Atmos. Chem. Phys., 5, 227 237, 2005
www.atmos-chem-phys.org/acp/5/227/
SRef-ID: 1680-7324/acp/2005-5-227
European Geosciences Union
Atmospheric
Chemistry
and Physics
Halogens and the chemistry of the free troposphere
D. J. Lary1,2
1Global Modelling and Assimilation Of ce, NASA Goddard Space Flight Center, Greenbelt, MD, USA
2GEST at the University of Maryland Baltimore County, Baltimore, MD, USA
Received: 20 August 2004 Published in Atmos. Chem. Phys. Discuss.: 16 September 2004
Revised: 12 November 2004 Accepted: 26 January 2005 Published: 27 January 2005
Abstract. The role of halogens in both the marine boundary
layer and the stratosphere has long been recognized, while
their role in the free troposphere is often not considered in
global chemical models. However, a careful examination of
free-tropospheric chemistry constrained by observations us-
ing a full chemical data assimilation system shows that halo-
gens do play a signi cant role in the free troposphere. In
particular, the chlorine initiation of methane oxidation in the
free troposphere can contribute more than 10%, and in some
regions up to 50%, of the total rate of initiation. The ini-
tiation of methane oxidation by chlorine is particularly im-
portant below the polar vortex and in northern mid-latitudes.
Likewise, the hydrolysis of BrONO2 alone can contribute
more than 35% of the HNO3 production rate in the free-
troposphere.
1 Introduction
Halogens play a variety of roles in atmospheric chemistry.
Most notable is their involvement in catalytic ozone loss and
the formation of the stratospheric ozone hole (Johnston and
Podolske, 1978; Cicerone et al., 1983; Farman et al., 1985).
Like OH, they are also involved in the initiation and catal-
ysis of hydrocarbon oxidation and consequently also play
a role in the partitioning of OH and HO2. Similarly they
are involved with the partitioning of NO and NO2. Some
of the same reactions involved in ozone hole chemistry also
lead to the production of nitric acid, namely the hydrolysis
of BrONO2 and ClONO2 on sulphate aerosols. These roles
are well known and accepted when stratospheric chemistry
is being discussed (DeMore et al., 2000). The role of halo-
gens is also important in the marine boundary layer (Vogt
et al., 1996; Sander and Crutzen, 1996; Richter et al., 1998;
Correspondence to: D. J. Lary
(David.Lary@umbc.edu)
Dickerson et al., 1999; Sander et al., 2003; von Glasow and
Crutzen, 2004; von Glasow et al., 2004). Hendricks et al.
(1999) presented box model calculations on the impact of
heterogeneous reactions of nitrogen, chlorine, and bromine
compounds on the chemistry of the mid-latitude tropopause
region. von Glasow et al. (2004) recently used observations
and a GCM to look at the role of BrO in the troposphere.
However, when the chemistry of the free troposphere is con-
sidered the role of chlorine is not normally considered im-
portant.
A chemical data assimilation analysis using a full Kalman
lter ( Fisher and Lary, 1995; Lary et al., 2003; Lary,
2003; Lary et al., 1995b; Lary, 1996) (http://gest.umbc.edu/
AutoChem/) starting in October 1991 and continuing till De-
cember 1998 reveals that halogens are also playing a signif-
icant role in the chemistry of the free troposphere. Compre-
hensive results from the analysis are also available online at
http://gest.umbc.edu/CDACentral/. Section 2 describes the
analysis system. Section 3 describes the observations used
and how they are handled. Section 4 describes our uncer-
tainty analysis. Section 5 describes the chemical Kalman l-
ter. Section 6 describes the results relevant to methane oxi-
dation. Section 7 describes the role of halogen compounds
in the production of nitric acid. Section 8 describes the role
of halogen compounds in the partitioning of OH and HO2.
Section 8 describes the role of halogen compounds in the
partitioning of NO and NO2. Section 10 resents the conclu-
sions.
2 Analysis System
This section describes the basic elements of the analy-
sis system infrastructure. A hyperlinked schematic of the
chemical assimilation system and automatic code generator
and documentor is available online at http://gest.umbc.edu/
AutoChem/Schematic.html.
' 2005 Author(s). This work is licensed under a Creative Commons License.

228 D. J. Lary: Halogens and free tropospheric chemistry
2.1 Automatic Code Generation
This study used AutoChem, an automatic code generator and
documenter for atmospheric chemistry. Given a set of reac-
tion databases and a user supplied list of required species it
will automatically select the reactions involving those con-
stituents. It then constructs the ordinary differential equation
(ODE) time derivatives, symbolically differentiates the time
derivatives to give the Jacobian, and symbolically differenti-
ates the Jacobian to give the Hessian. It also documents the
whole process in a set of LaTeX and PDF les.
The subset of reactions involving the user speci ed con-
stituents is extracted by the rst AutoChem preprocessor pro-
gram called Pick. This subset of reactions is then used by
the second AutoChem preprocessor program RoC (rate of
change) to generate the time derivatives, Jacobian, and Hes-
sian. Once the two preprocessor programs have been run
all the Fortran90 code has been generated that is necessary
for modelling and assimilating the kinetic processes. An on-
line manual of AutoChem is available at http://gest.umbc.
edu/AutoChem/.
2.2 Radiative Transfer Calculation of Photolysis Rates
A key part of the chemical model is the calculation of photol-
ysis rates. In this study they are calculated using full spheri-
cal geometry and multiple scattering (Anderson, 1983; Lary
and Pyle, 1991a,b; Meier et al., 1982; Nicolet et al., 1982)
corrected after Becker et al. (2000). The photolysis rate
used for each time step is obtained by ten point Gaussian-
Legendre integration of the photolysis rate over the time step
(Press et al., 1992). The photolysis rates are looked up in
a photolysis rate tabulation which is updated every day for
each latitude band to ensure that the current ozone and tem-
perature pro les are used to calculate the photolysis rates.
A total of 203 wavelength intervals are used from 116.7 to
850 nm (WMO, 1986). Daily solar irradiances are used for
each of the 203 wavelength intervals. The surface albedo
used for each latitude band is the median albedo observed by
TOMS for that month.
2.3 Flow-Tracking Coordinates
Because a major component of the variability of trace gases
is due to the atmospheric motions it makes sense to use a co-
ordinate system that ‘moves’ with the large scale ow pat-
tern to perform our analyses. In this study Lagrangian ow-
tracking coordinates are used.
Under adiabatic conditions air parcels move along isen-
tropic surfaces (surfaces of constant potential temperature,
θ ). So when considering tracer elds θ is a suitable vertical
coordinate, since it acknowledges the likely vertical motion
of air parcels. McIntyre and Palmer (1983, 1984); Hoskins
et al. (1985), and Hoskins (1991) have shown the value of
isentropic maps of Ertel’s potential vorticity (PV) in visu-
alising large scale dynamical processes. PV is an approx-
imate material tracer for motion along isentropic surfaces
only (Haynes and McIntyre, 1990). PV plays a central role
in large scale dynamics where it behaves as an approximate
material tracer (Hoskins et al., 1985).
As a result, PV can be used as the horizontal spatial coor-
dinate instead of latitude and longitude (Norton, 1994; Lary
et al., 1995a). PV is suf ciently monotonic in latitude on an
isentropic surface to act as a useful replacement coordinate
for both latitude and longitude, reducing the tracer eld from
three dimensions to two. These ideas have already led to
interesting studies correlating PV and chemical tracers such
as N2O and O3 (Schoeberl et al., 1989; Schoeberl and Lait,
1992; Prof tt et al. , 1989, 1993; Lait et al., 1990; Douglass
et al., 1990; Prof tt et al. , 1989, 1993; Atkinson, 1993). A
key result of these studies is that PV and ozone mixing ratios
are correlated on isentropic surfaces in the lower stratosphere
(Danielsen, 1968).
Since the absolute values of PV depend strongly upon
height and the meteorological condition, it is useful to nor-
malise PV and use PV equivalent latitude (φe) as the hori-
zontal coordinate instead of PV itself. φe is calculated by
considering the area enclosed within a given PV contour on
a given θ surface. The φe assigned to every point on this PV
contour is the latitude of a latitude circle which encloses the
same area as that PV contour. Therefore, for every level in
the atmosphere φe has the same range of values, −90◦ to 90◦.
This provides a vortex-tracking, and indeed a ow-tracking,
stratospheric coordinate system.
2.4 Analyses Grid
The analyses grid used in this study is cast in equivalent
PV latitude, potential temperature coordinates. With 32
latitudes between 80◦ S and 80◦ N, and 24 logarithmically
spaced isentropic surfaces between the earth’s surface and
2400 K. The grid resolution was carefully chosen to ensure
that there is usually a statistically signi cant number of ob-
servations per analysis grid cell. This allows meaningful rep-
resentativeness uncertainty statistics to be calculated based
on the observations alone. As the potential temperature at
the surface changes with time we use a xed number of isen-
tropic levels between the surface potential temperature for
a given day and equivalent latitude band and 500 K, above
500 K the levels remain xed with time. The isentropic lev-
els correspond approximately to the UARS surfaces spaced
at 6 per decade in pressure (c.f. the UARS reference atmo-
sphere levels http://code916.gsfc.nasa.gov/Public/Analysis/
UARS/urap/home.html).
3 Observations
The key difference between conventional modelling and data
assimilation is the use of observations and information on
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D. J. Lary: Halogens and free tropospheric chemistry 229
(a)
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Fig. 1. Panels (a) to (d) show the global ozone, nitric acid, methane and hydrochloric acid analyses from the surface up to the lower
mesosphere produced by chemical data assimilation for October 15, 1991 at local solar noon. The analyses are presented as equivalent PV
latitude - potential temperature cross sections. The background colors show the volume mixing ratio (in the case of HNO3 and HCl log10 of
the v.m.r.) and the overlaid color lled circles show the observations used. The thick red line overlaid on the plots is the thermal tropopause
diagnosed from the UKMO analyses minimum temperature, the dashed red line is the tropopause diagnosed using the WMO lapse rate
de nition. The white space at the bottom of the plots is because the analysis is terrain following and the surface potential temperature
changes with time and location. It can be seen that although the bulk of the observations are in the stratosphere many observations are also
available below the tropopause.
observational and other uncertainties (described in the next
section). In this study for each analysis grid cell we consider
a probability distribution function (PDF) of all the available
observations. The ‘observation’ used by the assimilation sys-
tem for a given grid cell is the median value of the PDF. The
criteria used to determine at what location we use an obser-
vation are equivalent PV latitude (φe), and potential tempera-
ture (θ ). An observation is used in φe-θ grid box where it lies.
That means that no interaction between the boxes (merid-
ional transport, mixing, diabatic ascent/descent) is consid-
ered.
Two criteria were used in choosing which observations to
assimilate. First, we chose constituents for which we had
observations over the entire period of 1991 to 1998. Sec-
ond, where more than one instrument was observing a con-
stituent we chose to use instruments that did not have sig-
ni cant relative biases. This was determined by looking at
observation PDFs. This analysis is also available online at:
http://gest.umbc.edu/PDFCentral/.
There appears to be good consistency between the spo-
radic observations of missions such as ATMOS and CRISTA
with the long-term HALOE and MLS data-sets used. This
was not the case for some possible combination of obser-
vations. For example, CLAES ozone and MLS ozone had
some large differences. After conducting the PDF analyses it
seems that the major problems are with CLAES. Another ex-
ample is MLS, HALOE and SAGE water, SAGE water was
not used after the results of the PDF analyses showed it has
bias issues.
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230 D. J. Lary: Halogens and free tropospheric chemistry
The resulting assimilated analyses are presented online,
where observations were used these are overlaid on the
assimilated analyses (http://gest.umbc.edu/CDACentral/) as
color- lled circles using the same color scale as the color-
lled contours used to depict the analyses. This allows ap-
propriate comparison with observations to validate the as-
similation. In addition, when observations of a constituent
were used the web site also provides an assimilation statistics
page (at the top of each page just below the java-script cal-
endar bar). This page presents the observations, the various
observation uncertainties, and the assimilation skill scores.
This study used sulphate aerosol observations from SAGE
II (Ackerman et al., 1989; Oberbeck et al., 1989; Rus-
sell and McCormick, 1989; Thomason, 1991, 1992; Bau-
man et al., 2003) and HALOE (Hervig et al., 1993, 1996;
Hervig and Deshler, 1998; Massie et al., 2003), ozone ob-
servations from UARS (Reber et al., 1993) MLS v6 (Froide-
vaux et al., 1996; Waters, 1998), HALOE v19 (Russell et al.,
1993), POAM, ozone sondes and LIDAR, nitric acid obser-
vations from UARS MLS v6 (Santee et al., 1997, 1999),
CLAES, ATMOS, CRISTA (Offermann and Conway, 1999)
and ILAS (Wood et al., 2002), hydrochloric acid observa-
tions from UARS HALOE and ATMOS, water observations
from UARS HALOE v19, ATMOS and MOZAIC (Marenco
et al., 1998), methane observations from UARS HALOE
v19, ATMOS and CRISTA were used. Although the bulk
of these observations were in the stratosphere a signi cant
number of satellite observations were available for the free
troposphere down to 5 km, and from sondes and aircraft data
is also available below 5 km (e.g. Fig. 1).
4 Uncertainties
This section describes the treatment of uncertainties of both
the observations and the model.
4.1 Observational Uncertainties
A key feature of this study is the quanti cation of a suite of
uncertainties associated with the observations all on the anal-
yses grid. The uncertainties provided are: The observational
uncertainty as supplied by the instrument teams. The rep-
resentativeness uncertainty, i.e. the concentration variability
over the analyses grid cell. The Kriging uncertainty, i.e. the
uncertainty associated with lling in the data gaps. The total
uncertainty due to all of the above. The representativeness
uncertainty is calculated by taking the average deviation of
the tracer concentrations from the median from the given grid
cell.
4.2 Observation Sanity Check
Where possible a zeroth order sanity check on the observa-
tions are performed. For example, the observations of HCl
should not be greater than the total atmospheric loading of
chlorine, ClOy, and the observations of HNO3 should not be
greater than the total atmospheric loading of nitrogen, NOy.
For this sanity check an 81 year run of the Goddard Space
Flight Center (GSFC) two-dimensional chemistry and trans-
port model run from 1970 to 2050 is used (Fleming et al.,
1999). This model run was used for international assess-
ments of ozone depletion and is constrained by the recom-
mended emission inventories of the various source gases.
During the period 1992 to 2000 it is constrained with the
observed residual circulation and gives realistic NOy, ClOy,
and BrOy distributions.
4.3 ClOy, BrOy, and NOy
The elds of total ClO y, BrOy, and NOy in our assimilation
were taken from the GSFC 2D model run just mentioned
(Fleming et al., 1999). The 2D model transport captures
much of the qualitative structure and seasonal variability ob-
served in stratospheric long lived tracers, such as isolation of
the tropics and the southern hemisphere winter polar vortex,
the well-mixed surf-zone region of the winter subtropics and
midlatitudes, and the latitudinal and seasonal variations of
total ozone. The generally good model-measurement agree-
ment of the 2-D tracer simulations demonstrate that a suc-
cessful formulation of zonal mean transport processes can
be constructed from currently available atmospheric data sets
(Fleming et al., 1999).
4.4 Accessing Model Uncertainty
A major new feature of this study is the detail and care with
which the observation and modeling uncertainties were de-
termined. At each time step the model uncertainty is ac-
cessed in detail by performing a set of sensitivity experi-
ments. The model is cast in equivalent PV latitude, potential
temperature (φe-θ ) coordinates that are derived from daily
meteorological analyses (UKMO, ECMWF or GEOS). For
each analysis grid cell in the ow tracking coordinates we
have a probability distribution function (PDF) of tempera-
tures, pressures, geographic latitudes (determining the solar
illumination) and sulfate aerosol loadings (derived from daily
SAGE and HALOE observations). The temperature, pres-
sure, geographic latitude and sulfate aerosol loading used for
the chemical analysis of each grid cell in the ow tracking
coordinates is the median value of the PDF. In order to con-
tinuously access the representativeness uncertainty for each
grid cell associated with the full PDF of temperatures, pres-
sures, geographic latitudes and sulfate aerosol loadings in
each grid cell an ensemble of sensitivity experiments is per-
formed at each time step. The average deviation from the
median is used as a robust estimator of the width of the PDF
and the time step is repeated for the median ± average de-
viation of the temperature, pressure, geographic latitude and
sulfate aerosol loading. This gives a total of eight simulations
for each time step that allow a continuous real assessment of
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D. J. Lary: Halogens and free tropospheric chemistry 231
the model representativeness uncertainty associated with the
analyses coordinate grid.
5 Chemical Kalman Filter
Khattatov et al. (1999) applied the Kalman lter for synoptic
mapping of short-lived species using UARS data. However
they ignored possible observational biases and skill scores.
Nor did they address the issue of mass non-conservation that
can occur. We have demonstrated how use of sophisticated
mathematical techniques in atmospheric chemistry can help
with data quality control and understanding limitations of
modern instruments and models. This aspect is expected to
be particularly important in the near future as more and more
satellite-based instruments are being deployed and scienti c
community faces a complicated task of integrating and vali-
dating the emerging extensive data sets.
The chemical Kalman lter ( Khattatov et al., 1999) al-
lows the optimal combination of model simulations and mea-
surements taking into account their respective uncertainties.
Consider a model of a physical system represented by opera-
tor (generally nonlinear) M, and let vector x with dimension
Nx be a set of input parameters for the model. So in this case
the model of our non-linear chemical system is represented
by M. These input parameters are used to predict the state
of the system, vector y with dimension Ny:
y =M(x) (1)
Assume that vector x represents the state of a time-dependent
numerical photochemical model, i.e. concentrations of mod-
eled species at model grid points in the atmosphere. In the
case of a box model that includes N species, the dimension
of vector x would be N. We will now limit the discussion to
the case when M is used to predict the state of the system at
some future time from past state estimates. Formally, in this
case
x = xt , y = xt+1t (2)
and xt+1t =M(t, xt) (3)
Let vector yo contain observations of the state (hence sub-
script o). Usually, the dimension of yo is less than Ny, the
dimension of the model space, since not all model species
are usually observed. The connection between yo and y can
be established through the so-called observational operator
H:
yo = H(y) (4)
Combining equations (1) and (4), we get
yo = H(M(x)) (5)
We now assume that that the probability density functions
associated with x and y can be satisfactorily approximated
by Gaussian functions:
PDF(y) ∼ exp
(
− (y − yt)
T C−1(y − yt)
2
)
(6)
where yt is the true value of y and C is the corresponding
error covariance matrix. Its diagonal elements are the uncer-
tainties (standard deviations) of y, and the off-diagonal ele-
ments represent correlation between uncertainties of differ-
ent elements of vector y. The covariance matrix C is de ned
as
C = 〈(y − yt)(y − yt)T 〉 (7)
where angle brackets represent averaging over all available
realizations of y.
For most practical applications we need to introduce the
linear approximation. In the linear approximation we assume
that for small perturbations of the parameter vector 1x the
following is approximately true:
M(x +1x) =M(x)+ L1x (8)
Formally, L is a derivative of M with respect to x:
L = dM
dx
(9)
For small variations of x one can show that the evolution of
error covariance matrix Ct is given by:
Ct+1t = LCtLT +Q (10)
Matrix Q is the error covariance matrix introduced to take
into account uncertainties of the model calculations. The
Kalman lter equations are
xt+1t =M(t, xt)
Ct+1t = LCtLT +Q
xˆt = xt + CtHT (HCtHT +O)−1(yo −Hxt) (11)
Cˆt = Ct + CtHT (HCtHT +O)−1HCt (12)
O is the observation error covariance matrix. At the end of
each analysis period the model value (xt ) and the correspond-
ing observation (yo) are ‘mixed’ (see Eq. 11) with weights
inversely proportional to their respective errors to produce
the analysis, xˆt. Then the model is integrated forward in
time starting from the obtained analysis. Once an observa-
tion has been incorporated in the model, the analysis error
covariance should be updated to re ect this (see Eq. 12). In
the absence of observations, the model state is updated using
Eq. (3), while evolution of the error covariance is obtained
from the linearized model equations as in Eq. (10).
If no observations are available, then
xˆt = xt (13)
Cˆt = Ct (14)
The following sections examine some of the roles halo-
gens play in tropospheric chemistry.
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232 D. J. Lary: Halogens and free tropospheric chemistry
Contributions to CH3 production on October 15, 1991 at local solar noon.
(a)
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+OH→ CH
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+H
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O Bimolecular
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(b)
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Bimolecular
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Contributions to CH3 production on January 15, 1993 at local solar noon.
(c)
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+OH→ CH
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+H
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(d)
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Bimolecular
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45
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55
Fig. 2. Based on the analyses produced by chemical data assimilation system panel (a) shows the percentage of the initiation of methane
oxidation due to OH for 15 October 1991. At rst glance it con rms the conventional position that in the free-troposphere the initiation by
OH is all that needs to be considered. However, on closer examination it can be seen that there are extensive regions within the troposphere
where the initiation of methane oxidation due to Cl (Panel (b)) contributes more than 10% and some regions where it contributes up to 50%.
The regions of signi cant initiation by Cl are, as would be expected, in the region below the polar vortex, and more surprisingly in northern
mid latitudes. The northern mid-latitude feature persists. For example, it can be seen that the mid-latitude role of chlorine initiation is greater
in January 1993 (panel (d)). Panels (c) and (d) are the analogues to panels (a) and (b) for 15 January 1993. It can be seen that the northern
mid-latitude role of chlorine initiation is slightly greater than for 1991.
6 Initiation of Hydrocarbon Oxidation
Methane and hydrocarbon oxidation are some of the most
signi cant atmospheric chemical processes. The hydroxyl
radical (OH) is an important cleansing agent of the lower
atmosphere, in particular, it provides the dominant sink for
CH4 and HFCs as well as the pollutants NOx, CO and VOCs.
Once formed, tropospheric OH reacts with CH4 or CO within
seconds. It is generally accepted that the local abundance
of OH is controlled by the local abundances of NOx, CO,
VOCs, CH4, O3, and H2O as well as the intensity of solar
UV; and thus it varies greatly with time of day, season, and
geographic location (Houghton and Ding, 2001).
Methane oxidation is usually initiated by hydrogen ab-
straction reactions such as
OH + CH4 −→ CH3 + H2O (15)
O(1D)+ CH4 −→ CH3 + OH (16)
Cl + CH4 −→ CH3 + HCl (17)
Br + CH4 −→ CH3 + HBr (18)
The rate at which hydrogen is abstracted from CH4
by OH and Cl is a strong function of temperature,
Atmos. Chem. Phys., 5, 227 237, 2005 www.atmos-chem-phys.org/acp/5/227/

D. J. Lary: Halogens and free tropospheric chemistry 233
October 15, 1991 at local solar noon.
(a)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of prod for HONO
2
due to OH+NO
2
→ HONO
2
+m Trimolecular
10
20
30
40
50
60
70
80
90
(b)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of prod for HONO
2
due to H
2
O+N
2
O
5
→ HONO
2
+HONO
2
(Heterogeneous SA)
10
20
30
40
50
60
(c)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of prod for HONO
2
due to H
2
O+ClONO
2
→ HOCl+HONO
2
(Heterogeneous SA)
0.5
1
1.5
2
2.5
3
(d)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of prod for HONO
2
due to H
2
O+BrONO
2
→ HOBr+HONO
2
(Heterogeneous SA)
5
10
15
20
25
30
35
Fig. 3. The contribution of four of the main HNO3 production channels. It is well known that two of the key nitric acid production channels
in the troposphere are the bimolecular reaction of OH with NO2 (panel (a)) and the heterogeneous hydrolysis of N2O5 on sulphate aerosols
(panel (b)). In the stratosphere the heterogeneous hydrolysis of ClONO2 (panel (c)) and BrONO2 (panel (d)) is also routinely considered. It
can be seen that they are also signi cant sources of HNO 3 in the free troposphere.
altitude, and the total reactive chlorine loading
(ClOy=2Cl2+Cl+ClO+2Cl2O2+HCl+HOCl+ClONO2).
It should be noted that Reaction (4) is very slow and just
included for the sake of completeness.
Initiation of methane oxidation by Cl is a strong function
of ClOy. Burnett and Burnett (1995) have inferred from their
OH column measurements that chlorine is likely to be in-
volved in the initiation and oxidation of methane. In agree-
ment with this, Fig. 2 shows that signi cant initiation of
methane oxidation is due to Cl.
However, the halogen initiation and catalysis of hydrocar-
bons is not usually considered in global chemistry models.
This is not due to a lack of kinetic knowledge but rather
an assumption that halogens play a minor role outside of
the boundary layer and stratosphere (Johnston and Podolske,
1978; Cicerone et al., 1983; Farman et al., 1985). Figure 2
shows that in the lower stratosphere and even in the free tro-
posphere, halogen-catalyzed, and halogen-initiated, methane
oxidation can be important. Halogen-catalyzed methane ox-
idation can play a signi cant role in the production of HO x
(=H+OH+HO2) radicals (Lary and Toumi, 1997) in just the
region where it is usually accepted that nitrogen-catalyzed
methane oxidation is one of the main sources of ozone
(Houghton and Ding, 2001). Aspects of methane oxida-
tion by halogens has been previously mentioned by Crutzen
et al. (1992); Burnett and Burnett (1995) and the mechanism
speci cally described by Lary and Toumi (1997).
Figure 1 panels (a) to (d) show the global ozone, nitric
acid, methane and hydrochloric acid analyses from the sur-
face up to the lower mesosphere produced by chemical data
assimilation for mid-October 1991. Based on the analyses
produced by chemical data assimilation system Fig. 1 panel
(e) shows the percentage of the initiation of methane oxida-
tion due to OH. At rst glance it con rms the conventional
www.atmos-chem-phys.org/acp/5/227/ Atmos. Chem. Phys., 5, 227 237, 2005

234 D. J. Lary: Halogens and free tropospheric chemistry
October 15, 1991 at local solar noon.
(a)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of prod for OH due to HOBr+hν→ OH+Br Photolysis
1
2
3
4
5
6
7
(b)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of loss for HO
2
due to BrO+HO
2
→ HOBr+O
2
Bimolecular
0.5
1
1.5
2
2.5
3
3.5
4
4.5
(c)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of loss for NO due to ClO+NO→ Cl+NO
2
Bimolecular
2
4
6
8
10
12
14
16
18
20
22
(d)
75 60 45 30 15 0 15 30 45 60 75
300
350
400
500
600
700
800
1000
1200
1400
1600
1800
2000
2200
2400
Equivalent PV Latitude
P
o
t
e
n
t
i
a
l

T
e
m
p
e
r
a
t
u
r
e
% of loss for NO due to BrO+NO→ Br+NO
2
Bimolecular
1
2
3
4
5
6
7
8
Fig. 4. HOBr is readily photolyzed in the visible and yields OH. Panel (a) shows that HOBr photolysis can contribute close to 10% of the
total OH production rate at high latitudes in the free-troposphere. Likewise panel (b) shows that the production of HOBr by the bimolecular
reaction of BrO with HO2 contributes more than 5% to the total HO2 loss rate at high latitudes in the free-troposphere. The tropospheric
partitioning of NO and NO2 is affected by halogen interactions. Panel (c) shows that there are large regions in northern mid-latitudes
and below the polar vortex where more than 10% of the loss of NO is due to reaction with ClO. Panel (d) shows that for much of the
free-troposphere the reaction of NO with BrO contributes more than 5% to the loss of NO.
position that in the free-troposphere the initiation by OH is
all that needs to be considered. However, on closer examina-
tion it can be seen that there are extensive regions within the
troposphere where the initiation of methane oxidation due to
Cl (Fig. 1 panel (f)) contributes more than 10% and some
regions where it contributes up to 50%. The regions of sig-
ni cant initiation by Cl are, as would be expected, in the re-
gion below the polar vortex, and more surprisingly in north-
ern mid latitudes. The northern mid-latitude feature persists.
For example, it can be seen that the mid-latitude role of chlo-
rine initiation is greater in January 1993 (Fig. 2 panel (d)).
7 Production of Nitric Acid
It is well known (Brasseur and Solomon, 1987; Wayne, 1991;
DeMore et al., 2000) that two of the key nitric acid pro-
duction channels are the bimolecular reaction of OH with
NO2 and the heterogeneous hydrolysis of N2O5 on sulphate
aerosols (please see Fig. 3a and b). In the stratosphere the
heterogeneous hydrolysis of ClONO2 and BrONO2 are also
routinely considered (DeMore et al., 2000). However, as
halogens are often normally not considered in models of
the free troposphere these channels are not normally consid-
ered in the troposphere. Figure 3c shows that the hydroly-
sis of BrONO2 alone can contribute more than 35% to the
HNO3 production rate (this percentage depends on the re-
action probability, here 0.9 was used). Therefore excluding
Atmos. Chem. Phys., 5, 227 237, 2005 www.atmos-chem-phys.org/acp/5/227/

D. J. Lary: Halogens and free tropospheric chemistry 235
halogen chemistry from global chemical models can lead to a
signi cant error in these regions, yet another reason for con-
sidering halogen chemistry in the free troposphere.
8 Partitioning of OH and HO2
HOBr is readily photolyzed in the visible and yields OH
(Rattigan et al., 1996). Figure 4a shows that HOBr photol-
ysis can contribute close to 10% of the total OH production
rate at high latitudes in the free-troposphere. Likewise Fig-
ure 4b shows that the production of HOBr by the bimolecular
reaction of BrO with HO2 contributes more than 5% to the
total HO2 loss rate at high latitudes in the free-troposphere.
9 Partitioning of NO and NO2
The tropospheric partitioning of NO and NO2 is affected by
halogen interactions. Figure 4 panel (c) shows that there are
large regions in northern mid-latitudes and below the south-
ern polar vortex where more than 10% of the loss of NO is
due to reaction with ClO. Figure 4 panel (d) shows that for
much of the free-troposphere the reaction of NO with BrO
contributes more than 5% to the loss of NO.
10 Conclusions
A careful constraint of a photochemical modelling system us-
ing chemical data assimilation and a variety of atmospheric
observations has been conducted. A detailed analysis of the
results shows that halogens are playing a role in the chem-
istry of the free troposphere. In particular, methane oxidation
is initiated by Cl as well as OH in the troposphere. The Cl ini-
tiation of methane oxidation can contribute more than 10%
to the total rate of initiation below the polar vortex and in
mid-latitudes. In addition, the hydrolysis of BrONO2 alone
can contribute more than 35% of the HNO3 production rate
in the free troposphere. The partitioning of NO and NO2 in
the free troposphere is also signi cantly affected by halogen
reactions.
Acknowledgements. It is a pleasure to acknowledge: NASA
for a distinguished Goddard Fellowship in Earth Science and
for research support; The Royal Society for a Royal Society
University Research Fellowship; The government of Israel for
an Alon Fellowship; The NERC, EU, and ESA for research support.
Edited by: R. Sander
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