3.3 % from isoprene oxidation, consistent with the observed relationship of total fine organic aerosol (OA) and formaldehyde (a product of isoprene oxidation). Isoprene SOA production is mainly contributed by two immediate gas-phase precursors, isoprene epoxydiols (IEPOX, 58% of isoprene SOA) from the low-NO(x) pathway and glyoxal (28%) from both low- and high-NO(x) pathways. This speciation is consistent with observations of IEPOX SOA from SOAS and SEAC(4)RS. Observations show a strong relationship between IEPOX SOA and sulfate aerosol that we explain as due to the effect of sulfate on aerosol acidity and volume. Isoprene SOA concentrations increase as NO(x) emissions decrease (favoring the low-NO(x) pathway for isoprene oxidation), but decrease more strongly as SO(2) emissions decrease (due to the effect of sulfate on aerosol acidity and volume). The US EPA projects 2013–2025 decreases in anthropogenic emissions of 34% for NO(x) (leading to 7% increase in isoprene SOA) and 48% for SO(2) (35% decrease in isoprene SOA). Reducing SO(2) emissions decreases sulfate and isoprene SOA by a similar magnitude, representing a factor of 2 co-benefit for PM(2.5) from SO(2) emission controls.

Formation of organic nitrates (RONO2) during oxidation of biogenic volatile organic compounds (BVOCs: isoprene, monoterpenes) is a significant loss pathway for atmospheric nitrogen oxide radicals (NOx), but the chemistry of RONO2 formation and degradation remains uncertain. Here we implement a new BVOC oxidation mechanism (including updated isoprene chemistry, new monoterpene chemistry, and particle uptake of RONO2) in the GEOS-Chem global chemical transport model with ∼25 × 25 km2 resolution over North America. We evaluate the model using aircraft (SEAC4RS) and ground-based (SOAS) observations of NOx, BVOCs, and RONO2 from the Southeast US in summer 2013. The updated simulation successfully reproduces the concentrations of individual gas- and particle-phase RONO2 species measured during the campaigns. Gas-phase isoprene nitrates account for 25-50% of observed RONO2 in surface air, and we find that another 10% is contributed by gas-phase monoterpene nitrates. Observations in the free troposphere show an important contribution from long-lived nitrates derived from anthropogenic VOCs. During both campaigns, at least 10% of observed boundary layer RONO2 were in the particle phase. We find that aerosol uptake followed by hydrolysis to HNO3 accounts for 60% of simulated gas-phase RONO2 loss in the boundary layer. Other losses are 20% by photolysis to recycle NOx and 15% by dry deposition. RONO2 production accounts for 20% of the net regional NOx sink in the Southeast US in summer, limited by the spatial segregation between BVOC and NOx emissions. This segregation implies that RONO2 production will remain a minor sink for NOx in the Southeast US in the future even as NOx emissions continue to decline.

The chemical link between isoprene and formaldehyde (HCHO) is a strong, non-linear function of NOx (= NO + NO2). This relationship is a linchpin for top-down isoprene emission inventory verification from orbital HCHO column observations. It is also a benchmark for overall photochemical mechanism performance with regard to VOC oxidation. Using a comprehensive suite of airborne in situ observations over the Southeast U.S., we quantify HCHO production across the urban-rural spectrum. Analysis of isoprene and its major first-generation oxidation products allows us to define both a “prompt” yield of HCHO (molecules of HCHO produced per molecule of freshly-emitted isoprene) and the background HCHO mixing ratio (from oxidation of longer-lived hydrocarbons). Over the range of observed NOx values (roughly 0.1 – 2 ppbv), the prompt yield increases by a factor of 3 (from 0.3 to 0.9 ppbv ppbv−1), while background HCHO increases by a factor of 2 (from 1.6 to 3.3 ppbv). We apply the same method to evaluate the performance of both a global chemical transport model (AM3) and a measurement-constrained 0-D steady state box model. Both models reproduce the NOx dependence of the prompt HCHO yield, illustrating that models with updated isoprene oxidation mechanisms can adequately capture the link between HCHO and recent isoprene emissions. On the other hand, both models under-estimate background HCHO mixing ratios, suggesting missing HCHO precursors, inadequate representation of later-generation isoprene degradation and/or under-estimated hydroxyl radical concentrations. Detailed process rates from the box model simulation demonstrate a 3-fold increase in HCHO production across the range of observed NOx values, driven by a 100% increase in OH and a 40% increase in branching of organic peroxy radical reactions to produce HCHO.

Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA), but the mechanism and yields are uncertain. Aerosol is prevailingly aqueous under the humid conditions typical of isoprene-emitting regions. Here we develop an aqueous-phase mechanism for isoprene SOA formation coupled to a detailed gas-phase isoprene oxidation scheme. The mechanism is based on aerosol reactive uptake probabilities (γ) for water-soluble isoprene oxidation products, including sensitivity to aerosol acidity and nucleophile concentrations. We apply this mechanism to simulation of aircraft (SEAC4RS) and ground-based (SOAS) observations over the Southeast US in summer 2013 using the GEOS-Chem chemical transport model. Emissions of nitrogen oxides (NOx ≡ NO + NO2) over the Southeast US are such that the peroxy radicals produced from isoprene oxidation (ISOPO2) react significantly with both NO (high-NOx pathway) and HO2 (low-NOx pathway), leading to different suites of isoprene SOA precursors. We find a mean SOA mass yield of 3.3 % from isoprene oxidation, consistent with the observed relationship of OA and formaldehyde (a product of isoprene oxidation). The yield is mainly contributed by two immediate gas-phase precursors, isoprene epoxydiols (IEPOX, 58 % of isoprene SOA) from the low-NOx pathway and glyoxal (28 %) from both low- and high-NOx pathways. This speciation is consistent with observations of IEPOX SOA from SOAS and SEAC4RS. Observations show a strong relationship between IEPOX SOA and sulfate aerosol that we explain as due to the indirect effect of sulfate on aerosol acidity and volume, rather than a direct mechanistic role for sulfate. Isoprene SOA concentrations increase as NOx emissions decrease (favoring the low-NOx pathway for isoprene oxidation), but decrease as SO2 emissions decrease (due to the effect of sulfate on aerosol acidity and volume). The US EPA projects 2013–2025 decreases in anthropogenic emissions of 34 % for NOx (leading to 7 % increase in isoprene SOA) and 48 % for SO2 (35 % decrease in isoprene SOA). The combined projected decreases in NOx and SO2 emissions reduce isoprene SOA yields from 3.3 to 2.3 %. Reducing SO2 emissions decreases sulfate and isoprene SOA by a similar magnitude, representing a factor of 2 co-benefit for PM2.5 from SO2 emission controls.

The interaction of atomic oxygen (O(3P)) with semifluorinated self-assembled monolayers (CF-SAMs), two different n-alkanethiolate self-assembled monolayers, and a carbonaceous overlayer derived from an x-ray modified n-alkanethiolate SAM have been studied using in situ x-ray photoelectron spectroscopy. For short atomic oxygen exposures, CF-SAMs remain intact, an effect ascribed to the inertness of C-F and C-C bonds toward atomic oxygen and the well-ordered structure of the CF-SAMs. Following this initial induction period, atomic oxygen permeates through the CF3(CF2)7 overlayer and initiates reactions at the film/substrate interface, evidenced by the formation of sulfonate (RSO3) species and Au2O3. These reactions lead to the desorption of intact adsorbate chains, evidenced by the loss of carbon and fluorine from the film while the C(1s) spectral envelope and the C(1s)/F(1s) ratio remain virtually constant. In contrast, the reactivity of atomic oxygen with alkanethiolate SAMs is initiated at the vacuum/film interface, producing oxygen-containing carbon functional groups. Subsequent reactions of these new species with atomic oxygen lead to erosion of the hydrocarbon film. Experiments on the different hydrocarbon-based films reveal that the atomic oxygen-induced kinetics are influenced by the thickness as well as the structural and chemical characteristics of the hydrocarbon overlayer. Results from this investigation are also discussed in the context of material erosion by AO in low Earth orbit.

Rapid urbanization and economic development in East Asia in past decades has led to photochemical air pollution problems such as excess photochemical ozone and aerosol formation. Asian megacities such as Seoul, Tokyo, Shanghai, Gangzhou, and Beijing are surrounded by densely forested areas and recent research has consistently demonstrated the importance of biogenic volatile organic compounds from vegetation in determining oxidation capacity in the suburban Asian megacity regions. Uncertainties in constraining tropospheric oxidation capacity, dominated by hydroxyl radical concentrations, undermine our ability to assess regional photochemical air pollution problems. We present an observational dataset of CO, NOx, SO2, ozone, HONO, and VOCs (anthropogenic and biogenic) from Taehwa Research Forest (TRF) near the Seoul Metropolitan Area (SMA) in early June 2012. The data show that TRF is influenced both by aged pollution and fresh BVOC emissions. With the dataset, we diagnose HOx (OH, HO2, and RO2) distributions calculated with the University of Washington Chemical Box Model (UWCM v 2.1). Uncertainty from unconstrained HONO sources and radical recycling processes highlighted in recent studies is examined using multiple model simulations with different model constraints. The results suggest that (1) different model simulation scenarios cause systematic differences in HOx distributions especially OH levels (up to 2.5 times) and (2) radical destruction (HO2+HO2 or HO2+RO2) could be more efficient than radical recycling (HO2+NO) especially in the afternoon. Implications of the uncertainties in radical chemistry are discussed with respect to ozone-VOC-NOx sensitivity and oxidation product formation rates. Overall, the VOC limited regime in ozone photochemistry is predicted but the degree of sensitivity can significantly vary depending on the model scenarios. The model results also suggest that RO2 levels are positively correlated with OVOCs production that is not routinely constrained by observations. These unconstrained OVOCs can cause higher than expected OH loss rates (missing OH reactivity) and secondary organic aerosol formation. The series of modeling experiments constrained by observations strongly urge observational constraint of the radical pool to enable precise understanding of regional photochemical pollution problems in the East Asian megacity region.

The Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics & Nitrogen (BEACHON) project seeks to understand the feedbacks and inter-relationships between hydrology, biogenic emissions, carbon assimilation, aerosol properties, clouds and associated feedbacks within water-limited ecosystems. The Manitou Experimental Forest Observatory (MEFO) was established in 2008 by the National Center for Atmospheric Research to address many of the BEACHON research objectives, and it now provides a fixed field site with significant infrastructure. MEFO is a mountainous, semi-arid ponderosa pine-dominated forest site that is normally dominated by clean continental air, but is periodically influenced by anthropogenic sources from Colorado Front Range cities. This article summarizes the past and ongoing research activities at the site, and highlights some of the significant findings that have resulted from these measurements. These activities include: – soil property measurements, – hydrological studies, – measurements of high-frequency turbulence parameters, – eddy covariance flux measurements of water, energy, aerosols and carbon dioxide through the canopy, – biogenic and anthropogenic volatile organic compound emissions and their influence on regional atmospheric chemistry, – aerosol number and mass distributions, – chemical speciation of aerosol particles, – characterization of ice and cloud condensation nuclei, – trace gas measurements, and – model simulations using coupled chemistry and meteorology. In addition to various long-term continuous measurement, three focused measurement campaigns with state-of-the-art instrumentation have taken place since the site was established, and two of these are the subjects of this special issue: BEACHON-ROCS (Rocky Mountain Organic Carbon Study, 2010) and BEACHON-RoMBAS (Rocky Mountain Biogenic Aerosol Study, 2011).

Organic peroxy (RO2) and hydroperoxy (HO2) radicals are key intermediates in the photochemical processes that generate ozone, secondary organic aerosol and reactive nitrogen reservoirs throughout the troposphere. In regions with ample biogenic hydrocarbons, the richness and complexity of peroxy radical chemistry presents a significant challenge to current-generation models, especially given the scarcity of measurements in such environments. We present peroxy radical observations acquired within a Ponderosa pine forest during the summer 2010 Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen – Rocky Mountain Organic Carbon Study (BEACHON-ROCS). Total peroxy radical mixing ratios reach as high as 180 pptv and are among the highest yet recorded. Using the comprehensive measurement suite to constrain a near-explicit 0-D box model, we investigate the sources, sinks and distribution of peroxy radicals below the forest canopy. The base chemical mechanism underestimates total peroxy radicals by as much as a factor of 3. Since primary reaction partners for peroxy radicals are either measured (NO) or under-predicted (HO2 and RO2, i.e. self-reaction), missing sources are the most likely explanation for this result. A close comparison of model output with observations reveals at least two distinct source signatures. The first missing source, characterized by a sharp midday maximum and a strong dependence on solar radiation, is consistent with photolytic production of HO2. The diel profile of the second missing source peaks in the afternoon and suggests a process that generates RO2 independently of sun-driven photochemistry, such as ozonolysis of reactive hydrocarbons. The maximum magnitudes of these missing sources (~ 120 and 50 pptv min−1, respectively) are consistent with previous observations alluding to unexpectedly intense oxidation within forests. We conclude that a similar mechanism may underlie many such observations.

Nitryl chloride (ClNO2) is produced at night by reactions of dinitrogen pentoxide (N2O5) on chloride containing surfaces. ClNO2 is photolyzed during the morning hours after sunrise to liberate highly reactive chlorine atoms (Cl·). This chemistry takes place primarily in polluted environments where the concentrations of N2O5 precursors (nitrogen oxide radicals and ozone) are high, though it likely occurs in remote regions at lower intensities. Recent field measurements have illustrated the potential importance of ClNO2 as a daytime Cl· source and a nighttime NOx reservoir. However, the fate of the Cl· and the overall impact of ClNO2 on regional photochemistry remain unclear. To this end, we have incorporated ClNO2 production, photolysis, and subsequent Cl· reactions into an existing Master Chemical Mechanism (MCM version 3.2) box model framework using observational constraints from the CalNex 2010 field study. Cl· reactions with a set of alkenes and alcohols, and the simplified multiphase chemistry of N2O5, ClNO2, HOCl, ClONO2, and Cl2, none of which are currently part of the MCM, have been added to the mechanism. The presence of ClNO2 produces significant changes to oxidants, ozone, and nitrogen oxide partitioning, relative to model runs excluding ClNO2 formation. From a nighttime maximum of 1.5 ppbv ClNO2, the daytime maximum Cl· concentration reaches 1 × 105 atoms cm−3 at 7 a.m., reacting mostly with a large suite of volatile organic compounds (VOC) to produce 2.2 times more organic peroxy radicals in the morning than in the absence of ClNO2. In the presence of several ppbv of nitrogen oxide radicals (NOx = NO + NO2), these perturbations lead to similar enhancements in hydrogen oxide radicals (HOx = OH + HO2). Neglecting contributions from HONO, the total integrated daytime radical source is 17% larger when including ClNO2, which leads to a similar enhancement in integrated ozone production of 15%. Detectable levels (tens of pptv) of chlorine containing organic compounds are predicted to form as a result of Cl· addition to alkenes, which may be useful in identifying times of active Cl· chemistry.

We present a detailed analysis of OH and HO2 observations from the BEACHON (Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen)-ROCS (Rocky Mountain Organic Carbon Study) 2010 field campaign at the Manitou Forest Observatory (MFO), which is a 2-methyl-3-butene-2-ol (MBO) and monoterpene (MT) dominated forest environment. A comprehensive suite of measurements was used to constrain primary production of OH via ozone photolysis, OH recycling from HO2, and OH chemical loss rates, in order to estimate the steady-state concentration of OH. In addition, the University of Washington Chemical Model (UWCM) was used to evaluate the performance of a near-explicit chemical mechanism. The diurnal cycle in OH from the steady-state calculations is in good agreement with measurement. A comparison between the photolytic production rates and the recycling rates from the HO2 + NO reaction shows that recycling rates are ~20 times faster than the photolytic OH production rates from ozone. Thus, we find that direct measurement of the recycling rates and the OH loss rates can provide accurate predictions of OH concentrations. More importantly, we also conclude that a conventional OH recycling pathway (HO2 + NO) can explain the observed OH levels in this non-isoprene environment. This is in contrast to observations in isoprene-dominated regions, where investigators have observed significant underestimation of OH and have speculated that unknown sources of OH are responsible. The highly-constrained UWCM calculation under-predicts observed HO2 by as much as a factor of 8. As HO2 maintains oxidation capacity by recycling to OH, UWCM underestimates observed OH by as much as a factor of 5. When the UWCM calculation is constrained by measured HO2, model calculated OH is in reasonable agreement with the observed OH levels. Conversely, constraining the model to observed OH only slightly reduces the model-measurement HO2 discrepancy, implying unknown HO2 sources. These findings demonstrate the importance of constraining both the inputs to, and recycling within, the ROx radical pool (OH + HO2 + RO2).

Acyl peroxy nitrates (APNs, also known as PANs) are formed from the oxidation of aldehydes and other oxygenated VOC (oVOC) in the presence of NO2. Formation of APNs suppresses NOx (NOx≡NO+NO2) in urban areas and enhances NOx downwind in urban plumes, increasing the rate of ozone production throughout an urban plume. APNs also redistribute NOx on global scales, enhancing NOx and thus ozone production. There are both anthropogenic and biogenic oVOC precursors to APNs, but a detailed evaluation of their chemistry against observations has proven elusive. Here we describe measurements of PAN, PPN, and MPAN along with the majority of chemicals that participate in their production and loss, including OH, HO2, numerous oVOC, and NO2. Observations were made during the Biosphere Effects on AeRosols and Photochemistry Experiment (BEARPEX 2007) in the outflow of the Sacramento urban plume. These observations are used to evaluate a detailed chemical model of APN ratios and concentrations. We find the ratios of APNs are nearly independent of the loss mechanisms and thus an especially good test of our understanding of their sources. We show that oxidation of methylvinyl ketone, methacrolein, methyl glyoxal, biacetyl and acetaldehyde are all significant sources of the PAN+peroxy acetyl (PA) radical reservoir, with methylvinyl ketone (MVK) often being the primary non-acetaldehyde source. At high temperatures, oxidation of non-acetaldehyde PA radical sources contributes over 60% to the total PA production rate. An analysis of absolute APN concentrations reveals a missing APN sink that can be resolved by increasing the PA+∑RO2 rate constant by a factor of 3.

Metastatic lesions occur in up to 36% of patients with pheochromocytoma. Currently there is no way to reliably detect or predict which patients are at risk for metastatic pheochromocytoma. Thus, the discovery of biomarkers that could distinguish patients with benign disease from those with metastatic disease would be of great clinical value. Using surface-enhanced laser desorption ionization protein chips combined with high-resolution mass spectrometry, we tested the hypothesis that pheochromocytoma pathologic states can be reflected as biomarker information within the low molecular weight (LMW) region of the serum proteome. LMW protein profiles were generated from the serum of 67 pheochromocytoma patients from four institutions and analyzed by two different bioinformatics approaches employing pattern recognition algorithms to determine if the LMW component of the circulatory proteome contains potentially useful discriminatory information. Both approaches were able to identify combinations of LMW molecules which could distinguish all metastatic from all benign pheochromocytomas in a separate blinded validation set. In conclusion, for this study set low molecular mass biomarker information correlated with pheochromocytoma pathologic state using blinded validation. If confirmed in larger validation studies, efforts to identify the underlying diagnostic molecules by sequencing would be warranted. In the future, measurement of these biomarkers could be potentially used to improve the ability to identify patients with metastatic disease.