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3.6: Biogeochemical reactions in the troposphere

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    Dec 27, 2023
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The planetary boundary layer, PBL, is the initial recipient of substances from ground sources. Because of the dynamic character of the atmosphere, material from the PBL will mix into the free troposphere and can be transported horizontally over great distances. Vertical transport across the PBL is significantly enhanced in the presence of deep convective cloud systems. These dynamic processes provide a transition from high mixing ratios of trace gases near source regions to low mixing ratios in the remote troposphere. These changes in mixing ratios result in changes in chemical reaction paths, thus justifying a chemical classification of the troposphere into the background troposphere, the source region, and a "transition" regime between the two. The troposphere is governed by heterogeneous chemistry far more so than the stratosphere. Heterogeneous processes of interest here involve scavenging of trace gases by aerosols, cloud and precipitation elements leading to aqueous phase chemical reactions and to temporary and permanent removal of material from the gas phase. They also include exchange of material with the earth's surface, such as dry deposition. Dry deposition is a major removal process for ozone, as well as for other gases of importance in tropospheric photochemistry (e.g., NO2 ).

The Chemistry of Ozone

Ozone is formed by the association reaction of ground state O atoms with O2 :
O(3P)+O2+M→O3+M
and is removed by photolysis
O3+hv→O(1D)+O2O3+hv→O(3P)+O2.
The metastable O(′D) is quenched by O2 and N2
O(1D)+M→O(3P)+M
though it can also react with H2O to form the hydroxyl radical HO
O(1D)+H2O→HO+HO
Nitric oxide reacts with ozone to form NO2
NO+O3→NO2+O2
with NO2 removed by photolysis
NO2+hv→O(3P)+NO
Ozone removed by (6) is reconstituted by (7) followed by (1). It is convenient, because of the cyclic nature of the chemistry, to define a family of species undergoing rapid reactions leading to formation or removal of ozone. We define this family, odd oxygen, as the sum of O3,O(1D),O(3P) and NO2.

Odd oxygen is conserved in reactions (1)-(4), (6) and (7). It is formed by reactions of NO with HO2, CH3O2, and RO2.
HO2+NO→HO+NO2
CH3O2+NO→CH3O+NO2RO2+NO−RO+NO2
The species RO2 represents a variety of complex organic peroxy radicals. These reactions occur during the photooxidation of CO,CH4 and hydrocarbons, for example by
HO+CO+O2→HO2+CO2HO2+NO→NO2+HONO2+hv→NO+OO+O2+M→O3+MNET:CO+2O2→CO2+O3
and by
HO+CH4→CH3+H2OCH3+O2+M→CH3O2+MCH3O2+NO→CH3O+NO2CH3O+O2→CH2O+HO2HO2+NO→NO2+HO2×(NO2+hv→NO+O(3P))λ<420 nm2×(O(3P)+O2+M→O3+M)NET:CH4+4O2→CH2O+H2O+2O3
Odd oxygen is removed by reaction of O(1D) with H2O, by reaction of O3 with HO2 and HO,
HO2+O3→OH+2O2HO+O3→HO2+O2
by formation of nitric acid from NO2,
HO+NO2+M→HNO3
and by heterogeneous reactions of O3 and NO2 at the earth's surface.

Oxidation of CO,CH4 and hydrocarbons leads to net production of odd oxygen in the presence of adequate NOx. The rate for production of ozone is roughly proportional to the concentration of NO, while the rate of loss is almost independent of NOx(NO+NO2) for concentrations below 200 ppt (Fishman et al., 1979). Loss of odd oxygen, primarily by reactions (5) and (11) is balanced by production in reactions (8) and (9) for concentrations of NO near 30 ppt (Fishman et al., 1979; Logan et al., 1981; Crutzen, 1983). Hence, regions of the globe characterized by extremely low concentrations of NO, such as the remote Pacific, are likely to provide a net photochemical sink for odd oxygen (Liu et al., 1983), while the continental boundary layer at midlatitudes, characterized by higher concentrations of NO, is likely to provide a net source. Measurements of NOx in the troposphere are few, and the lack of data for NOx contributes significantly to uncertainties in global estimates for the photochemical source of ozone.
Production of ozone in the troposphere is limited ultimately by supply of CO,CH4, and hydrocarbons, if NOx is available. One molecule of ozone may be formed for each molecule of CO (Crutzen, 1973b), while the yield of ozone from oxidation of CH4 could be as large as 3.5 (e.g., Logan et al., 1981). Production of ozone from nonmethane hydrocarbons is discussed in more detail later in this chapter.

The Chemistry of HO

Reaction with HO in the troposphere is the primary removal mechanism for many trace gases which influence the chemical composition and radiative balance of the stratosphere. Consequently, tropospheric and stratospheric chemistry are inextricably linked through the HO radical.

The hydroxyl radical is formed by reaction (2) followed by (5). It is removed by reaction with carbon monoxide and methane,
HO+CO+O2→HO2+CO2HO+CH4+O2→CH3O2+H2O
with reaction (14) dominant over (15). HO2 is removed by reaction (8), and (16)
HO2+O3→HO+2O2
leading to regeneration of HO, or by
HO2+HO2→H2O2+O2
Hydrogen peroxide is photolysed,
H2O2+hv→HO+HO
it can react with HO,
HO+H2O2→H2O+HO2
or may be removed by heterogeneous processes such as precipitation scavenging, as discussed below.
H2O2+ rain → removal. 

It is convenient, because of the fairly rapid interconversion of H,HO,HO2 and H2O2 to consider these species as a family, odd hydrogen (=H+HO+HO2+2×H2O2). Reaction (5) provides the dominant source for odd hydrogen, while reactions (19) and (20) provide important sinks for odd hydrogen. Reactions (8), (14) and (16)-(18) do not influence the concentration of odd hydrogen.

Atmospheric oxidation of methane (Figure 2-1) may also provide sources and sinks for odd hydrogen, in addition to providing a source for odd oxygen. CH3O2, formed in (15), is removed primarily by reaction with NO or HO2.
CH3O2+NO→CH3O+NO2CH3O2+HO2→CH3OOH+O2
Subsequent reaction of methyl hydroperoxide with HO leads to loss of odd hydrogen.
CH3OOH+HO→CH3O2+H2O
HO2+HO→H2O+O2.
Recent measurements of a relatively fast rate for reaction (22) (Niki et al., 1983) indicate that this reaction may provide an important sink for odd hydrogen at low concentrations of NOx (Logan, 1985, private communication).

The net source of odd hydrogen is determined first by competition between reaction (9) and reaction (21), and second by competition between reactions (22)-(23) which remove odd hydrogen,
CH3OOH+ rain → removal 
and reaction (24)
CH3OOH+hv→CH3O+HO
which recycles odd hydrogen. Reaction of the methoxy radical with oxygen yields formaldehyde.
CH3O+O2→CH2O+HO2
Photolysis of CH2O
CH2O+hv→H+HCOCH2O+hv→H2+CO
via path (26a) provides an important source for odd hydrogen in the upper troposphere, while path (26b) and reaction of HO with CH2O have no net effect on odd hydrogen.

The major pathways in the methane oxidation chain are thought to be understood fairly well. Recent kinetic data for some of the intermediate species have changed the net effect of the cycle on the budget of odd hydrogen. It should be emphasized that the influence of CH4 chemistry on the budgets of both odd hydrogen and odd oxygen depends critically on ambient concentrations of NOx, because of competition between reactions (9) and (21). A discussion of the chemistry of HO and associated uncertainties may be found in Chameides and Tan (1981), Logan et al. (1981) and NRC (1984). Logan et al. (1981) present a detailed discussion of the potential influence of CH4 chemistry on odd hydrogen.

The Chemistry of Oxides of Nitrogen

Nitrogen oxides act as catalysts in the photochemical production of ozone. Any reaction which converts NO to NO2, other than the reaction of NO with ozone, provides a photochemical source of ozone. Present measurements of NOx are inadequate for definition of its distribution. Preliminary data indicate that ambient concentrations are highly variable in space and time, as discussed in Chapter 3. The lack of data for NOx precludes accurate quantification of the net global chemical source for ozone.

Nitrogen oxides are produced in the troposphere primarily in the form of NO. Nitric oxide and nitrogen dioxide are rapidly interconverted by reactions (6), (7), (8) and (9) on a time scale of minutes. Nitrogen oxides are removed from the atmosphere by conversion to nitric acid,
HO+NO2+M→HNO3
followed by heterogeneous processes, i.e., rainout or surface deposition of HNO3. Surface deposition of NO2 could provide another important tropospheric sink. There have been few field studies of the rate of uptake of NOx by surfaces, as discussed later in this chapter, and removal rates of NOx are not well defined at present.

Current models suggest that NOx is converted to HNO3 by reaction (13) within 1-2 days in summer. Nitric acid may be converted to aerosol nitrate, for example by reaction with sea-salt aerosol (Savoie and Prospero, 1982) or by reaction with ammonia (Tang, 1980). Nitric acid and aerosol nitrate are likely to be removed from the atmosphere by precipitation and surface deposition, with mean lifetimes of a few days (Junge, 1963; Levine and Schwartz, 1982). Nitric acid is converted back to NOx by reactions (20) and (21) more slowly, with a time scale of 2-4 weeks.
HNO3+HO→H2O+NO3HNO3+hv→HO+NO2
These processes are significant primarily in the upper troposphere.
Nitric oxide and NO2 may be converted to HNO2,HO2NO2,NO3, N2O5 and organic nitrates in addition to HNO3. Most of these molecules decompose thermally or photolytically and therefore provide temporary reservoirs for NOx. Peroxynitric acid is formed by reaction of HO2 with NO2
HO2+NO2+M→HO2NO2+M.
It decomposes rapidly in the lower troposphere,
HO2NO2→HO2+NO2

but it is thermally stable in the colder upper troposphere, where it is removed by photolysis and by reaction with HO. Current models suggest that a significant fraction of acidic nitrate may be present in the form of HO2NO2 in the upper troposphere, but there are no observational data at present.

Peroxyacetyl nitrate (PAN) is formed during the degradation of hydrocarbons (see below). PAN is more stable than HO2NO2 with respect to thermal decomposition, with a lifetime of about a day at 275∘K and several years at temperatures characteristic of the upper troposphere (Cox and Coffey, 1977; Hendry and Kenley, 1979). Recent kinetic data indicate that the lifetime of PAN towards photolysis is about four months (Senum et al., 1984), with a similar value for attack by HO (Wallington et al., 1984). Recent measurements of PAN show that it is an important reservoir for NOx in clean marine air (Singh and Salas, 1983a, b) and in rural air in North America (Bottenheim et al., 1984; Spicer et al., 1983) and in Europe (Brice et al., 1984).
The nitrate radical (NO3) is formed by
NO2+O3→NO3+O2
and is photolysed rapidly during the day. At night a steady state should be established between NO3 and N2O5.
NO3+NO2+M⇆NO2O5+M.
The nitrate radical has been observed in a variety of "clean-air" locations including Hawaii and rural Colorado. In most cases the concentration of NO3 at a given level of NO2 was lower than predicted by model calculations (Noxon et al., 1980; Platt et al., 1980b, 1981, 1984; Platt and Perner, 1980; Noxon, 1983). Some processes, as yet unidentified, appear to be removing NO3 and/or N2O5 from the atmosphere at night. If these processes lead to removal of NOx, then nighttime removal of NOx by reactions involving NO3 could be comparable to daytime by reaction (13). Platt et al. (1981,1984) speculate that reactions of NO3, or more likely N2O5, on wet aerosols may account for rapid removal of NO3 under conditions of high humidity, and may provide another sink for NOx in clouds and fog. A detailed discussion of NO3 scavenging by cloud droplets, and its possible conversion to NO−3by chemical reactions in the liquid phase is given in the section on heterogeneous chemistry. The rate of the homogeneous gas-phase reaction between N2O5 and water vapor,
N2O5+H2O→HNO3+HNO3
is extremely slow, but this reaction could provide an important source for HNO3 if it proceeds at the upper limit (k<1.3×10−21 cm3 molecule −1sec−1) given by Tuazon et al. (1983). The role of (33) in nighttime chemistry will remain uncertain until its rate constant is better defined.

CHEMISTRY OF OZONE FORMATION IN THE POLLUTED TROPOSPHERE

The discussion on clean tropospheric chemistry indicated that the oxidation of CO,CH4, and possibly other biogenic hydrocarbons leads to a net production of odd oxygen, if sufficient NOx is present (i.e., NOx>30ppt ). In the polluted troposphere, unlike the clean troposphere, the rate of ozone formation is not necessarily proportional to the concentration of NOx, but varies in a complex way that is dependent upon the ratios and concentrations of the hydrocarbons and NOx as well as the chemical composition of the hydrocarbons themselves. The chemistry of ozone in the polluted troposphere has been studied for over thirty years. The research emphasis has been predominantly in elucidating the processes for oxidant/ozone formation in urban areas. The focus of interest in urban areas is due mainly to the high emission densities of ozone precursors (hydrocarbons and NOx ) which result typically in very high ozone concentrations under summertime meteorological conditions. In many cases the concentration levels of ozone in urban areas exceed ambient air quality standards which have been set to protect public health and welfare.
Several reviews of the chemistry of polluted atmospheres are available (Leighton, 1961; Stern, 1977; Seinfeld, 1975; Heiklen, 1976), as are detailed discussions of reaction mechanisms (Demerjian et al., 1974; Carter et al., 1979; Baldwin et al., 1977; Falls and Seinfeld, 1978; Whitten et al., 1980) and reaction rate constant reviews (Baulch et al., 1980; Demerjian et al., 1980; Baulch et al., 1982). The discussions which follows provides an overview of the chemistry of the polluted troposphere.

The chemistry that occurs in sunlight-irradiated polluted atmospheres involves the interaction of a host of chemical species. These include: hydrocarbons such as alkanes, alkenes, and aromatics; other organics such as aldehydes and ketones; nitric oxide (NO); nitrogen dioxide (NO2); ozone (O3); peroxyacetyl nitrate (PAN); nitric acid (HNO3); atomic oxygen (O3P) and its first electronic excited state O(1D); hydroxy radical (HO); hydroperoxyl radical (HO2); alkylperoxyl radicals (RO2); acylperoxyl radicals (R(O)O2); nitrogen trioxide (NO3); and dinitrogen pentoxide (N2O5).

This chemistry explains the rapid conversion of NO to NO2 observed in the ambient polluted atmosphere (Leighton, 1961; Altshuller and Bufalini, 1965; Demerjian et al., 1974). The key lies in a sequence of reactions involving the same free radical species thought to be important in the chemistry of the clean troposphere and a number of organic radicals derived from the host of more complex hydrocarbon and organic molecules present additionally in the polluted atmosphere.

The most important atmospheric reactions governing the decomposition of alkanes, alkenes, and aromatics involve their reaction with hydroxyl radical. Reaction sequences describing the pathways for their oxidation as a result of HO attack have been studied extensively (Demerjian et al., 1974; Carter et al., 1979; Niki, 1978; Falls and Seinfeld, 1978; Perry et al., 1977; Atkinson et al., 1985; Grosjean, 1984). In a very simplified form this may be represented as follows:
HO+ Hydrocarbon →R+H2O
The alkyl radical (R) produced as a result of the HO attack on the hydrocarbon reacts with an oxygen molecule to form an alkylperoxyl radical (RO2)
R+O2→RO2

The alkylperoxyl radical reacts with NO to form NO2 and an alkoxy radical (RO)
RO2+NO→RO+NO2
Hydrogen abstraction from the alkoxy radical by molecular oxygen will produce a hydroperoxyl radical (HO2) and a carbonyl compound (R(C=O)H) :
RO+O2→R(C=O)H+HO2
The aldehydes formed in the RO oxidation, or emitted as such from combustion sources, react with HO or photolyze, introducing another important source of radicals to the atmosphere.
R(C=O)H+HO→R(C=O)+H2OR(C=O)H+hν(λ<400 nm)→R+H(C=O)
The hydroperoxyl radical can then react with NO to form NO2 and another hydroxyl radical, which reenters the cycle.
HO2+NO→HO+NO2
Reactions (8) and (10) taken together provide an efficient mechanism for the rapid conversion of NO to NO2. This increase in the concentration of "odd oxygen" (previous section) results in an increase of ozone through the perturbation of the chemical steady state relationship (39) derived from the following reactions:
NO2+hν→NO+O(3P)O(3P)+O2+M→O3+MO3+NO→NO2+O2
The chemical steady state relationship (39) has been shown to be a valid approximation over a considerable range of atmospheric pollutant conditions (Stedman and Jackson, 1975; Calvert, 1976).
[O3]=J7[NO2]k6[NO]
Ratios of NO2 and NO emitted into the atmosphere by man's activities are typically less than one and would lead to very low ozone steady state concentrations under typical atmospheric solar irradiation conditions. The impact of reactions (8) and (10) is to drive the ratio of NO2 to NO up by oxidizing the NO to NO2, in direct competition with the ozone-nitric oxide reaction and thereby allowing ozone to build up in concentration.

Typical observations made in a polluted atmosphere of this phenomenon are shown in Figures 4-1a and b. The diurnal pattern begins with the emission of hydrocarbons, carbon monoxide and NOx from motor vehicles in the early morning. The NO is converted to NO2 and ozone accumulation begins when

most of the NO has been oxidized. The ozone concentration maximizes and then declines either as a result of reaction with additional emissions of NO through the day, dilution due to meteorology, or in the case of extended periods of time and transport, by interaction with the ground surface, which is a major sink for ozone in the atmosphere as will be discussed later in this chapter.

The interaction of organic free radicals produced by hydrocarbon oxidation with NO and NO2 represents an important aspect of the chemistry of the oxides of nitrogen in the polluted atmosphere. They represent key processes in the conversion of NO to NO2 and the formation of organic nitrates. It has recently been found that the more complex peroxyalkyl radicals formed during alkane photooxidation can add NO to form alkyl nitrates in non-negligible yields, in competition with reaction (10) (Atkinson et al., 1985):
RO2+NO→RONO2
Also the hydroperoxyl radical formed from hydrocarbon oxidation in reaction (36) supplements that formed in reactions (12) and (14) to create hydrogen peroxide via reaction (17), and aldehydes react with the hydroxy radical to produce peroxyacyl radicals and ultimately peroxyacyl nitrates by reaction with NO2
RCHO+OH→RCO+H2ORCO+O2→R(C=O)O2R(C=O)O2+NO2→R(C=O)O2NO2
A thermal equilibrium exists between the peroxyacyl nitrate and its components
R(C=O)O2NO2⇆R(C=O)O2+NO2
and the peroxyacyl radical is removed from the atmosphere by reaction with NO (Cox and Coffey 1977)
R(C=O)O2+NO→R(C=O)O+NO2
The most commonly occurring peroxyacyl nitrate is peroxyacetyl nitrate or PAN and there is a great similarity between the behavior of PAN and ozone in polluted atmospheres. Their diurnal variations at ground based sites are virtually identical on many occasions (Garland and Penkett 1976) primarily because their formation and removal mechanisms are very similar. PAN is thus an excellent tracer of the photochemical reactivity of the troposphere and since it has no large stratospheric source it can be used in studies designed to investigate the seasonal behavior of tropospheric photochemical activity (Brice et al., 1984).
4.2.2 Night-time Chemistry of the Source Region
The nitrate radical NO3 can be formed by reaction of NO2 with ozone
NO2+O3→NO3+O2
During the day NO3 is rapidly photolyzed back to its precursors but during the night an equilibrium with N2O5 can be established
NO3+NO2=N2O5

Night-time concentrations of NO3 as high as 355pptv have been recorded in the Los Angeles basin (Platt et al., 1980b, 1984). Some NO3 is converted to HNO3 by reactions with hydrocarbons and aldehydes,
NO3+RH→R+HNO3NO3+R(C=O)H→R(C=O)+HNO3
but in the absence of NO no chain reactions can be initiated by the peroxy radicals, which will be rapidly lost. The N2O5 which is formed will be stable until sunrise or it can be removed either by hydrolysis in deliquescent aerosols or by uptake on ground surfaces.

It is quite possible that heterogeneous chemistry is important in the overall NOx cycle particularly in the formation of nitrous acid, HONO, which can act as an efficient source of HO radicals in conditions of low light intensity, but this is an area where much more research is required before definite statements can be made.

Excerpted from:

V.A. Mohnen, W. Chameides K.L. Demerjian D. H. Lenschow J.A. Logan R.J. McNeal, S.A. Penkett, U. Platt, U. Schurath, P. da Silva Dias. Tropospheric Chemistry, in Atmospheric Ozone 1985: Assessment of Our Understanding of the Processes Controlling Its Present Distribution and Change, World Meteorological Organization. Accessed November 2023 at https://csl.noaa.gov/assessments/ozone/1985/report.html

3.6: Biogeochemical reactions in the troposphere is shared under a Public Domain license and was authored, remixed, and/or curated by NOAA Tropospheric Chemistry https://csl.noaa.gov/assessments/ozone/1985/vol1/chapter4.pdf.

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