Siyuan Wang | Research - Ch 5. N2O5-ClNO2

Ch 5. N2O5-ClNO2: a source of Cl atoms

OVERVIEW

- In previous chapters, we have learnt how to load KPP mechanism, as well as how to manually type-in mechanism. We also played around with VOC-NOx chemistry. Moreover, we set up the model to mimic the ambient conditions, such set diurnal variations for photolysis, mixing layer height, and set up depositions and emissions, etc.
- In this chapter, we will briefly introduce heterogeneous chemistry and its treatment in the model. We will do this by playing around with a very interesting chemistry system: N2O5-ClNO2.
- We will manually add a few more reactions. Burkholder et al JPL compication 2015 is a very good source for kinetics!!
- Finally, we will take a look at some unique VOC signatures due to Cl oxidation!

1. BACKGROUND: N2O5-ClNO2

- We have learnt from previous chapters that N2O5 is an important nighttime NOx reservoir. We also mentioned that N2O5 is quite "sticky", such that when a molecule of N2O5 hits a surface, the chance that N2O5 "permanently" lost at the surface is quite high. Not all molecules striking a surface would trigger a chemical reaction. The probability of a molecule stick to a surface and triggers a chemical reaction is called reactive uptake coefficient.
- So, when N2O5 hits a surface, what does it do? Well, if the N2O5 hits a "wet" surface (almost all surface has at least a teeny tiny amount of surfacial water) it would produce two HNO3 molecules (which would usually rapidly disassociate into hydrogen ions and nitrate ions). But, if there is chloride on the surface, N2O5 may react with chloride and release ClNO2 into the gas-phase. In the ambient air, you'll amost always find at least some chloride.
- ClNO2 is quite stable at night. In the morning, ClNO2 would undergo photolysis and produce Cl atoms, which is super reactive and can oxidize a lots VOCs, much faster than OH radicals. More interestingly, Cl oxidation has unique "signatures" that can be distinguished from OH oxidation.

2. GET OUR HANDS DIRTY!

Firstly go to the MCM website, and download the KPP mechanism containing the following VOCs:

Methane (CH4), ethane (C2H6), propane (C3H8), n-butane (n-C4H10), and i-butane (i-C4H10)

Don't forget to include inorganic reactions as well.

Now load the mechanism into IGOR! There are 249 species and 765 reactions.
But before you generate your own ODE_ScratchBoard, add the following four reactions into the BIG TABLE:

R765 N2O5 = ClNO2 R766 N2O5 = R767 ClNO2 = CL + NO2 R768 CL + NO2 = ClNO2

Also add one more species in to the species list: ClNO2. Note that chlorine chemistry could be quite complicated, but here we deal with the very simple ones.
Now once you added these into the BIG TABLE, run the model for a second or two, abort, then press the button to generate your ODE_ScratchBoard.
Don't forget to generate your kr list. You've done all these for multiple times already, should take you no more than a few minutes.

3. SET NEW RATE COEFFICIENTS:

CTRL+M find the section where we define the rate coefficients (kr). Add the rate coefficients for the four new reactions:

kr[765] = Yield_ClNO2 * (1/4) * Gamma_N2O5* (AerosolSurfaceArea_um2_cm3*1E-8) * 100 * Sqrt(8*8.314*TEMP*1000/3.14159/108) kr[766] = (1 - Yield_ClNO2) * (1/4) * Gamma_N2O5* (AerosolSurfaceArea_um2_cm3*1E-8) * 100 * Sqrt(8*8.314*TEMP*1000/3.14159/108) kr[767] = 0.005 * Jvalue[4] // ClNO2 = Cl + NO2. scaled to j_NO2 kr[768] = k_termolecular(1.3E-30, 2, 1e-10, 1, TEMP, M) // Cl + NO2 = ClNO2

I'll walk you thru:

kr[767] is the photolysis frequency of ClNO2. For the sake of simplicity, let's scale it to j_NO2, which is about 0.5%. You know how to estimate this? Simply integrate the absorption cross section of ClNO2 in the 290-700 nm range, and normalized to the absorption cross section of NO2.
kr[768] is the termolecular reaction. You can find the parameterization in Burkholder et al 2015. I got the termolecular rate coefficient function for you, you can copy-paste it into the procedure window.

Function k_termolecular(k0_300, n, kinf_300, m, TEMP, c_M) Variable k0_300, n, kinf_300, m, TEMP, c_M Variable k0_T = k0_300 * (TEMP/300)^(-1*n) Variable kinf_T = kinf_300 * (TEMP/300)^(-1*m) Return (k0_T*c_M/(1 + k0_T*c_M/kinf_T)) * 0.6^((1+(log(k0_T*c_M/kinf_T))^2)^-1) End

Don't put this inside any other functions or macros ;)

Now kr[765] and kr[766] are heterogeneous reactions, i.e. a reaction between a gas and a surface:

k_het = (1/4) * γ * 100 * ThermalSpeed * SurfaceAreaDensity ThermalSpeed = sqrt( 8*R*T/pi/MW )

where k_het (s^-1) is the pseudo 1st order rate coefficient of a heterogeneous reaction, γ (dimensionless) is the reactive uptake coefficient, ThermalSpeed (m/s) and SurfaceAreaDensity (cm^2 / cm^-3) are exactly what they look like. MW (kg/mol) is the molecular weight. T (K) is temperature.

In this example we assume N2O5 react with chloride-containing particles, therefore SurfaceAreaDensity is for particles. This section looks something like this:

As we mentioned before, N2O5 reactive uptake on aerosols may either produce ClNO2, or something else. We only care about ClNO2 here, as you can see Reaction 766 doesn't even have products on the right-hand-side. Therefore we only specify the stoichiometric yield of ClNO2, and the yield of the other channel is 1 - Yield_ClNO2.
Now scroll up and set up the initial concentrations, uptake coefficient of N2O5, ClNO2 yield, and aerosol surface area:

// =============== // Initial concentrations // =============== Concentration_Matrix[0][154] = (20)*Pressure*(6.0232E+8)/(8.314*TEMP) // NO Concentration_Matrix[0][19] = (40)*Pressure*(6.0232E+8)/(8.314*TEMP) // O3 Concentration_Matrix[0][169] = (100)*Pressure*(6.0232E+8)/(8.314*TEMP) // CO
Concentration_Matrix[0][37] = (2000)*Pressure*(6.0232E+8)/(8.314*TEMP) // CH4 Concentration_Matrix[0][112] = (5)*Pressure*(6.0232E+8)/(8.314*TEMP) // C2H6 Concentration_Matrix[0][79] = (2)*Pressure*(6.0232E+8)/(8.314*TEMP) // C3H8 Concentration_Matrix[0][64] = (1)*Pressure*(6.0232E+8)/(8.314*TEMP) // n-C4H10 Concentration_Matrix[0][39] = (1)*Pressure*(6.0232E+8)/(8.314*TEMP) // i-C4H10 // ================================ // N2O5 uptake on aerosols producing ClNO2 // ================================ Variable Yield_ClNO2 = 0.6 Variable Gamma_N2O5 = 0.03 Variable AerosolSurfaceArea_um2_cm3 = 200

ABOUT THE HETEROGENEOUS REACTIONS

There are underlying assumptions the way we treated the N2O5-ClNO2 chemistry in this example:

This reaction involves N2O5 and chloride (two reactants), but we write it as a pseudo-1st order reaction, assuming N2O5 is the local limiting reagent. This mostly is not the worst assumption, and also is consistent with most laboratory studies measuring N2O5 reactive uptake coefficient.
Assume gas diffusion is not limiting. See the next section for details.
We here use fixed N2O5 uptake coefficient and ClNO2. In reality these two depend on chemical composition, aerosol mixing state, etc, and can vary a lot! We will not cover this here.

MASS TRANSPORT CONSIDERATIONS

I strongly recommend Stephen Schwartz's work (1986), which is one of my all time favorate! From the mass transport point-of-view, heterogeneous reaction between a gas-phase molecule and a particle consists of multiple steps:

diffusion in the gas-phase, which sets the upper bound of gas-to-particle flux;
interfacial transport: not all molecules colliding the surface will stick to the surface, and the probability of the molecule sticking to the surface over all the molecules striking the surface is often called mass accommodation coefficient, which sets the upper bound of the reactive uptake coefficient.
diffusion in the bulk, which is largely affected by the viscosity of the particle (imagine a particle behaves like water, oily, honey, peanut butter, ... all the way to tar).
chemical reaction within the bulk (including hydration).

Rule of thumb: the slowest step limits the overall rate. Gas diffusion (1) is fast in most cases; but for "very sticky" compounds (with high mass accommodation coefficient), gas diffusion (1) might be limiting. This is often the case for radicals. For very soluble species, interfacial transport (2) may be limiting. For example, glyoxal. For very reactive species, chemical reaction (4) may be faster than the diffusion in the bulk (3), this would lead to quick depletion at the surface and possibly accumulation of product(s) at the surface.

In the case of N2O5 uptake, it reacts quite fast at the surface containing chloride: on average a N2O5 molecule would not penetrate more than a few nm (Gaston et al 2016) into the particle, therefore the overall rate is mostly limited by interfacial transport. However, there are circumstances when N2O5 surface uptake is so fast that it's depleted near the surface, and hence the gas diffusion limits the overall rate. This may be the case if you have high surface area density (e.g. laboratory experiments Lopez-Hilfiker et al 2012), and if yes, you may want to correct for the gas diffusion too.

4. EMISSION, DEPOSITIONS, DIURNAL VARIATIONS, etc

Now set up emissions, depositions, and diurnal variations as we did in the last chapter. Set dry deposition velocities of HNO3 and N2O5 to 0.5 cm/s. Don't forget to add the lines in the ODE_ScratchBoard.
In this example we don't need emissions. But feel free to add some NOx emissions!
Almost there! Let's set up in the GUI a few more things: let's ask the model to run for 4 days, and output results every 1 hour (3600 s), and run the model!!

5. PRODUCTION OF CL RADICALS

Once the model is finished, check out a few things. Take a look at N2O5 and ClNO2. As shown, N2O5 increases at hight and drops down to pretty much zero during daytime. ClNO2 accumulates to pretty high levels at night, due to N2O5 heterogeneous reaction, and starts to decrease during daytime.
In this example, the depositions of HNO3 and N2O5 are the major sink of total NOy. Feel free to tune the deposition velocities!
With the presence of light, ClNO2 photolysis produces Cl atoms. Now compare the model Cl atoms concentration to that of OH radicals. You'll see that OH radicals are still like two orders of magnitude higher than Cl. However, we mention that Cl radicals are much more reactive than OH radicals!

6. CHLORINE OXIDATION SIGNATURE

Not only Cl oxidation is faster than OH oxidation, it leaves unique signatures in the atmosphere too! One thing that can be used to examine if Cl oxidation actually plays a role is to look at certain VOC ratios. Impact of dilution on concentrations would be cancelled out.
i-butane and n-butane have fairly similar OH rate coefficients. Therefore, if OH oxidation dominates, the ratio of i-butane / n-butane wouldn't change much over the course of time. However, their Cl rate coefficients are very different! Therefore if Cl oxidation dominates, the ratio of i-butane / n-butane would change drastically,
i-butane and propane are the other way around: their OH rate coefficients are very different but OH rate coefficients are fairly similar. Therefore if OH oxidation dominates, the ratio of i-butane / propane would vastly change; but if Cl oxidation dominates, this ratio wouldn't change much.

7. CHANGE CHEMISTRY HOWEVER YOU WANT

Now here is the fun part: you're the boss of the fake world you just created and you can do whatever you want! For example, to examine the VOC signature with OH oxdiation only, you can simply set Yield_ClNO2 to zero, and in this case N2O5 will still react with aerosols but no ClNO2 will be produced, and hence [Cl] would be zero.
You can also turn of OH oxidation and examine only Cl oxidation! There are multiple ways to do this. Here let's do it in an interesting way: let's directly touch the ordinary different equations in the ODE_ScratchBoard!
Press the button and bring up the ODE_ScratchBoard, scrool all the way down to the bottom, and type in this line:

YDOT[59] = 0 // OH

what this does is simply set d[OH]/dt to zero, such that no OH will be produced or removed! Since the intial [OH] is zero, if you set this, [OH] will remain zero always.

7. VOC RATIO-RATIO PLOT

Now make a new wave of the ratio of i-butane / n-butane, and another wave of i-butane / propane, and make the ratio-ratio plot. You may type in the commandline:

Make/O/N=(DimSize(Concentration_Matrix,0)) Ratio_iButane_nButane = Concentration_Matrix[p][39] / Concentration_Matrix[p][64] Make/O/N=(DimSize(Concentration_Matrix,0)) Ratio_iButane_Propane = Concentration_Matrix[p][39] / Concentration_Matrix[p][79]

in my case the species indies of i-butane, n-butane, and propane are 39, 64, and 79, respectively.

Then run the model two more times: one with OH turned off, and another one with Cl turned off, and compare the ratio-ratio plot. You should get something like this (I color-coded the points with time):
Cool huh? As you can see that with OH only, the ratio-ratio line evolves sort of horizontally. But with Cl only, the line evolves vertically! And if you have them both on, the line is kinda line a mixture of both!

8. SUMMARY

In this chapter we briefly introduced heterogeneous, and we examined simple N2O5 heterogeneous reaction on chloride-containng particles producing ClNO2, which could be an important source of Cl radicals. We also examined the unique VOC fingerprint of Cl oxidation in the atmosphere.
One trick we learnt is that, by setting YDOT[n] to zero, you shut off all production and removal path ways, and the concentration of specie n will stay unchanged until you reset to new concentration (if you ever do so). This is useful if you want to load measurements into the model and would like to constrain to measurements.
Constraining the modeled species to measurements is sometimes quite useful, depending on what question you would like to ask. For example, if you wanna examine a compound B that is produced from a given precursor A, and that precursor A is both produced from other processes and also can be directly emitted. Emissions often times could be highly uncertain, and hence if you compare the modeled compound B to measurements and the results don't look good, it's hard to say if it's because of chemistry is wrong, or if the emission is off. But if you constrain species A in the model, and still modeled B is off, then it's more likely that the chemistry needs to be improved.
Last but not least, chlorine chemistry in the atmosphere is way more complicated than we had in this example. For example, chlorine chemistry is the major culprit of the ozone hole. Chlorine chemistry also plays a role in the Arctic boundary layer.

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