Atmospheric Chemistry and Physics Discussions www.atmos-chem-phys-discuss.net 1680-7367 1680-7375 9 5 2009 10.5194/acpd-9-19243-2009 http://www.atmos-chem-phys-discuss.net/9/19243/2009/ http://www.atmos-chem-phys-discuss.net/9/19243/2009/acpd-9-19243-2009.html http://www.atmos-chem-phys-discuss.net/9/19243/2009/acpd-9-19243-2009.pdf 19243 19278 2009-09-16 Simulating atmospheric composition over a South-East Asian tropical rainforest: Performance of a chemistry box model T. A. M. Pugh A. R. MacKenzie C. N. Hewitt B. Langford P. M. Edwards K. L. Furneaux D. E. Heard J. R. Hopkins C. E. Jones A. Karunaharan J. Lee G. Mills P. Misztal S. Moller P. S. Monks L. K. Whalley Lancaster Environment Centre, Lancaster University, Lancaster, UK School of Chemistry, University of Leeds, Leeds, UK National Centre for Atmospheric Science, University of York, York, UK Department of Chemistry, University of York, York, UK Department of Chemistry, University of Leicester, Leicester, UK School of Environmental Sciences, University of East Anglia, UK Centre for Ecology and Hydrology Edinburgh, UK School of Chemistry, The University of Edinburgh, UK Sadly passed away on 28 July 2009 Atmospheric composition and chemistry above tropical rainforests is currently not well established, particularly for south-east Asia. In order to examine our understanding of chemical processes in this region, the performance of a box model of atmospheric boundary layer chemistry is tested against measurements made at the top of the rainforest canopy near Danum Valley, Malaysian Borneo. Multi-variate optimisation against ambient concentration measurements was used to estimate average canopy-scale emissions for isoprene, total monoterpenes and nitric oxide. The excellent agreement between estimated values and measured fluxes of isoprene and total monoterpenes provides confidence in the overall modelling strategy, and suggests that this method may be applied where measured fluxes are not available. The largest contributors to the optimisation cost function at the point of best-fit are OH (41%), NO (18%) and total monoterpenes (16%). Several factors affect the modelled VOC chemistry. In particular concentrations of methacrolein (MACR) and methyl-vinyl ketone (MVK) are substantially overestimated, and the hydroxyl radical [OH] concentration is substantially underestimated; as has been seen before in tropical rainforest studies. It is shown that inclusion of dry deposition of MACR and MVK and wet deposition of species with high Henry's Law values substantially improves the fit of these oxidised species, whilst also substantially decreasing the OH sink. Increasing [OH] production arbitrarily, through a simple OH recycling mechanism, adversely affects the model fit for volatile organic compounds (VOCs). Given the constraints on isoprene flux provided by measurements, a substantial decrease in the rate of reaction of VOCs with OH is the only remaining option to explain the measurement/model discrepancy for OH. A reduction in the isoprene + OH rate constant of 50–70% is able to produce both isoprene and OH concentrations within error of those measured. Whilst we cannot rule out an important role for missing chemistry, particularly in areas of higher isoprene flux, this study demonstrates that the inadequacies apparent in box and global model studies of tropical VOC chemistry may be more strongly influenced by representation of detailed physical and micrometeorological effects than errors in the chemical scheme. Andreae, M. and Merlet, P.: Emissions of trace gases and aerosols from biomass burning, Global Biogeochem. Cy., 15, 955–966, 2001. Butler, T., Taraborrelli, D., Brühl, C., Fischer, H., Harder, H., Martinez, M., Williams, J., Lawrence, M., 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, 2008. Chappell, N., Bidin, K., and Tych, W.: Modelling rainfall and canopy controls on net-precipitation beneath selectively-logged forest, Plant Ecol., 153, 215–229, 2001. Cook, P., Savage, N., Turquety, S., Carver, G., O'Connor, F., Heckel, A., Stewart, D., Whalley, L., Parker, A., Schlager, H., Avery, H. S M., Sachse, G., Brune, W., Richter, A., Burrows, J., Purvis, R., Lewis, A., Reeves, C., Monks, P., Levine, J., and Pyle., J.: Forest fire plumes over the North Atlantic: p-TOMCAT model simulations with aircraft and satellite measurements from the ITOP/ICARTT campaign, J. Geophys. Res., 112, \doi0.1029/2006JD007563, 2007. Dillon, T. and Crowley, J.: Direct detection of OH formation in the reactions of \chemHO_2 with \chemCH_3C(O)O_2 and other substituted peroxy radicals, Atmos. Chem. Phys., 8, 4877–4889, 2008. Donovan, R., Hope, E., Owen, S., Mackenzie, A., and Hewitt, C.: Development and Application of an Urban Tree Air Quality Score for Photochemical Pollution Episodes Using the Birmingham, United Kingdom, Area as a Case Study, Environ. Sci. Technol., 39, 6730–6738, 2005. Emmerson, K., MacKenzie, A., Owen, S., Evans, M., and Shallcross, D.: A Lagrangian model with simple primary and secondary aerosol scheme 1: comparison with UK \chemPM_10 data, Atmos. Chem. Phys., 4, 2161–2170, 2004. Emmerson, K., Carslaw, N., Carslaw, D., Lee, J., McFiggans, G., Bloss, W., Gravestock, T., Heard, D., Hopkins, J., Ingham, T., Pilling, M., Smith, S., Jacob, M., and Monks, P.: Free radical modelling studies during the UK TORCH Campaign in Summer 2003, Atmos. Chem. Phys., 7, 167–181, 2007. Evans, M., Shallcross, D., Law, K., Wild, J., Simmonds, P., Spain, T., Berrisford, P., Methven, J., Lewis, A., McQuaid, J., Pilling, M., Bandy, B., Penkett, S., and Pyle, J.: Evaluation of a Lagrangian box model using field measurements from EASE (Eastern Atlantic Summer Experiment) 1996, Atmos. Environ., 34, 3843–3863, 2000. Fuentes, J., Lerdau, M., Atkinson, R., Baldocchi, D., Bottenheim, J., Ciccioli, P., Lamb, B., Geron, C., Gu, L., Guenther, A., Sharkey, T., and Stockwell, W.: Biogenic hydrocarbons in the atmospheric boundary layer: A review, B. Am. Meteor. Soc., 81, 1537–1575, 2000. Ganzeveld, L., Eerdekens, G., Feig, G., Fischer, H., Harder, H., Konigstedt, R., Kubistin, D., Martinez, M., Meixner, F X., Scheeren, H A., Sinha, V., Taraborrelli, D., Williams, J., de~Arellano, J. V.-G., 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, 2008. Gao, W. and Li, B.: Wavelet analysis of coherent structure at the atmosphere-forest interface, J. Appl. Meteorol., 32, 1717–1725, 1993. Geyer, A. and Stutz, J.: The vertical structure of OH-\chemHO_2-\chemRO_2 chemistry in the nocturnal boundary layer: A one-dimensional model study, J. Geophys. Res., 109, \doi10.1029/2003JD004425, 2004. Guenther, A., Hewitt, C., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P., Klinger, L., Lerdau, M., McKay, W., 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. Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P I., and Geron, C.: Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature), Atmos. Chem. Phys., 6, 3181–3210, 2006. Hasson, A., Tyndall, G., and Orlando, J.: A product yield study of the reaction of \chemHO_2 radicals with ethyl peroxy (\chemC_2H_5O_2), acetyl peroxy (\chemCH_3C(O)O_2), and acetonyl peroxy (\chemCH_3C(O)CH_2O_2) radicals, J. Phys. Chem. A, 108, 5979–5989, \doi10.1021/jp048873t, 2004. Hewitt, C. N., Lee, J., Barkley, M. P., Carslaw, N., Chappell, N. A., Coe, H., Collier, C., Commane, R., Davies, F., DiCarlo, P., Di Marco, C. F., 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., MacKenzie, A. R., 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., Palmer, P. I., Phillips, G. J., Plane, J. M. C., Pugh, T., Pyle, J. A., Reeves, C. E., Robinson, N. H., Stewart, D., Stone, D., and Whalley, L. K.: Oxidant and particle photochemical processes above a south-east Asian tropical rain forest (the OP3 project): introduction, rationale, location characteristics and tools, Atmos. Chem. Phys. Discuss., 9, 18899–18963, 2009. 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, \doi10.1126/science.1164566, 2009. 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., 112, \doi10.1029/2006JD007747, 2007. IUPAC: Evaluated kinetic data, prefixhttp://www.iupac-kinetic.ch.cam.ac.uk/, last access: 19th March 2009, 2009. Jenkin, M.: Chemical Mechanisms forming condensable material, Tech. Rep. AEA/RAMP/2001 0010/002, AEA, 1996. Jenkin, M E., Hurley, M D., and Wallington, T J.: Investigation of the radical product channel of the \chemCH_3C(O)O_2+\chemHO_2 reaction in the gas phase, Phys. Chem. Chem. Phys., 9, 3149–3162, \doi10.1039/b702757e, 2007. Karl, T., Potosnak, M., Guenther, A., Clark, D., Walker, J., Herrick, J., 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, \doi10.1029/2004JD004738, 2004. Karl, T., Guenther, A., Yokelson, R J., Greenberg, J., Potosnak, M., Blake, D R., and Artaxo, P.: The tropical forest and fire emissions experiment: Emission, chemistry, and transport of biogenic volatile organic compounds in the lower atmosphere over Amazonia, J. Geophys. Res., 112, \doi10.1029/2007JD008539, 2007. Krol, M., Molemaker, M., and 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. Kubistin, D., Harder, H., Martinez, M., Rudolf, M., Sander, R., Bozem, H., Eerdekens, G., Fischer, H., Gurk, C., Klüpfel, T., Königstedt, R., Parchatka, U., Schiller, C., Stickler, A., Taraborrelli, D., Williams, J., and Lelieveld, J.: Hydroxyl radicals in the tropical troposphere over the Suriname rainforest: comparison of measurements with the box model MECCA, Atmos. Chem. Phys. Discuss., 8, 15239–15289, 2008. Kuhn, U., Rottenberger, S., Biesenthal, T., Wolf, A., Schebeske, G., Ciccioli, P., Brancaleoni, E., Frattoni, M., Tavares, T., and Kesselmeier, J.: Seasonal differences in isoprene and light-dependent monoterpene emission by Amazonian tree species, Glob. Change Biol., 10, 663–682, \doi10.1111/j.1529-8817.2003.00771.x, 2004. Kuhn, U., Andreae, M O., Ammann, C., Araujo, A C., Brancaleoni, E., Ciccioli, P., Dindorf, T., Frattoni, M., Gatti, L V., Ganzeveld, L., Kruijt, B., Lelieveld, J., Lloyd, J., Meixner, F X., Nobre, A D., Poeschl, U., Spirig, C., Stefani, P., Thielmann, A., Valentini, R., and Kesselmeier, J.: Isoprene and monoterpene fluxes from Central Amazonian rainforest inferred from tower-based and airborne measurements, and implications on the atmospheric chemistry and the local carbon budget, Atmos. Chem. Phys., 7, 2855–2879, 2007. Langford, B., Davison, B., Nemitz, E., and Hewitt, C N.: Mixing ratios and eddy covariance flux measurements of volatile organic compounds from an urban canopy (Manchester, UK), Atmos. Chem. Phys., 9, 1971–1987, 2009. 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, \doi10.1038/nature06870, 2008. Müller, J.-F., Stavrakou, T., Wallens, S., De Smedt, I., Van Roozendael, M., Potosnak, M. J., Rinne, J., Munger, B., Goldstein, A., and Guenther, A. B.: Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model, Atmos. Chem. Phys., 8(5), 1329–1341, 2008. Ohara, T., Akimoto, H., Kurokawa, J., Horii, N., Yamaji, K., Yan, X., and Hayasaka, T.: An Asian emission inventory of anthropogenic emission sources for the period 1980-2020, Atmos. Chem. Phys., 7, 4419–4444, 2007. Pearson, G. and et al.: Remote sensing of the tropical rain forest boundary layer using pulsed Doppler lidar, in preparation for Atmos. Chem. Phys. Discuss., 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, \doi10.1039/b908511d, 2009. Pike, R. C., Lee, J. D., Young, P. J., Moller, S., Misztal, P., Langford, B., Yang, X., Carver, G., and Pyle, J. A.: Can a GCM mechanism reproduce NO, NO₂ and O₃ data above a tropical rainforest?, in preparation for Atmos. Chem. Phys. Discuss., 2009. Pinho, P., Pio, C., and Jenkin, M.: Evaluation of isoprene degradation in the detailed tropospheric chemical mechanism, MCM v3, using environmental chamber data, Atmos. Environ., 39, 1303–1322, \doi10.1016/j.atmosenv.2004.11.014, 2005. Poisson, N., Kanakidou, M., and Crutzen, P.: 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, 2000. Pugh, T. and et al.: Nocturnal profiles of NO_x and \chemO_3 over a South-East Asian rainforest, in preparation, 2009. Real, E., Law, K S., Schlager, H., Roiger, A., Huntrieser, H., Methven, J., Cain, M., Holloway, J., Neuman, J A., Ryerson, T., Flocke, F., de~Gouw, J., Atlas, E., Donnelly, S., and Parrish, D.: Lagrangian analysis of low altitude anthropogenic plume processing across the North Atlantic, Atmos. Chem. Phys., 8, 7737–7754, 2008. Sander, R.: Compilation of Henry's Law Constants for Inorganic and Organic Species of Potential Importance in Environmental Chemistry (Version 3), online available at: prefixhttp://www.henrys-law.org, 2009. Saunders, S., Jenkin, M., Derwent, R., and Pilling, M.: Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds, Atmos. Chem. Phys., 3, 161–180, 2003. Stockwell, W., Kirchner, F., Kuhn, M., and Seefeld, S.: A new mechanism for regional atmospheric chemistry modeling, J. Geophys. Res., 102, 25847–25879, 1997. Tan, D., Faloona, I., Simpas, J., Brune, W., Olson, J., Crawford, J., Avery, M., Sachse, G., Vay, S., Sandholm, S., Guan, H., Vaughn, T., Mastromarino, J., Heikes, B., Snow, J., Podolske, J., and Singh, H.: OH and \chemHO_2 in the tropical Pacific: Results from PEM-Tropics B, J. Geophys. Res., 106, 32667–32681, 2001. Taraborrelli, D., Lawrence, M G., Butler, T M., Sander, R., and Lelieveld, J.: Mainz Isoprene Mechanism 2 (MIM2): an isoprene oxidation mechanism for regional and global atmospheric modelling, Atmos. Chem. Phys., 9, 2751–2777, 2009. Turner, B., Leclerc, M., Gauthier, M., Moore, K., and Fitzjarrald, D.: Identification of turbulence structures above a forest canopy using a wavelet transform, J. Geophys. Res., 99, 1919–1926, 1994. van Dijk, S. and Duyzer, J.: Nitric oxide emissions from forest soils, J. Geophys. Res., 104, 15955–15961, 1999. Wild, O., Law, K., McKenna, D., Bandy, B., Penkett, S., and Pyle, J.: Photochemical trajectory modeling studies of the North Atlantic region during August 1993, J. Geophys. Res., 101, 29269–29288, 1996. WMO: Scientific assessment of ozone depletion: 1995 Global Ozone Research and Monitoring Project, Geneva, Switzerland, 1995. Yienger, J. and Levy, H.: Empirical model of global soil biogenic NO_x emissions, J. Geophys. Res., 100, 11447–11464, 1995. Zhang, L., Moran, M., Maker, P., Brook, J., and Gong, S.: Modelling gaseous dry deposition in AURAMS: a unified regional air-quality modelling system, Atmos. Environ., 36, 537–560, 2002.