ACP Atmospheric Chemistry and Physics ACP 1680-7324 Copernicus GmbH Göttingen, Germany 10.5194/acp-12-8829-2012 In-canopy gas-phase chemistry during CABINEX 2009: sensitivity of a 1-D canopy model to vertical mixing and isoprene chemistry Bryan A. M. 1 Bertman S. B. 2 Carroll M. A. 1 Dusanter S. 3 4 5 Edwards G. D. 6 Forkel R. 7 Griffith S. 8 Guenther A. B. 9 Hansen R. F. 8 Helmig D. 10 Jobson B. T. 11 Keutsch F. N. 12 Lefer B. L. 13 Pressley S. N. 11 Shepson P. B. 14 15 Stevens P. S. 8 Steiner A. L. 1 Department of Atmospheric, Oceanic, and Space Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, 49008, USA School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana, 47405, USA EMDouai, CE, 59508 Douai, France Univ Lille Nord de France, 59000, Lille, France Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, 48197, USA Karlsruhe Institute of Technology (KIT), IMK-IFU, 82467 Garmisch-Partenkirchen, Germany Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA Atmospheric Chemistry Division, National Center for Atmospheric Research, Boulder, Colorado, 80307, USA Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309, USA Department of Civil & Environmental Engineering, Washington State University, Pullman, Washington, 99164, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, USA Department of Earth and Atmospheric Sciences, University of Houston, Houston, Texas, 77004, USA Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA Department of Earth and Atmospheric Sciences, Purdue University, West Lafayette, Indiana, 47907, USA 28 09 2012 12 18 8829 8849 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/12/8829/2012/acp-12-8829-2012.html The full text article is available as a PDF file from http://www.atmos-chem-phys.net/12/8829/2012/acp-12-8829-2012.pdf

Vegetation emits large quantities of biogenic volatile organic compounds (BVOC). At remote sites, these compounds are the dominant precursors to ozone and secondary organic aerosol (SOA) production, yet current field studies show that atmospheric models have difficulty in capturing the observed HO<sub>x</sub> cycle and concentrations of BVOC oxidation products. In this manuscript, we simulate BVOC chemistry within a forest canopy using a one-dimensional canopy-chemistry model (Canopy Atmospheric CHemistry Emission model; CACHE) for a mixed deciduous forest in northern Michigan during the CABINEX 2009 campaign. We find that the base-case model, using fully-parameterized mixing and the simplified biogenic chemistry of the Regional Atmospheric Chemistry Model (RACM), underestimates daytime in-canopy vertical mixing by 50–70% and by an order of magnitude at night, leading to discrepancies in the diurnal evolution of HO<sub>x</sub>, BVOC, and BVOC oxidation products. Implementing observed micrometeorological data from above and within the canopy substantially improves the diurnal cycle of modeled BVOC, particularly at the end of the day, and also improves the observation-model agreement for some BVOC oxidation products and OH reactivity. We compare the RACM mechanism to a version that includes the Mainz isoprene mechanism (RACM-MIM) to test the model sensitivity to enhanced isoprene degradation. RACM-MIM simulates higher concentrations of both primary BVOC (isoprene and monoterpenes) and oxidation products (HCHO, MACR+MVK) compared with RACM simulations. Additionally, the revised mechanism alters the OH concentrations and increases HO<sub>2</sub>. These changes generally improve agreement with HO<sub>x</sub> observations yet overestimate BVOC oxidation products, indicating that this isoprene mechanism does not improve the representation of local chemistry at the site. Overall, the revised mechanism yields smaller changes in BVOC and BVOC oxidation product concentrations and gradients than improving the parameterization of vertical mixing with observations, suggesting that uncertainties in vertical mixing parameterizations are an important component in understanding observed BVOC chemistry.

 References Alaghmand, M., Shepson, P B., Starn, T K., Jobson, B T., Wallace, H W., Carroll, M A., Bertman, S B., Lamb, B., Edburg, S L., Zhou, X., Apel, E., Riemer, D., Stevens, P., and Keutsch, F.: The Morning NO$_\text x$ maximum in the forest atmosphere boundary layer, Atmos. Chem. Phys. Discuss., 11, 29251–29282, http://dx.doi.org/10.5194/acpd-11-29251-2011doi:10.5194/acpd-11-29251-2011, 2011. Apel, E C., Riemer, D D., Hills, A., Baugh, W., Orlando, J., Faloona, I., Tan, D., Brune, W., Lamb, B., Westberg, H., Carroll, M A., Thornberry, T., and Geron, C D.: Measurement and interpretation of isoprene fluxes and isoprene, methacrolein, and methyl vinyl ketone mixing ratios at the PROPHET site during the 1998 Intensive, J. Geophys. Res., 107, 4034, http://dx.doi.org/10.1029/2000JD000225doi:10.1029/2000JD000225, 2002. Asner, G P.: Biophysical and Biochemical Sources of Variability in Canopy Reflectance, Remote Sens. Environ., 64, 234–253, http://dx.doi.org/10.1016/S0034-4257(98)00014-5doi:10.1016/S0034-4257(98)00014-5, 1998. Baldocchi, D.: A multi-layer model for estimating sulfur dioxide deposition to a deciduous oak forest canopy, Atmos. Environ., 22, 869–884, http://dx.doi.org/10.1016/0004-6981(88)90264-8doi:10.1016/0004-6981(88)90264-8, 1988. Baldocchi, D., Falge, E., Gu, L., Olson, R., Hollinger, D., Running, S., Anthoni, P., Bernhofer, C., Davis, K., Evans, R., Fuentes, J., Goldstein, A., Katul, G., Law, B., Lee, X., Malhi, Y., Meyers, T., Munger, W., Oechel, W., Paw~U, K T., Pilegaard, K., Schmid, H P., Valentini, R., Verma, S., Vesala, T., Wilson, K., and Wofsyn, S.: FLUXNET: A New Tool to Study the Temporal and Spatial Variability of Ecosystem-Scale Carbon Dioxide, Water Vapor, and Energy Flux Densities, B. Am. Meteor. Soc., 82, 2415–2434, 2001. Barkley, M P., Palmer, P I., Ganzeveld, L., Arneth, A., Hagberg, D., Karl, T., Guenther, A., Paulot, F., Wennberg, P O., Mao, J., Kurosu, T P., Chance, K., Müller, J.-F., De~Smedt, I., Van~Roozendael, M., Chen, D., Wang, Y., and Yantosca, R M.: Can a "state of the art" chemistry transport model simulate Amazonian tropospheric chemistry?, J. Geophys. Res., 116, D16302, http://dx.doi.org/10.1029/2011JD015893doi:10.1029/2011JD015893, 2011. Blackadar, A K.: High-resolution models of the planetary boundary layer, in: Advances in Environmental Science and Engineering, 1, 50–85, Gordon and Breech Science Publishers, Inc., New York, USA, 1979. 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, 2009. Boy, M., Sogachev, A., Lauros, J., Zhou, L., Guenther, A., and Smolander, S.: SOSA – a new model to simulate the concentrations of organic vapours and sulphuric acid inside the ABL – Part 1: Model description and initial evaluation, Atmos. Chem. Phys., 11, 43–51, http://dx.doi.org/10.5194/acp-11-43-2011doi:10.5194/acp-11-43-2011, 2011. Butler, T M., Taraborrelli, D., Brühl, C., Fischer, H., Harder, H., Martinez, M., Williams, J., Lawrence, M G., and Lelieveld, J.: Improved simulation of isoprene oxidation chemistry with the ECHAM5/MESSy chemistry-climate model: lessons from the GABRIEL airborne field campaign, Atmos. Chem. Phys., 8, 4529–4546, http://dx.doi.org/10.5194/acp-8-4529-2008doi:10.5194/acp-8-4529-2008, 2008. Carlton, A G., Wiedinmyer, C., and Kroll, J H.: A review of Secondary Organic Aerosol (SOA) formation from isoprene, Atmos. Chem. Phys., 9, 4987–5005, http://dx.doi.org/10.5194/acp-9-4987-2009doi:10.5194/acp-9-4987-2009, 2009. Carroll, M A., Bertman, S B., and Shepson, P B.: Overview of the Program for Research on Oxidants: PHotochemistry, Emissions, and Transport (PROPHET) summer 1998 measurements intensive, J. Geophys. Res., 106, 24275–24288, 2001. Carslaw, N. and Carslaw, D.: The gas-phase chemistry of urban atmospheres, Surv. Geophys., 22, 31–53, 2001. Claeys, M., Graham, B., Vas, G., Wang, W., Vermeylen, R., Pashynska, V., Cafmeyer, J., Guyon, P., Andreae, M O., Artaxo, P., and Maenhaut, W.: Formation of Secondary Organic Aerosols Through Photooxidation of Isoprene, Science, 303, 1173–1176, http://dx.doi.org/10.1126/science.1092805doi:10.1126/science.1092805, 2004. Cooper, O R., Moody, J L., Thornberry, T D., Town, M S., and Carroll, M A.: PROPHET 1998 meteorological overview and air-mass classification, J. Geophys. Res., 106, 24289–24299, 2001. de~Gouw, J. and Warneke, C.: Measurements of volatile organic compounds in the Earth's atmosphere using proton-transfer-reaction mass spectrometry, Mass. Spectrom. Rev., 26, 223–257, 2007. Di~Carlo, P., Brune, W H., Martinez, M., Harder, H., Lesher, R., Ren, X., 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, http://dx.doi.org/10.1126/science.1094392doi:10.1126/science.1094392, 2004. Dusanter, S., Vimal, D., Stevens, P S., Volkamer, R., and Molina, L T.: Measurements of OH and HO<sub>2</sub> concentrations during the MCMA-2006 field campaign – Part 1: Deployment of the Indiana University laser-induced fluorescence instrument, Atmos. Chem. Phys., 9, 1665–1685, http://dx.doi.org/10.5194/acp-9-1665-2009doi:10.5194/acp-9-1665-2009, 2009. Faloona, I., Tan, D., Brune, W., Hurst, J., Barket, Dennis, J., 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., 106, 24315–24333, 2001. Finkelstein, P L., Ellestad, T G., Clarke, J F., Meyers, T P., Schwede, D B., Hebert, E O., and Neal, J A.: Ozone and sulfur dioxide dry deposition to forests: Observations and model evaluation, J. Geophys. Res., 105, 15365–15377, 2000. Finnigan, J.: Turbulence in Plant Canopies, Annu. Rev. Fluid Mech., 32, 519–571, http://dx.doi.org/10.1146/annurev.fluid.32.1.519doi:10.1146/annurev.fluid.32.1.519, 2000. Forkel, R., Seidl, W., Dlugi, R., and Deigele, E.: A One-Dimensional Numerical-Model to Simulate Formation and Balance of Sulfate during Radiation Fog Events, J. Geophys. Res., 95, 18501–18515, 1990. Forkel, R., Klemm, O., Graus, M., Rappenglück, 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, 28–42, http://dx.doi.org/10.1016/j.atmosenv.2005.11.070doi:10.1016/j.atmosenv.2005.11.070, 2006. Fuchs, H., Bohn, B., Hofzumahaus, A., Holland, F., Lu, K D., Nehr, S., Rohrer, F., and Wahner, A.: Detection of HO<sub>2</sub> by laser-induced fluorescence: calibration and interferences from RO<sub>2</sub> radicals, Atmos. Meas. Tech., 4, 1209–1225, http://dx.doi.org/10.5194/amt-4-1209-2011doi:10.5194/amt-4-1209-2011, 2011. Ganzeveld, L., Valverde-Canossa, J., Moortgat, G., and Steinbrecher, R.: Evaluation of peroxide exchanges over a coniferous forest in a single-column chemistry-climate model, Atmos. Environ., 40, 68–80, http://dx.doi.org/10.1016/j.atmosenv.2006.01.062doi:10.1016/j.atmosenv.2006.01.062, 2006. Ganzeveld, L., Eerdekens, G., Feig, G., Fischer, H., Harder, H., Königstedt, R., Kubistin, D., Martinez, M., Meixner, F X., Scheeren, H A., Sinha, V., Taraborrelli, D., Williams, J., Vilà-Guerau~de Arellano, J., and Lelieveld, J.: Surface and boundary layer exchanges of volatile organic compounds, nitrogen oxides and ozone during the GABRIEL campaign, Atmos. Chem. Phys., 8, 6223–6243, http://dx.doi.org/10.5194/acp-8-6223-2008doi:10.5194/acp-8-6223-2008, 2008. Ganzeveld, L N., Lelieveld, J., Dentener, F J., Krol, M C., Bouwman, A J., and Roelofs, G J.: Global soil-biogenic NO$_\text x$ emissions and the role of canopy processes, J. Geophys. Res., 107, 4298, http://dx.doi.org/10.1029/2001JD001289doi:10.1029/2001JD001289, 2002. Gao, W., Wesely, M L., and Doskey, P V.: Numerical Modeling of the Turbulent Diffusion and Chemistry of NO$_x$, O<sub>3</sub>, Isoprene, and Other Reactive Trace Gases in and Above a Forest Canopy, J. Geophys. Res., 98, 18339–18353, 1993. Geiger, H., Barnes, I., Bejan, I., Benter, T., and Spittler, M.: The tropospheric degradation of isoprene: an updated module for the regional atmospheric chemistry mechanism, Atmos. Environ., 37, 1503–1519, http://dx.doi.org/10.1016/S1352-2310(02)01047-6doi:10.1016/S1352-2310(02)01047-6, 2003. Goldstein, A H. and Galbally, I E.: Known and Unexplored Organic Constituents in the Earth's Atmosphere, Environ. Sci. Technol., 41, 1514–1521, http://dx.doi.org/10.1021/es072476pdoi:10.1021/es072476p, 2007. Guenther, A., Hewitt, C N., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P., Klinger, L., Lerdau, M., 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. Hallquist, M., Wenger, J C., Baltensperger, U., Rudich, Y., Simpson, D., Claeys, M., Dommen, J., Donahue, N M., George, C., Goldstein, A H., Hamilton, J F., Herrmann, H., Hoffmann, T., Iinuma, Y., Jang, M., Jenkin, M E., Jimenez, J L., Kiendler-Scharr, A., Maenhaut, W., McFiggans, G., Mentel, T F., Monod, A., Prévôt, A. S H., Seinfeld, J H., Surratt, J D., Szmigielski, R., and Wildt, J.: The formation, properties and impact of secondary organic aerosol: current and emerging issues, Atmos. Chem. Phys., 9, 5155–5236, http://dx.doi.org/10.5194/acp-9-5155-2009doi:10.5194/acp-9-5155-2009, 2009. Hanson, D T. and Sharkey, T D.: Rate of acclimation of the capacity for isoprene emission in response to light and temperature, Plant Cell. Environ., 24, 937–946, http://dx.doi.org/10.1046/j.1365-3040.2001.00745.xdoi:10.1046/j.1365-3040.2001.00745.x, 2001. Hari, P., Raivonen, M., Vesala, T., Munger, J W., Pilegaard, K., and Kulmala, M.: Atmospheric science: Ultraviolet light and leaf emission of NO$_\text x$, Nature, 422, p 134, 2003. Heus, T., van Heerwaarden, C C., Jonker, H. J J., Pier~Siebesma, A., Axelsen, S., van~den Dries, K., Geoffroy, O., Moene, A F., Pino, D., de~Roode, S R., and Vilà-Guerau~de Arellano, J.: Formulation of the Dutch Atmospheric Large-Eddy Simulation (DALES) and overview of its applications, Geosci. Model Dev., 3, 415–444, http://dx.doi.org/10.5194/gmd-3-415-2010doi:10.5194/gmd-3-415-2010, 2010. Hewitt, C N., Lee, J D., MacKenzie, A R., Barkley, M P., Carslaw, N., Carver, G D., Chappell, N A., Coe, H., Collier, C., Commane, R., Davies, F., Davison, B., DiCarlo, P., Di~Marco, C F., Dorsey, J R., Edwards, P M., Evans, M J., Fowler, D., Furneaux, K L., Gallagher, M., Guenther, A., Heard, D E., Helfter, C., Hopkins, J., Ingham, T., Irwin, M., Jones, C., Karunaharan, A., Langford, B., Lewis, A C., Lim, S F., MacDonald, S M., Mahajan, A S., Malpass, S., McFiggans, G., Mills, G., Misztal, P., Moller, S., Monks, P S., Nemitz, E., Nicolas-Perea, V., Oetjen, H., Oram, D E., Palmer, P I., Phillips, G J., Pike, R., Plane, J. M C., Pugh, T., Pyle, J A., Reeves, C E., Robinson, N H., Stewart, D., Stone, D., Whalley, L K., and Yin, X.: Overview: oxidant and particle photochemical processes above a south-east Asian tropical rainforest (the OP3 project): introduction, rationale, location characteristics and tools, Atmos. Chem. Phys., 10, 169–199, http://dx.doi.org/10.5194/acp-10-169-2010doi:10.5194/acp-10-169-2010, 2010. 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, http://dx.doi.org/10.1111/j.1600-0889.2007.00269.xdoi:10.1111/j.1600-0889.2007.00269.x, 2007. Huisman, A J., Hottle, J R., Galloway, M M., DiGangi, J P., Coens, K L., Choi, W., Faloona, I C., Gilman, J B., Kuster, W C., de~Gouw, J., Bouvier-Brown, N C., Goldstein, A H., LaFranchi, B W., Cohen, R C., Wolfe, G M., Thornton, J A., Docherty, K S., Farmer, D K., Cubison, M J., Jimenez, J L., Mao, J., Brune, W H., and Keutsch, F N.: Photochemical modeling of glyoxal at a rural site: observations and analysis from BEARPEX 2007, Atmos. Chem. Phys., 11, 8883–8897, http://dx.doi.org/10.5194/acp-11-8883-2011doi:10.5194/acp-11-8883-2011, 2011. Hurst, J M., Barket, Dennis~J., J., Herrera-Gomez, O., Couch, T L., Shepson, P B., Faloona, I., Tan, D., Brune, W., Westberg, H., Lamb, B., Biesenthal, T., Young, V., Goldstein, A., Munger, J W., Thornberry, T., and Carroll, M A.: Investigation of the nighttime decay of isoprene, J. Geophys. Res., 106, 24335–24346, 2001. Jarvis, P G.: The interpretation of the variations in leaf water potential and stomatal conductance found in canopies in the field, Philos. T. Roy. Soc. B, 273, 593–610, 1976. Jobson, B T. and McCoskey, J K.: Sample drying to improve HCHO measurements by PTR-MS instruments: laboratory and field measurements, Atmos. Chem. Phys., 10, 1821–1835, http://dx.doi.org/10.5194/acp-10-1821-2010doi:10.5194/acp-10-1821-2010, 2010. Karl, T., Potosnak, M., Guenther, A., Clark, D., Walker, J., Herrick, J D., and Geron, C.: Exchange processes of volatile organic compounds above a tropical rain forest: Implications for modeling tropospheric chemistry above dense vegetation, J. Geophys. Res., 109, D18306, http://dx.doi.org/10.1029/2004JD004738doi:10.1029/2004JD004738, 2004. Karl, T., Guenther, A., Turnipseed, A., Tyndall, G., Artaxo, P., and Martin, S.: Rapid formation of isoprene photo-oxidation products observed in Amazonia, Atmos. Chem. Phys., 9, 7753–7767, http://dx.doi.org/10.5194/acp-9-7753-2009doi:10.5194/acp-9-7753-2009, 2009. 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, http://dx.doi.org/10.1126/science.1192534doi:10.1126/science.1192534, 2010. Kim, S., Guenther, A., Karl, T., and Greenberg, J.: Contributions of primary and secondary biogenic VOC tototal OH reactivity during the CABINEX (Community Atmosphere-Biosphere INteractions Experiments)-09 field campaign, Atmos. Chem. Phys., 11, 8613–8623, http://dx.doi.org/10.5194/acp-11-8613-2011doi:10.5194/acp-11-8613-2011, 2011. Kim, S W., Barth, M C., and Trainer, M.: Influence of fair-weather cumulus clouds on isoprene chemistry, J. Geophys. Res., 117, D10302, http://dx.doi.org/10.1029/2011JD017099doi:10.1029/2011JD017099, 2012. Kovacs, T A. and Brune, W H.: Total OH Loss Rate Measurement, J. Atmos. Chem., 39, 105–122, http://dx.doi.org/10.1023/A:1010614113786doi:10.1023/A:1010614113786, 2001. Krol, M C., Molemaker, M J., and Vilà-Guerau~de Arellano, J.: Effects of turbulence and heterogeneous emissions on photochemically active species in the convective boundary layer, J. Geophys. Res., 105, 6871–6884, 2000. LADCO: Regional Network Assessment: States of Illinois, Indiana, Michigan, Minnesota, Ohio, and Wisconsin, Tech. rep., Lake Michigan Air Directors Consortium (LADCO), Des Plaines, IL, http://www.ladco.org/reports/general/Regional_Network_Assessment/Regional_Network_Assessment_Report_Version_5.0_May_27_2010.pdf, draft report, 27 May 2010. 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, 2008. Logan, J A.: Tropospheric Ozone: Seasonal Behavior, Trends, and Anthropogenic Influence, J. Geophys. Res., 90, 10463–10482, 1985. 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. Martin, R S., Westberg, H., Allwine, E., Ashman, L., Farmer, J C., and Lamb, B.: Measurement of isoprene and its atmospheric oxidation products in a central Pennsylvania deciduous forest, J. Atmos. Chem., 13, 1–32, http://dx.doi.org/10.1007/BF00048098doi:10.1007/BF00048098, 1991. Martin, S T., Andreae, M O., Althausen, D., Artaxo, P., Baars, H., Borrmann, S., Chen, Q., Farmer, D K., Guenther, A., Gunthe, S S., Jimenez, J L., Karl, T., Longo, K., Manzi, A., Müller, T., Pauliquevis, T., Petters, M D., Prenni, A J., Pöschl, U., Rizzo, L V., Schneider, J., Smith, J N., Swietlicki, E., Tota, J., Wang, J., Wiedensohler, A., and Zorn, S R.: An overview of the Amazonian Aerosol Characterization Experiment 2008 (AMAZE-08), Atmos. Chem. Phys., 10, 11415–11438, http://dx.doi.org/10.5194/acp-10-11415-2010doi:10.5194/acp-10-11415-2010, 2010. Meyers, T P.: The sensitivity of modeled $SO_2$ fluxes and profiles to stomatal and boundary layer resistances, Water Air Soil Poll., 35, 261–278, http://dx.doi.org/10.1007/BF00290935doi:10.1007/BF00290935, 1987. Meyers, T P. and Baldocchi, D D.: A comparison of models for deriving dry deposition fluxes of O<sub>3</sub> and SO<sub>2</sub> to a forest canopy, Tellus B, 40B, 270–284, http://dx.doi.org/10.1111/j.1600-0889.1988.tb00297.xdoi:10.1111/j.1600-0889.1988.tb00297.x, 1988. Misztal, P K., Nemitz, E., Langford, B., Di~Marco, C F., Phillips, G J., Hewitt, C N., MacKenzie, A R., Owen, S M., Fowler, D., Heal, M R., and Cape, J N.: Direct ecosystem fluxes of volatile organic compounds from oil palms in South-East Asia, Atmos. Chem. Phys., 11, 8995–9017, http://dx.doi.org/10.5194/acp-11-8995-2011doi:10.5194/acp-11-8995-2011, 2011. Molemaker, M J. and Vilà-Guerau~de Arellano, J.: Control of Chemical Reactions by Convective Turbulence in the Boundary Layer, J. Atmos. Sci., 55, 568–579, 1998. Ortega, J. and Helmig, D.: Approaches for quantifying reactive and low-volatility biogenic organic compound emissions by vegetation enclosure techniques – Part A, Chemosphere, 72, 343–364, http://dx.doi.org/10.1016/j.chemosphere.2007.11.020doi:10.1016/j.chemosphere.2007.11.020, 2008. Ortega, J., Helmig, D., Guenther, A., Harley, P., Pressley, S., and Vogel, C.: Flux estimates and OH reaction potential of reactive biogenic volatile organic compounds (BVOCs) from a mixed northern hardwood forest, Atmos. Environ., 41, 5479–5495, http://dx.doi.org/10.1016/j.atmosenv.2006.12.033doi:10.1016/j.atmosenv.2006.12.033, 2007. Pang, X., Mu, Y., Zhang, Y., Lee, X., and Yuan, J.: Contribution of isoprene to formaldehyde and ozone formation based on its oxidation products measurement in Beijing, China, Atmos. Environ., 43, 2142–2147, http://dx.doi.org/10.1016/j.atmosenv.2009.01.022doi:10.1016/j.atmosenv.2009.01.022, 2009. Patton, E., Davis, K., Barth, M., and Sullivan, P.: Decaying Scalars Emitted By A Forest Canopy: A Numerical Study, Bound.-Lay. Meteor., 100, 91–129, http://dx.doi.org/10.1023/A:1019223515444doi:10.1023/A:1019223515444, 2001. 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, 2009. Peeters, J., Nguyen, T L., and Vereecken, L.: HO$_x$ radical regeneration in the oxidation of isoprene, Phys. Chem. Chem. Phys., 11, 5935–5939, http://dx.doi.org/10.1039/B908511-Ddoi:10.1039/B908511-D, 2009. Perterer, J. and Körner, C.: The problem of reference parameters in physiological-ecological research with conifer needles, Forstwissenschaftliches Centralblatt, 109, 220–241, 1990. Pétron, G., Harley, P., Greenberg, J., and Guenther, A.: Seasonal temperature variations influence isoprene emission, Geophys. Res. Lett., 28, 1707–1710, 2001. Poisson, N., Kanakidou, M., and Crutzen, P J.: Impact of Non-Methane Hydrocarbons on Tropospheric Chemistry and the Oxidizing Power of the Global Troposphere: 3-Dimensional Modelling Results, J. Atmos. Chem., 36, 157–230, http://dx.doi.org/10.1023/A:1006300616544doi:10.1023/A:1006300616544, 2000. Pöschl, U., von Kuhlmann, R., Poisson, N., and Crutzen, P J.: Development and Intercomparison of Condensed Isoprene Oxidation Mechanisms for Global Atmospheric Modeling, J. Atmos. Chem., 37, 29–52, http://dx.doi.org/10.1023/A:1006391009798doi:10.1023/A:1006391009798, 2000. Pratt, K A., Mielke, L H., Shepson, P B., Bryan, A M., Steiner, A L., Ortega, J., Daly, R., Helmig, D., Vogel, C S., Griffith, S., Dusanter, S., Stevens, P S., and Alaghmand, M.: A one-dimensional model study of individual reactive biogenic volatile organic compounds and their contributions to organic nitrates above a mixed forest, Atmos. Chem. Phys. Discuss., submitted, 2012. Pressley, S., Lamb, B., Westberg, H., Flaherty, J., Chen, J., and Vogel, C.: Long-term isoprene flux measurements above a northern hardwood forest, J. Geophys. Res., 110, D07301, http://dx.doi.org/10.1029/2004JD005523doi:10.1029/2004JD005523, 2005. Pugh, T. A M., MacKenzie, A R., Hewitt, C N., Langford, B., Edwards, P M., Furneaux, K L., Heard, D E., Hopkins, J R., Jones, C E., Karunaharan, A., Lee, J., Mills, G., Misztal, P., Moller, S., Monks, P S., and Whalley, L K.: Simulating atmospheric composition over a South-East Asian tropical rainforest: performance of a chemistry box model, Atmos. Chem. Phys., 10, 279–298, http://dx.doi.org/10.5194/acp-10-279-2010doi:10.5194/acp-10-279-2010, 2010. Raupach, M R.: A practical Lagrangian method for relating scalar concentrations to source distributions in vegetation canopies, Q. J. Roy. Meteor. Soc., 115, 609–632, http://dx.doi.org/10.1002/qj.49711548710doi:10.1002/qj.49711548710, 1989. Raupach, M R., Finnigan, J J., and Brunei, Y.: Coherent eddies and turbulence in vegetation canopies: The mixing-layer analogy, Bound.-Lay. Meteor., 78, 351–382, http://dx.doi.org/10.1007/BF00120941doi:10.1007/BF00120941, 1996. Schmid, H P., Su, H.-B., Vogel, C S., and Curtis, P S.: Ecosystem-atmosphere exchange of carbon dioxide over a mixed hardwood forest in northern lower Michigan, J. Geophys. Res., 108, 4417, http://dx.doi.org/10.1029/2002JD003011doi:10.1029/2002JD003011, 2003. Sillman, S., Carroll, M A., Thornberry, T., Lamb, B K., Westberg, H., Brune, W H., Faloona, I., Tan, D., Shepson, P B., Sumner, A L., Hastie, D R., Mihele, C M., Apel, E C., Riemer, D D., and Zika, R G.: Loss of isoprene and sources of nighttime OH radicals at a rural site in the United States: Results from photochemical models, J. Geophys. Res., 107, 4043, http://dx.doi.org/10.1029/2001JD000449doi:10.1029/2001JD000449, 2002. Simpson, D., Guenther, A., Hewitt, C N., and Steinbrecher, R.: Biogenic emissions in Europe 1. Estimates and uncertainties, J. Geophys. Res., 100, 22875–22890, 1995. Stavrakou, T., Peeters, J., and Müller, J.-F.: Improved global modelling of HO$_x$ 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. Steinbrecher, R., Hauff, K., Hakola, H., and Rössler, J.: A Revised Parametrisation for Emission Modelling of Isoprenoids for Boreal Plants, in: Biogenic VOC emissions and photochemistry in the boreal regions of Europe – Biphorep, edited by Laurila, T. and Lindfors, V., no 70 in Air pollution research report, pp. 29–43, Commission of the European Communities, EUR 18910 EN. EC, Brussels, 1999. Steiner, A L., Pressley, S N., Botros, A., Jones, E., Chung, S H., and Edburg, S L.: Analysis of coherent structures and atmosphere-canopy coupling strength during the CABINEX field campaign, Atmos. Chem. Phys., 11, 11921–11936, http://dx.doi.org/10.5194/acp-11-11921-2011doi:10.5194/acp-11-11921-2011, 2011. Stevens, P., Mather, J., and Brune, W.: Measurement of tropospheric OH and HO<sub>2</sub> by laser-induced fluorescence at low pressure, J. Geophys. Res., 99, 3543–3557, 1994. Stockwell, W R., Kirchner, F., Kuhn, M., and Seefeld, S.: A new mechanism for regional atmospheric chemistry modeling, J. Geophys. Res., 102, 25847–25879, 1997. Stroud, C., Makar, P., Karl, T., Guenther, A., Geron, C., Turnipseed, A., Nemitz, E., Baker, B., Potosnak, M., and Fuentes, J D.: Role of canopy-scale photochemistry in modifying biogenic-atmosphere exchange of reactive terpene species: Results from the CELTIC field study, J. Geophys. Res., 110, D17303, http://dx.doi.org/10.1029/2005JD005775doi:10.1029/2005JD005775, 2005. Stull, R B.: An Introduction to Boundary Layer Meteorology, p 382, Kluwer Academic Publishers, Dordrecht/Boston/London, 1988. Sumner, A L., Shepson, P B., Couch, T L., Thornberry, T., Carroll, M A., Sillman, S., Pippin, M., Bertman, S., Tan, D., Faloona, I., Brune, W., Young, V., Cooper, O., Moody, J., and Stockwell, W.: A study of formaldehyde chemistry above a forest canopy, J. Geophys. Res., 106, 24387–24405, 2001. 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$_x$ budgets in a deciduous forest: Results from the PROPHET summer 1998 campaign, J. Geophys. Res., 106, 24407–24427, 2001. Wesely, M L.: Parameterization of surface resistances to gaseous dry deposition in regional-scale numerical models, Atmos. Environ., 23, 1293–1304, http://dx.doi.org/10.1016/0004-6981(89)90153-4doi:10.1016/0004-6981(89)90153-4, 1989. 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., Bouvier-Brown, N C., Goldstein, A H., Park, J.-H., McKay, M., Matross, D M., Mao, J., Brune, W H., LaFranchi, B W., Browne, E C., Min, K.-E., Wooldridge, P J., Cohen, R C., Crounse, J D., Faloona, I C., Gilman, J B., Kuster, W C., de~Gouw, J A., Huisman, A., and Keutsch, F N.: The Chemistry of Atmosphere-Forest Exchange (CAFE) Model – Part 2: Application to BEARPEX-2007 observations, Atmos. Chem. Phys., 11, 1269–1294, http://dx.doi.org/10.5194/acp-11-1269-2011doi:10.5194/acp-11-1269-2011, 2011.