ACP Atmospheric Chemistry and Physics ACP 1680-7324 Copernicus GmbH Göttingen, Germany 10.5194/acp-11-1269-2011 The Chemistry of Atmosphere-Forest Exchange (CAFE) Model – Part 2: Application to BEARPEX-2007 observations Wolfe G. M. 1 2 Thornton J. A. 2 Bouvier-Brown N. C. 3 11 Goldstein A. H. 3 Park J.-H. 3 McKay M. 3 12 Matross D. M. 3 13 Mao J. 4 14 Brune W. H. 4 LaFranchi B. W. 5 15 Browne E. C. 5 Min K.-E. 5 Wooldridge P. J. 5 Cohen R. C. 5 Crounse J. D. 6 Faloona I. C. 7 Gilman J. B. 8 9 Kuster W. C. 8 de Gouw J. A. 8 9 Huisman A. 10 Keutsch F. N. 10 Department of Chemistry, University of Washington, Seattle, WA, USA Department of Atmospheric Sciences, University of Washington, Seattle, WA, USA Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA Department of Meteorology, Pennsylvania State University, University Park, PA, USA Department of Chemistry, University of California, Berkeley, CA, USA Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA Department of Land, Air and Water Resources, University of California, Davis, CA, USA NOAA Earth System Research Laboratory, Boulder, CO, USA Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA Department of Chemistry, University of Wisconsin, Madison, WI, USA now at: Chemistry and Biochemistry Department, Loyola Marymount University, Los Angeles, CA, USA now at: California Air Resources Board, Sacramento, CA, USA now at: KEMA, Inc., Oakland, CA, USA now at: School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA now at: Center for Accelerator Mass Spectrometry (CAMS), Lawrence Livermore National Lab, Livermore, CA, USA 15 02 2011 11 3 1269 1294 This is an open-access article ditributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This article is available from http://www.atmos-chem-phys.net/11/1269/2011/acp-11-1269-2011.html The full text article is available as a PDF file from http://www.atmos-chem-phys.net/11/1269/2011/acp-11-1269-2011.pdf

In a companion paper, we introduced the Chemistry of Atmosphere-Forest Exchange (CAFE) model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we apply CAFE to noontime observations from the 2007 Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007). In this work we evaluate the CAFE modeling approach, demonstrate the significance of in-canopy chemistry for forest-atmosphere exchange and identify key shortcomings in the current understanding of intra-canopy processes. <br><br> CAFE generally reproduces BEARPEX-2007 observations but requires an enhanced radical recycling mechanism to overcome a factor of 6 underestimate of hydroxyl (OH) concentrations observed during a warm (~29 °C) period. Modeled fluxes of acyl peroxy nitrates (APN) are quite sensitive to gradients in chemical production and loss, demonstrating that chemistry may perturb forest-atmosphere exchange even when the chemical timescale is long relative to the canopy mixing timescale. The model underestimates peroxy acetyl nitrate (PAN) fluxes by 50% and the exchange velocity by nearly a factor of three under warmer conditions, suggesting that near-surface APN sinks are underestimated relative to the sources. Nitric acid typically dominates gross dry N deposition at this site, though other reactive nitrogen (NO<sub>y</sub>) species can comprise up to 28% of the N deposition budget under cooler conditions. Upward NO<sub>2</sub> fluxes cause the net above-canopy NO<sub>y</sub> flux to be ~30% lower than the gross depositional flux. CAFE under-predicts ozone fluxes and exchange velocities by ~20%. Large uncertainty in the parameterization of cuticular and ground deposition precludes conclusive attribution of non-stomatal fluxes to chemistry or surface uptake. Model-measurement comparisons of vertical concentration gradients for several emitted species suggests that the lower canopy airspace may be only weakly coupled with the upper canopy. Future efforts to model forest-atmosphere exchange will require a more mechanistic understanding of non-stomatal deposition and a more thorough characterization of in-canopy mixing processes.

 References % vor jede Referenz Atkinson, R. and Arey, J.: Gas-phase tropospheric chemistry of biogenic volatile organic compounds: a review, Atmos. Environ., 37, S197–S219, 2003. Baker, B., Guenther, A., Greenberg, J., Goldstein, A., and Fall, R.: Canopy fluxes of 2-methyl-3-buten-2-ol over a ponderosa pine forest by relaxed eddy accumulation: Field data and model comparison, J. Geophys. Res., 104, 26107–26114, 1999. Bouvier-Brown, N. C., Goldstein, A. H., Gilman, J. B., Kuster, W. C., and de Gouw, J. A.: In-situ ambient quantification of monoterpenes, sesquiterpenes, and related oxygenated compounds during BEARPEX 2007: implications for gas- and particle-phase chemistry, Atmos. Chem. Phys., 9, 5505–5518, http://dx.doi.org/10.5194/acp-9-5505-2009doi:10.5194/acp-9-5505-2009, 2009a. Bouvier-Brown, N. C., Goldstein, A. H., Worton, D. R., Matross, D. M., Gilman, J. B., Kuster, W. C., Welsh-Bon, D., Warneke, C., de Gouw, J. A., Cahill, T. M., and Holzinger, R.: Methyl chavicol: characterization of its biogenic emission rate, abundance, and oxidation products in the atmosphere, Atmos. Chem. Phys., 9, 2061–2074, http://dx.doi.org/10.5194/acp-9-2061-2009doi:10.5194/acp-9-2061-2009, 2009b. Bouvier-Brown, N. C., Holzinger, R., Palitzsch, K., and Goldstein, A. H.: Large emissions of sesquiterpenes and methyl chavicol quantified from branch enclosure measurements, Atmos. Environ., 43, 389–401, 2009c. Brune, W. H., van Duin, D., Mao, J., and Ren, X.: OH and HO<sub>2</sub> Measurement in Blodgett Forest, CA during BEARPEX 2009, 2010 AGU Fall Meeting, San Francisco, CA, Abstract A51G-02, 2010. Bytnerowicz, A. and Fenn, M. E.: Nitrogen deposition in California forests: a review, Environ. Pollut., 92, 127–146, 1996. Cantrell, C. A., Lind, J. A., Shetter, R. E., Calvert, J. G., Goldan, P. D., Kuster, W., Fehsenfeld, F. C., Montzka, S. A., Parrish, D. D., Williams, E. J., Buhr, M. P., Westberg, H. H., Allwine, G., and Martin, R.: Peroxy-Radicals In The Rose Experiment – Measurement And Theory, J. Geophys. Res.-Atmos., 97, 20671–20686, 1992. Choi, W., Faloona, I. C., Bouvier-Brown, N. C., McKay, M., Goldstein, A. H., Mao, J., Brune, W. H., LaFranchi, B. W., Cohen, R. C., Wolfe, G. M., Thornton, J. A., Sonnenfroh, D. M., and Millet, D. B.: Observations of elevated formaldehyde over a forest canopy suggest missing sources from rapid oxidation of arboreal hydrocarbons, Atmos. Chem. Phys., 10, 8761–8781, http://dx.doi.org/10.5194/acp-10-8761-2010doi:10.5194/acp-10-8761-2010, 2010. Ciccioli, P., Brancaleoni, E., Frattoni, M., Di Palo, V., Valentini, R., Tirone, G., Seufert, G., Bertin, N., Hansen, U., Csiky, O., Lenz, R., and Sharma, M.: Emission of reactive terpene compounds from orange orchards and their removal by within-canopy processes, J. Geophys. Res.-Atmos., 104, 8077–8094, 1999. Coe, H., Gallagher, M. W., Choularton, T. W., and Dore, C.: Canopy Scale Measurements Of Stomatal And Cuticular O-3 Uptake By Sitka Spruce, Atmos. Environ., 29, 1413–1423, 1995. Da Silva, G., Graham, C., and Wang, Z. F.: Unimolecular beta-Hydroxyperoxy Radical Decomposition with OH Recycling in the Photochemical Oxidation of Isoprene, Environ. Sci. Technol., 44, 250–256, 2010. Darrall, N. M.: The Effect Of Air-Pollutants On Physiological Processes In Plants, Plant Cell Environ., 12, 1–30, 1989. Day, D. A., Wooldridge, P. J., and Cohen, R. C.: Observations of the effects of temperature on atmospheric HNO<sub>3</sub>, $§igma $ANs, $§igma $PNs, and NO<sub>x</sub>: evidence for a temperature-dependent HO<sub>x</sub> source, Atmos. Chem. Phys., 8, 1867–1879, http://dx.doi.org/10.5194/acp-8-1867-2008doi:10.5194/acp-8-1867-2008, 2008. Day, D. A., Farmer, D. K., Goldstein, A. H., Wooldridge, P. J., Minejima, C., and Cohen, R. C.: Observations of NO<sub>x</sub>, $§igma $PNs, $§igma $ANs, and HNO<sub>3</sub> at a Rural Site in the California Sierra Nevada Mountains: summertime diurnal cycles, Atmos. Chem. Phys., 9, 4879–4896, http://dx.doi.org/10.5194/acp-9-4879-2009doi:10.5194/acp-9-4879-2009, 2009. Di Carlo, P., Brune, W. H., Martinez, M., Harder, H., Lesher, R., Ren, X. R., Thornberry, T., Carroll, M. A., Young, V., Shepson, P. B., Riemer, D., Apel, E., and Campbell, C.: Missing OH reactivity in a forest: Evidence for unknown reactive biogenic VOCs, Science, 304, 722–725, 2004. Dillon, M. B., Lamanna, M. S., Schade, G. W., Goldstein, A., and Cohen, R. C.: Chemical evolution of the Sacramento urban plume: Transport and oxidation, J. Geophys. Res., 107, 4045, http://dx.doi.org/10.1029/2001JD000969doi:10.1029/2001JD000969, 2002. Dorsey, J. R., Duyzer, J. H., Gallagher, M. W., Coe, H., Pilegaard, K., Weststrate, J. H., Jensen, N. O., and Walton, S.: Oxidized nitrogen and ozone interaction with forests. I: Experimental observations and analysis of exchange with Douglas fir, Q. J. Roy. Meteorol. Soc., 130, 1941–1955, 2004. Dreyfus, G. B., Schade, G. W., and Goldstein, A. H.: Observational constraints on the contribution of isoprene oxidation to ozone production on the western slope of the Sierra Nevada, California, J. Geophys. Res.-Atmos., 107, 4365–4382, http://dx.doi.org/10.1029/2001JD001490doi:10.1029/2001JD001490, 2002. Duyzer, J. H., Dorsey, J. R., Gallagher, M. W., Pilegaard, K., and Walton, S.: Oxidized nitrogen and ozone interaction with forests. II: Multi-layer process-oriented modelling results and a sensitivity study for Douglas fir, Q. J. Roy. Meteorol. Soc., 130, 1957–1971, 2004. Erisman, J. W., Draaijers, G. P. J., Steingrover, E., Van Dijk, H., Boxman, A., and de Vries, W.: Assessment of the exposure and loads of acidifying and eutrophying pollutants and ozone, as well as their, harmful influence on the vitality of the trees and the Speulder forest ecosystem as a whole, Water Air Soil Pollut., 105, 539–571, 1998. Faloona, I., Tan, D., Brune, W., Hurst, J., Barket, D., Couch, T. L., Shepson, P., Apel, E., Riemer, D., Thornberry, T., Carroll, M. A., Sillman, S., Keeler, G. J., Sagady, J., Hooper, D., and Paterson, K.: Nighttime observations of anomalously high levels of hydroxyl radicals above a deciduous forest canopy, J. Geophys. Res.-Atmos., 106, 24315–24333, 2001. Fares, S., McKay, M., Holzinger, R., and Goldstein, A. H.: Ozone fluxes in a Pinus ponderosa ecosystem are dominated by non-stomatal processes: Evidence from long-term continuous measurements, Agr. Forest Meteorol., 150, 420–431, 2010a. Fares, S., Park, J. H., Ormeno, E., Gentner, D. R., McKay, M., Loreto, F., Karlik, J., and Goldstein, A. H.: Ozone uptake by citrus trees exposed to a range of ozone concentrations, Atmos. Environ., 44, 3404–3412, 2010b. Farmer, D. K. and Cohen, R. C.: Observations of HNO<sub>3</sub>, $§igma $AN, $§igma $PN and NO<sub>2</sub> fluxes: evidence for rapid HO<sub>x</sub> chemistry within a pine forest canopy, Atmos. Chem. Phys., 8, 3899–3917, http://dx.doi.org/10.5194/acp-8-3899-2008doi:10.5194/acp-8-3899-2008, 2008. Fischer, M. L. and Littlejohn, D.: Ammonia at Blodgett Forest, Sierra Nevada, USA, Atmos. Chem. Phys. Discuss., 7, 14139–14169, http://dx.doi.org/10.5194/acpd-7-14139-2007doi:10.5194/acpd-7-14139-2007, 2007. Forkel, R., Klemm, O., Graus, M., Rappengluck, B., Stockwell, W. R., Grabmer, W., Held, A., Hansel, A., and Steinbrecher, R.: Trace gas exchange and gas phase chemistry in a Norway spruce forest: A study with a coupled 1-dimensional canopy atmospheric chemistry emission model, Atmos. Environ., 40, S28–S42, 2006. Fowler, D., Pilegaard, K., Sutton, M. A., Ambus, P., Raivonen, M., Duyzer, J., Simpson, D., Fagerli, H., Fuzzi, S., Schjoerring, J. K., Granier, C., Neftel, A., Isaksen, I. S. A., Laj, P., Maione, M., Monks, P. S., Burkhardt, J., Daemmgen, U., Neirynck, J., Personne, E., Wichink-Kruit, R., Butterbach-Bahl, K., Flechard, C., Tuovinen, J. P., Coyle, M., Gerosa, G., Loubet, B., Altimir, N., Gruenhage, L., Ammann, C., Cieslik, S., Paoletti, E., Mikkelsen, T. N., Ro-Poulsen, H., Cellier, P., Cape, J. N., Horvath, L., Loreto, F., Niinemets, U., Palmer, P. I., Rinne, J., Misztal, P., Nemitz, E., Nilsson, D., Pryor, S., Gallagher, M. W., Vesala, T., Skiba, U., Brueggemann, N., Zechmeister-Boltenstern, S., Williams, J., O'Dowd, C., Facchini, M. C., de Leeuw, G., Flossman, A., Chaumerliac, N., and Erisman, J. W.: Atmospheric composition change: Ecosystems-Atmosphere interactions, Atmos. Environ., 43, 5193–5267, 2009. Ganzeveld, L. N., Lelieveld, J., Dentener, F. J., Krol, M. C., Bouwman, A. J., and Roelofs, G. J.: Global soil-biogenic NOx emissions and the role of canopy processes, J. Geophys. Res.-Atmos., 107(D16), 4298, doi:10.1029/2001JD001289, 2002a. Ganzeveld, L. N., Lelieveld, J., Dentener, F. J., Krol, M. C., and Roelofs, G.-J.: Atmosphere-biosphere trace gas exchanges simulated with a single-column model, J. Geophys. Res., 107, 4297–4318, http://dx.doi.org/10.1029/2001JD000684doi:10.1029/2001JD000684, 2002b. Ganzeveld, L., Valverde-Canossa, J., Moortgat, G. K., and Steinbrecher, R.: Evaluation of peroxide exchanges over a coniferous forest un a single-column chemistry-climate model, Atmos. Environ., 40, S68–S80, http://dx.doi.org/10.1016/j.atmosenv.2006.01.062doi:10.1016/j.atmosenv.2006.01.062, 2006. Gao, W., Wesely, M. L., and Lee, I. Y.: A numerical study of the effects of air chemistry on fluxes of NO, NO<sub>2</sub>, and O<sub>3</sub> near the surface, J. Geophys. Res., 96, 18761–18769, 1991. Gao, W., Wesely, M. L., and Doskey, P. V.: Numerical modeling of the turbulent diffusion and chemistry of NO<sub>x</sub>, O<sub>3</sub>, isoprene, and other reactive trace gases in and above a forest canopy, J. Geophys. Res., 98, 18339–18353, 1993. Goldstein, A. H., Hultman, N. E., Fracheboud, J. M., Bauer, M. R., Panek, J. A., Xu, M., Qi, Y., Guenther, A. B., and Baugh, W.: Effects of climate variability on the carbon dioxide, water, and sensible heat fluxes above a ponderosa pine plantation in the Sierra Nevada (CA), Agr. Forest Meteorol., 101, 113–129, 2000. Goldstein, A. H., Schade, G. W., and Dreyfus, G.: Whole Ecosystem Measurements of Biogenic Hydrocarbon Emissions, Final Report, State of California Air Resources Board Award No. 98–328, 2001. Goldstein, A. H., McKay, M., Kurpius, M. R., Schade, G. W., Lee, A., Holzinger, R., and Rasmussen, R. A.: Forest thinning experiment confirms ozone deposition to forest canopy is dominated by reaction with biogenic VOCs, Geophys. Res. Lett., 31, L22106, http://dx.doi.org/10.1029/2004GL021259doi:10.1029/2004GL021259, 2004. Goldstein, A. H., Koven, C. D., Heald, C. L., and Fung, I. Y.: Biogenic carbon and anthropogenic pollutants combine to form a cooling haze over the southeastern United States, P. Natl. Acad. Sci. USA, 106, 8835–8840, 2009. Goodman, A. L., Underwood, G. M., and Grassian, V. H.: Heterogeneous reaction of NO2: Characterization of gas-phase and adsorbed products from the reaction, 2NO(2)(g)+H2O(a)-> HONO(g)+HNO3(a) on hydrated silica particles, J. Phys. Chem. A, 103, 7217–7223, 1999. Gray, D. W., Lerdau, M. T., and Goldstein, A. H.: Influences of temperature history, water stress, and needle age on methylbutenol emissions, Ecology, 84, 765–776, 2003. Gray, D. W., Goldstein, A. H., and Lerdau, M. T.: Thermal history regulates methylbutenol basal emission rate in Pinus ponderosa, Plant Cell Environ., 29, 1298–1308, 2006. Guenther, A., Hewitt, C. N., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P., Klinger, L., Lerdau, M. T., McKay, W. A., Pierce, T., Scholes, B., Steinbrecher, R., Tallamraju, R., Taylor, J., and Zimmerman, P.: A global model of natural volatile organic compound emissions, J. Geophys. Res., 100, 8873–8892, 1995. Hall, B. D. and Claiborn, C. S.: Measurements of the dry deposition of peroxides to a Canadian boreal forest, J. Geophys. Res.-Atmos., 102, 29343–29353, 1997. Harley, P., Fridd-Stroud, V., Greenberg, J., Guenther, A., and Vasconcellos, P.: Emission of 2-methyl-3-buten-2-ol by pines: A potentially large natural source of reactive carbon to the atmosphere, J. Geophys. Res., 103, 25479–25486, 1998. He, Y., Zhou, X. L., Hou, J., Gao, H. L., and Bertman, S. B.: Importance of dew in controlling the air-surface exchange of HONO in rural forested environments, Geophys. Res. Lett., 33, L02813, doi:10.1029/2005GL024348, 2006. Herman, D. J., Halverson, L. J., and Firestone, M. K.: Nitrogen Dynamics in an Annual Grassland: Oak Canopy, Climate, and Microbial Population Effects, Ecological Applications, 13, 593–604, 2003. Hofzumahaus, A., Rohrer, F., Lu, K., Bohn, B., Brauers, T., Chang, C.-C., Fuchs, H., Holland, F., Kita, K., Kondo, Y., Li, X., Lou, S., Shao, M., Zeng, L., Wahner, A., and Zhang, Y.: Amplified Trace Gas Removal in the Troposphere, Science, 324, 1702–1704, http://dx.doi.org/10.1126/science.1164566doi:10.1126/science.1164566, 2009. Hogg, A., Uddling, J., Ellsworth, D., Carroll, M. A., Pressley, S., Lamb, B., and Vogel, C.: Stomatal and non-stomatal fluxes of ozone to a northern mixed hardwood forest, Tellus B, 59, 514–525, 2007. Holzinger, R., Lee, A., Paw, K. T., and Goldstein, U. A. H.: Observations of oxidation products above a forest imply biogenic emissions of very reactive compounds, Atmos. Chem. Phys., 5, 67–75, http://dx.doi.org/10.5194/acp-5-67-2005doi:10.5194/acp-5-67-2005, 2005. Horii, C. V., Munger, J. W., Wofsy, S. C., Zahniser, M., Nelson, D., and McManus, J. B.: Atmospheric reactive nitrogen concentration and flux budgets at a Northeastern U.S. forest site, Agr. Forest Meteorol., 136, 159–174, 2006. Horowitz, L. W., Fiore, A. M., Milly, G. P., Cohen, R. C., Perring, A., Wooldridge, P. J., Hess, P. G., Emmons, L. K., and Lamarque, J. F.: Observational constraints on the chemistry of isoprene nitrates over the eastern United States, J. Geophys. Res.-Atmos., 112, D12S08, doi:10.1029/2006JD007747, 2007. Isaksen, I. S. A., Granier, C., Myhre, G., Berntsen, T. K., Dalsoren, S. B., Gauss, M., Klimont, Z., Benestad, R., Bousquet, P., Collins, W., Cox, T., Eyring, V., Fowler, D., Fuzzi, S., Jockel, P., Laj, P., Lohmann, U., Maione, M., Monks, P., Prevot, A. S. H., Raes, F., Richter, A., Rognerud, B., Schulz, M., Shindell, D., Stevenson, D. S., Storelvmo, T., Wang, W. C., van Weele, M., Wild, M., and Wuebbles, D.: Atmospheric composition change: Climate-Chemistry interactions, Atmos. Environ., 43, 5138–5192, 2009. Jacobson, M. Z.: Fundamentals of Atmospheric Modeling, Cambridge University Press, New York, 2005. Jaeglé, L., Steinberger, L., Martin, R. V., and Chance, K.: Global partitioning of NO<sub>x</sub> sources using satellite observations: Relative roles of fossil fuel combustion, biomass burning and soil emissions, Faraday Discuss., 130, 407–423, http://dx.doi.org/10.1039/b502128fdoi:10.1039/b502128f, 2005. Karl, T., Harley, P., Guenther, A., Rasmussen, R., Baker, B., Jardine, K., and Nemitz, E.: The bi-directional exchange of oxygenated VOCs between a loblolly pine (Pinus taeda) plantation and the atmosphere, Atmos. Chem. Phys., 5, 3015–3031, http://dx.doi.org/10.5194/acp-5-3015-2005doi:10.5194/acp-5-3015-2005, 2005. Karl, T., Harley, P., Emmons, L., Thornton, B., Guenther, A., Basu, C., Turnipseed, A., and Jardine, K.: Efficient Atmospheric Cleansing of Oxidized Organic Trace Gases by Vegetation, Science, 330, 816–819, 2010. Kurpius, M. R. and Goldstein, A. H.: Gas-phase chemistry dominates O<sub>3</sub> loss to a forest, implying a source of aerosols and hydroxyl radicals to the atmosphere, Geophys. Res. Lett., 30, 1371–1374, http://dx.doi.org/10.1029/2002GL016785doi:10.1029/2002GL016785, 2003. LaFranchi, B. W., Wolfe, G. M., Thornton, J. A., Harrold, S. A., Browne, E. C., Min, K. E., Wooldridge, P. J., Gilman, J. B., Kuster, W. C., Goldan, P. D., de Gouw, J. A., McKay, M., Goldstein, A. H., Ren, X., Mao, J., and Cohen, R. C.: Closing the peroxy acetyl nitrate budget: observations of acyl peroxy nitrates (PAN, PPN, and MPAN) during BEARPEX 2007, Atmos. Chem. Phys., 9, 7623–7641, http://dx.doi.org/10.5194/acp-9-7623-2009doi:10.5194/acp-9-7623-2009, 2009. Lee, A., Goldstein, A. H., Keywood, M. D., Gao, S., Varutbangkul, V., Bahreini, R., Ng, N. L., Flagan, R. C., and Seinfeld, J. H.: Gas-phase products and secondary aerosol yields from the ozonolysis of ten different terpenes, J. Geophys. Res., 111, 1–18, http://dx.doi.org/10.1029/2005JD006437doi:10.1029/2005JD006437, 2006a. Lee, A., Goldstein, A. H., Kroll, J. H., Ng, N. L., Varutbangkul, V., Flagan, R. C., and Seinfeld, J. H.: Gas-phase products and secondary aerosol yields from the photooxidation of 16 different terpenes, J. Geophys. Res., 111, 1–25, http://dx.doi.org/10.1029/2006JD007050doi:10.1029/2006JD007050, 2006b. Lelieveld, J., Butler, T. M., Crowley, J. N., Dillon, T. J., Fischer, H., Ganzeveld, L., Harder, H., Lawrence, M. G., Martinez, M., Taraborrelli, D., and Williams, J.: Atmospheric oxidation capacity sustained by a tropical forest, Nature, 452, 737–740, http://dx.doi.org/10.1038/nature06870doi:10.1038/nature06870, 2008. Li, Y. J., Chen, Q., Guzman, M. I., Chan, C. K., and Martin, S. T.: Second-generation products contribute substantially to the particle-phase organic material produced by β-caryophyllene ozonolysis, Atmos. Chem. Phys., 11, 121–132, http://dx.doi.org/10.5194/acp-11-121-2011doi:10.5194/acp-11-121-2011, 2011. Magnani, F., Mencuccini, M., Borghetti, M., Berbigier, P., Berninger, F., Delzon, S., Grelle, A., Hari, P., Jarvis, P. G., Kolari, P., Kowalski, A. S., Lankreijer, H., Law, B. E., Lindroth, A., Loustau, D., Manca, G., Moncrieff, J. B., Rayment, M., Tedeschi, V., Valentini, R., and Grace, J.: The human footprint in the carbon cycle of temperate and boreal forests, Nature, 447, 849–851, 2007. Makar, P. A., Fuentes, J. D., Wang, D., Staebler, R. M., and Wiebe, H. A.: Chemical processing of biogenic hydrocarbons within and above a temperate deciduous forest, J. Geophys. Res., 104, 3581–3603, 1999. Mao, J., Ren, X., Chen, Z., Brune, W., LaFranchi, B., Cohen, R., Gilman, J., and deGouw, J.: HO<sub>x</sub> chemistry in and above a forest canopy in seasonal transition, AGU Fall Meeting, Abstract A32C-03, 2008. Mao, J., Ren, X., Brune, W. H., Olson, J. R., Crawford, J. H., Fried, A., Huey, L. G., Cohen, R. C., Heikes, B., Singh, H. B., Blake, D. R., Sachse, G. W., Diskin, G. S., Hall, S. R., and Shetter, R. E.: Airborne measurement of OH reactivity during INTEX-B, Atmos. Chem. Phys., 9, 163–173, http://dx.doi.org/10.5194/acp-9-163-2009doi:10.5194/acp-9-163-2009, 2009. Martinez, M., Harder, H., Kovacs, T. A., Simpas, J. B., Bassis, J., Lesher, R., Brune, W. H., Frost, G. J., Williams, E. J., Stroud, C. A., Jobson, B. T., Roberts, J. M., Hall, S. R., Shetter, R. E., Wert, B., Fried, A., Alicke, B., Stutz, J., Young, V. L., White, A. B., and Zamora, R. J.: OH and HO2 concentrations, sources, and loss rates during the Southern Oxidants Study in Nashville, Tennessee, summer 1999, J. Geophys. Res.-Atmos., 108, D194617, doi:10.1029/2003JD003551, 2003. Murphy, J. G., Day, D. A., Cleary, P. A., Wooldridge, P. J., and Cohen, R. C.: Observations of the diurnal and seasonal trends in nitrogen oxides in the western Sierra Nevada, Atmos. Chem. Phys., 6, 5321–5338, http://dx.doi.org/10.5194/acp-6-5321-2006doi:10.5194/acp-6-5321-2006, 2006. Paulot, F., Beaver, M. R., St. Clair, J., Spencer, K. M., Crounse, J., and Wennberg, P. O.: Exchange of hydrogen peroxide and nitric acid over a ponerosa forest measured by eddy covariance, AGU Fall Meeting, San Francisco, CA, Abstract A41D-0133, 2009a. Paulot, F., Crounse, J. D., Kjaergaard, H. G., Kroll, J. H., Seinfeld, J. H., and Wennberg, P. O.: Isoprene photooxidation: new insights into the production of acids and organic nitrates, Atmos. Chem. Phys., 9, 1479–1501, http://dx.doi.org/10.5194/acp-9-1479-2009doi:10.5194/acp-9-1479-2009, 2009b. Paulot, F., Crounse, J. D., Kjaergaard, H. G., Kurten, A., St Clair, J. M., Seinfeld, J. H., and Wennberg, P. O.: Unexpected Epoxide Formation in the Gas-Phase Photooxidation of Isoprene, Science, 325, 730–733, 2009c. Paulson, S. E., Chung, M., Sen, A. D., and Orzechowska, G.: Measurement of OH radical formation from the reaction of ozone with several biogenic alkenes, J. Geophys. Res.-Atmos., 103, 25533–25539, 1998. Peeters, J., Nguyen, T. L., and Vereecken, L.: HO<sub>x</sub> radical regeneration in the oxidation of isoprene, Phys. Chem. Chem. Phys., 11, 5935–5939, 2009. Pérez, I. M., LaFranchi, B. W., and Cohen, R. C.: Nitrogen oxide chemistry in an urban plume: investigation of the chemistry of peroxy and multifunctional organic nitrates with a Lagrangian model, Atmos. Chem. Phys. Discuss., 9, 27099–27165, http://dx.doi.org/10.5194/acpd-9-27099-2009doi:10.5194/acpd-9-27099-2009, 2009. Perring, A. E., Bertram, T. H., Wooldridge, P. J., Fried, A., Heikes, B. G., Dibb, J., Crounse, J. D., Wennberg, P. O., Blake, N. J., Blake, D. R., Brune, W. H., Singh, H. B., and Cohen, R. C.: Airborne observations of total RONO2: new constraints on the yield and lifetime of isoprene nitrates, Atmos. Chem. Phys., 9, 1451–1463, http://dx.doi.org/10.5194/acp-9-1451-2009doi:10.5194/acp-9-1451-2009, 2009a. Perring, A. E., Wisthaler, A., Graus, M., Wooldridge, P. J., Lockwood, A. L., Mielke, L. H., Shepson, P. B., Hansel, A., and Cohen, R. C.: A product study of the isoprene+NO<sub>3</sub> reaction, Atmos. Chem. Phys., 9, 4945–4956, http://dx.doi.org/10.5194/acp-9-4945-2009doi:10.5194/acp-9-4945-2009, 2009b. Pryor, S. C. and Klemm, O.: Experimentally derived estimates of nitric acid dry deposition velocity and viscous sub-layer resistance at a conifer forest, Atmos. Environ., 38, 2769–2777, 2004. Qi, B., Takami, A., and Hatakeyama, S.: Peroxy radical concentrations measured at a forest canopy in Nikko, Japan, in summer 2002, J. Atmos. Chem., 52, 63–79, 2005. Raivonen, M., Bonn, B., Sanz, M. J., Vesala, T., Kulmala, M., and Hari, P.: UV-induced NOy emissions from Scots pine: Could they originate from photolysis of deposited HNO<sub>3</sub>?, Atmos. Environ., 40, 6201–6213, 2006. Raupach, M. R.: A practical Lagrangian method for relating scalar concentrations to source distributions in vegetation canopies, Q. J. Roy. Meteorol. Soc., 115, 609–632, 1989. Ren, X. R., Olson, J. R., Crawford, J. H., Brune, W. H., Mao, J. Q., Long, R. B., Chen, Z., Chen, G., Avery, M. A., Sachse, G. W., Barrick, J. D., Diskin, G. S., Huey, L. G., Fried, A., Cohen, R. C., Heikes, B., Wennberg, P. O., Singh, H. B., Blake, D. R., and Shetter, R. E.: HO<sub>x</sub> chemistry during INTEX-A 2004: Observation, model calculation, and comparison with previous studies, J. Geophys. Res.-Atmos., 113, D05310, doi:10.1029/2003JD003551, 2008. Ren, X., Gao, H., Zhou, X., Crounse, J. D., Wennberg, P. O., Browne, E. C., LaFranchi, B. W., Cohen, R. C., McKay, M., Goldstein, A. H., and Mao, J.: Measurement of atmospheric nitrous acid at Bodgett Forest during BEARPEX2007, Atmos. Chem. Phys., 10, 6283–6294, http://dx.doi.org/10.5194/acp-10-6283-2010doi:10.5194/acp-10-6283-2010, 2010. Rollins, A. W., Kiendler-Scharr, A., Fry, J. L., Brauers, T., Brown, S. S., Dorn, H.-P., Dubé, W. P., Fuchs, H., Mensah, A., Mentel, T. F., Rohrer, F., Tillmann, R., Wegener, R., Wooldridge, P. J., and Cohen, R. C.: Isoprene oxidation by nitrate radical: alkyl nitrate and secondary organic aerosol yields, Atmos. Chem. Phys., 9, 6685–6703, http://dx.doi.org/10.5194/acp-9-6685-2009doi:10.5194/acp-9-6685-2009, 2009. Rondon, A., Johansson, C., and Granat, L.: Dry Deposition Of Nitrogen-Dioxide And Ozone To Coniferous Forests, J. Geophys. Res.-Atmos., 98, 5159–5172, 1993. Rummel, U., Ammann, C., Kirkman, G. A., Moura, M. A. L., Foken, T., Andreae, M. O., and Meixner, F. X.: Seasonal variation of ozone deposition to a tropical rain forest in southwest Amazonia, Atmos. Chem. Phys., 7, 5415–5435, http://dx.doi.org/10.5194/acp-7-5415-2007doi:10.5194/acp-7-5415-2007, 2007. Schade, G. W. and Goldstein, A. H.: Plant physiological influences on the fluxes of oxygenated volatile organic compounds from ponderosa pine trees, J. Geophys. Res.-Atmos., 107, 4082–4091, 2002. Schade, G. W., Goldstein, A. H., Gray, D. W., and Lerdau, M. T.: Canopy and leaf level 2-methyl-3-buten-2-ol fluxes from a ponderosa pine plantation, Atmos. Environ., 34, 3535–3544, 2000. Seinfeld, J. H. and Pandis, S. N.: Atmospheric Chemistry and Physics, 2nd ed., John Wiley and Sons, Inc., Hoboken, NJ, 2006. Sievering, H., Kelly, T., McConville, G., Seibold, C., and Turnipseed, A.: Nitric acid dry deposition to conifer forests: Niwot Ridge spruce-fir-pine study, Atmos. Environ., 35, 3851–3859, 2001. Sitch, S., Cox, P. M., Collins, W. J., and Huntingford, C.: Indirect radiative forcing of climate change through ozone effects on the land-carbon sink, Nature, 448, 791–794, 2007. Sparks, J. P., Walker, J., Turnipseed, A., and Guenther, A.: Dry nitrogen deposition estimates over a forest experiencing free air CO<sub>2</sub> enrichment, Glob. Change Biol., 14, 768–781, 2008. Stavrakou, T., Peeters, J., and Müller, J.-F.: Improved global modelling of HO<sub>x</sub> recycling in isoprene oxidation: evaluation against the GABRIEL and INTEX-A aircraft campaign measurements, Atmos. Chem. Phys., 10, 9863–9878, http://dx.doi.org/10.5194/acp-10-9863-2010doi:10.5194/acp-10-9863-2010, 2010. Steiner, A. L., Tonse, S., Cohen, R. C., Goldstein, A. H., and Harley, R. A.: Influence of future climate and emissions on regional air quality in California, J. Geophys. Res.-Atmos., 111, D18303, doi:10.1029/2007GL030802, 2006. Steiner, A. L., Tonse, S., Cohen, R. C., Goldstein, A. H., and Harley, R. A.: Biogenic 2-methyl-3-buten-2-ol increases regional ozone and HO<sub>x</sub> sources, Geophys. Res. Lett., 34, L15806, http://dx.doi.org/10.1029/2007GL030802doi:10.1029/2007GL030802, 2007. Stroud, C., Makar, P., Karl, T., Guenther, A., Geron, C., Turnipseed, A. A., Nemitz, E., Baker, B., Potosnak, M., and Fuentes, J. D.: Role of canopy-scale photochemistry in modifying biogenic-atmosphere exchange of reactive terpenoid species: Results from the CELTIC field study, J. Geophys. Res., 110, D17303, http://dx.doi.org/10.1029/2005JD005775doi:10.1029/2005JD005775, 2005. Tan, D., Faloona, I., Simpas, J. B., Brune, W., Shepson, P. B., Couch, T. L., Sumner, A. L., Carroll, M. A., Thornberry, T., Apel, E., Riemer, D., and Stockwell, W.: HO<sub>x</sub> budgets in a deciduous forest: Results from the PROPHET summer 1998 campaign, J. Geophys. Res.-Atmos., 106, 24407–24427, 2001. Thomas, R. Q., Canham, C. D., Weathers, K. C., and Goodale, C. L.: Increased tree carbon storage in response to nitrogen deposition in the US, Nature Geoscience, 3, 13–17, http://dx.doi.org/10.1038/ngeo721doi:10.1038/ngeo721, 2010. Thornton, J. A., Wooldridge, P. J., Cohen, R. C., Martinez, M., Harder, H., Brune, W. H., Williams, E. J., Roberts, J. M., Fehsenfeld, F. C., Hall, S. R., Shetter, R. E., Wert, B. P., and Fried, A.: Ozone production rates as a function of NOx abundances and HO<sub>x</sub> production rates in the Nashville urban plume, J. Geophys. Res., 107, 4146–4163, http://dx.doi.org/10.1029/2001JD000932doi:10.1029/2001JD000932, 2002. Turnipseed, A. A., Huey, L. G., Nemitz, E., Stickel, R., Higgs, J., Tanner, D. J., Slusher, D. L., Sparks, J. P., Flocke, F., and Guenther, A.: Eddy covariance fluxes of peroxyacetyl nitrates (PANs) and NO<sub>y</sub> to a coniferous forest, J. Geophys. Res., 111, D09304, http://dx.doi.org/10.1029/2005JD006631doi:10.1029/2005JD006631, 2006. Walton, S., Gallagher, M. W., and Duyzer, J. H.: Use of a detailed model to study the exchange of NO<sub>x</sub> and O-3 above and below a deciduous canopy, Atmos. Environ., 31, 2915–2931, 1997. Wesely, M. L.: Parameterization of surface resistances to gaseous dry deposition in regional-scale numerical models, Atmos. Environ., 23, 1293–1304, 1989. Wesely, M. L. and Hicks, B. B.: A review of the current status of knowledge on dry deposition, Atmos. Environ., 34, 2261–2282, 2000. Williams, E. J., Guenther, A., and Fehsenfeld, F. C.: An inventory of nitric oxide emissions from soils in the united states, J. Geophys. Res., 97, 7511–7519, 1992. Wolfe, G. M. and Thornton, J. A.: The Chemistry of Atmosphere-Forest Exchange (CAFE) Model – Part 1: Model description and characterization, Atmos. Chem. Phys., 11, 77–101, http://dx.doi.org/10.5194/acp-11-77-2011doi:10.5194/acp-11-77-2011, 2011. Wolfe, G. M., Thornton, J. A., Yatavelli, R. L. N., McKay, M., Goldstein, A. H., LaFranchi, B., Min, K.-E., and Cohen, R. C.: Eddy covariance fluxes of acyl peroxy nitrates (PAN, PPN and MPAN) above a Ponderosa pine forest, Atmos. Chem. Phys., 9, 615–634, http://dx.doi.org/10.5194/acp-9-615-2009doi:10.5194/acp-9-615-2009, 2009. Wooldridge, P. J., Perring, A. E., Bertram, T. H., Flocke, F. M., Roberts, J. M., Singh, H. B., Huey, L. G., Thornton, J. A., Wolfe, G. M., Murphy, J. G., Fry, J. L., Rollins, A. W., LaFranchi, B. W., and Cohen, R. C.: Total Peroxy Nitrates (SPNs) in the atmosphere: the Thermal Dissociation-Laser Induced Fluorescence (TD-LIF) technique and comparisons to speciated PAN measurements, Atmos. Meas. Tech., 3, 593–607, http://dx.doi.org/10.5194/amt-3-593-2010doi:10.5194/amt-3-593-2010, 2010. Yienger, J. J. and Levy, H.: Empirical-Model Of Global Soil-Biogenic Nox Emissions, J. Geophys. Res.-Atmos., 100, 11447–11464, 1995. Zhang, L., Brook, J. R., and Vet, R.: A revised parameterization for gaseous dry deposition in air-quality models, Atmos. Chem. Phys., 3, 2067–2082, http://dx.doi.org/10.5194/acp-3-2067-2003doi:10.5194/acp-3-2067-2003, 2003. Zhang, L. M., Moran, M. D., Makar, P. A., Brook, J. R., and Gong, S. L.: Modelling gaseous dry deposition in AURAMS: a unified regional air-quality modelling system, Atmos. Environ., 36, 537–560, 2002. Zhou, X. L., Gao, H. L., He, Y., Huang, G., Bertman, S. B., Civerolo, K., and Schwab, J.: Nitric acid photolysis on surfaces in low-NOx environments: Significant atmospheric implications, Geophys. Res. Lett., 30, 2217, doi:10.1029/2003GL018620, 2003.