The Master Chemical Mechanism
1. Extract the trans-2-butene oxidation mechanism from the MCM website.
To do this, go to the main MCM website, and click on "Browse the mechanism". Under ‘Select a Primary VOC’, choose ‘alkenes’. Then, select trans-2-butene. This takes you to a page that gives the radical reactions which initiate the oxidation of trans-2-butene in the troposphere. Click ‘mark’ under any of the TBUT2ENE structures. Notice that if you mark one, they are all marked. When you click ‘mark’, TBUT2ENE appears in the ‘Mark List’ near the top of the page. This list includes any species that you have marked. If you accidentally mark something that you did not wish to, you can click ‘clear’, and that species is erased from the ‘Mark List’. Now that you have marked TBUT2ENE as the species for which you want an MCM oxidation mechanism, click on ‘Extract’ in the blue band at the top of the page. This page lets you extract a subset of the MCM using your mark list as the set of primary species. A variety of formats are available here; however, we are using FACSIMILE, so specify ‘FACSIMILE input format’ by clicking next to it. Click the ‘extract’ button near the bottom of the page, and specify where you want the TBUT2ENE oxidation mechanism to be saved.
2. Open the file containing the mechanism that you have just extracted with word pad or another text editor.
It includes 3 main parts:
Note that we get a warning in the extracted mechanism. It tells us that we have a species in our mechanism that doesn’t have a smiles string and is therefore not included in the RO2 summation. If this species is a peroxy radical, then the RO2 summation step will not give the correct value. The species is CH3CHOOB. Examination of the mechanism shows that CH3CHOOB first appears in the third reaction in the extracted mechanism, which is the reaction of O3 and t-butene. Thus, CH3CHOOB is the Criegee biradical intermediate. It is not a peroxy radical and we can proceed without worrying about an erroneous RO2 summation.
3. You will now import these bits of FACSIMILE code into a chamber mechanism that has been used to describe t-butene + O3 reactions in the recently constructed Leeds HIRAC chamber.
The model you will be using is called tbut_i.fac and can be saved to your computer by right clicking on the file name. If you have any problems at any stage you can compare syntax with the tbut.fac model, which runs without errors.
tbut_i.fac is a fairly simple model because it does not have variable photolysis rates that change according to the solar zenith angle. If the lights are on, then the photolysis rates have constant values (in theory at least). In the case of t-butene + O3, the experiments are carried out in the dark, and all the photolysis rates are set to zero, further simplifying matters.
This model also does not include chemistry that happens on the walls. A brief outline of the structure of this code is given in the introduction.
Identify where the three components of the extracted MCM mechanism (see the introduction for an outline of FACSIMILE code structure) should be pasted into tbut_i.fac, and paste them in the appropriate places. tbut_i.fac includes within it more inorganic species, more inorganic reactions, and more generic rate coefficients than actually occur in the MCM extracted mechanism for the oxidation of trans-2-butene. These extra components assure that the present model may be used with any MCM subset.
NOTE: when constructing MCM models from scratch the generic rate coefficients, the inorganic reaction mechanism and the photolysis rate parameterisations will also have to be added to the model in addition to the VOC mechanism(s) of interest. These are available from the MCM website.
Because the inorganic reactants are declared as variables separate from the organic ones (in the code, the inorganic variable declarations are immediately before the organic variable declarations), you will have to delete the inorganic species from the MCM variable declarations that you paste into tbut_i.fac. Otherwise, you will get error messages when you run the model, because FACSIMILE doesn’t like variable declarations to occur twice. Also remember that FACSIMILE also only reads 72 characters of each line. If a line is longer than 72 characters, FACSIMILE will most likely give errors in the *.006 file. The mechanism that you extracted from the MCM website and pasted into tbut_i.fac has lines longer than 72 characters (in the VARIABLE declaration and the peroxy radical summation lines). You will notice this because the lines that you import will be longer than all the lines currently in the code. Thus, the lines in the VARIABLE declarations and peroxy radical summations need to be rearranged or truncated if tbut_i.fac is to run without errors. This may be done with a simple <enter> at the point where the line is too long.
4. Run the model as follows:
When the model is running, the FACSIMILE commands will be greyed out and inaccessible. This model runs in a few seconds.
5. After the model has run, you will get 3 files in the directory where you have run the program:
i. A *.log file that gives information on the initial stages of program execution such as the model’s path and memory allocation. It is very important to note that FACSIMILE has a limit to the number of characters in the path of the model. If the number of characters is exceeded, then FACSIMILE will truncate the path in the *.log file, indicating that the path needs to be shortened. Inspect this file and see if your path to tbut_i.fac has been truncated. If it has, shorten the path.
ii. A *.006 file, which provides information regarding whether FACSIMILE was successfully able to step through each part of the program. This file is very helpful for identifying the cause of run time errors, which often have to do with bad syntax. tbut_i.fac was tested before we gave it to you and ran without errors. If your tbut_i.fac model does not run correctly (i.e., if errors are identified in the *.006 file), then it is most likely due to syntax errors. To check if any errors have occurred in running tbut_i.fac, open the *.006 file and do a search for ‘error’. FACSIMILE identifies the number of errors that it encounters in each section of the code, so that you can locate where the error occurred. If you have errors, check that the syntax format in tbut_i.fac after pasting the code from the mcm_subset.fac file is identical to that in tbut.fac.
iii. A *.007 file, which provides species concentrations at the times specified in the WHENEVER statement. If the *.006 file indicates errors, then the results in the *.007 file are not reliable.
6. To visualize results of this MCM run, import the results from the *.007 file into excel and plot [O3] as a function of time. It is difficult to back out a rate constant for O3 + trans-2-butene from this plot, since [trans-2-butene] is also being depleted by the OH radicals that are generated from the O3 + trans-2-butene reaction. In order to back out a rate constant, the model must be run under pseudo first order conditions or with a scavenger that will react with the nascent OH at a rate much faster than the OH can react with trans-2-butene. In this case an ideal scavenger to use would have to be very reactive with OH but not with O3. Typical scavengers used when studying the reactions of ozone with alkenes include cyclohexane, 1-butanol, and alkyl substituted mono-aromatics.
7. Go into tbut_i.fac and change the initial concentration of trans-2-butene to ≥ 10 ppm in order to simulate psuedo first order conditions (i.e., one reactant maintains a ‘constant’ concentration throughout the reaction). Then re-run your model in FACSIMILE and import the results (*.007) into excel. For those time points where [O3] > 1.0 molecule cm-3, plot ln([O3]) as a function of time. You should get a straight line with a negative slope. Taking the opposite of this slope and dividing it by the ‘constant’ trans-2-butene concentration will give the rate constant for O3 + trans-2-butene.
8. Now, use the MCM to simulate addition of a scavenger. Do the following:
iv. Go to the MCM website, browse the mechanism, and mark trans-2-butene (TBUT2ENE) and 1,3,5-trimethylbenzene (TM135B).
v. Extract the mechanism for the oxidation of these two species and save it to a directory separate from the other models that you have run.
vi. Copy tbut_i.fac to this directory and rename the copy tbut_ii.fac.
vii. Paste the VARIABLE declarations, the peroxy radical summation, and the chemical reactions from the extracted mechanism into tbut_ii.fac (remember to remove the previous TBUT2ENE mechanism first). Don’t forget to: (1) delete the inorganics from the MCM VARIABLE declarations so that there aren’t multiple declarations of the same variable and (2) check the length of lines so that they don’t exceed 72 characters.
viii. Set the initial conditions to 1 ppm O3, 1 ppm trans-2-butene, and 50 ppm 1,3,5-trimethylbenzene.
ix. Run the model. Check the *.006 file to see that FACSIMILE does not give any error messages. If you do get errors, use the *.006 file to locate where they have occurred (any errors will mostly likely pertain to syntax, line lengths, or multiple VARIABLE declarations), and alter tbut_ii.fac accordingly, comparing it with tbut_i.fac or tbut.fac if necessary.
x. When the model has run without errors, open the *.007 file with excel and construct a bimolecular plot of O3 or trans-2-butene as a function of time (plot 1/[O3] or 1/[trans-2-butene] over time). The slope of this line should give the rate constant of O3 + trans-2-butene.
xi. Go back to the MCM, browse the mechanism for trans-2-butene, and note the expression that the MCM uses to calculate the rate constant of the O3 + trans-2-butene reaction. Calculate this rate constant (you need the temperature at which your simulations were run) and compare it with the rate constants that you derived from both pseudo-first order conditions and from the bimolecular plot. Calculate the rate constant that the MCM uses for trimethylbenzene + OH at your simulation temperature.
Q1. At the time where [OH] peaks, how does the rate of reaction of OH + trans-2-butene compare to the rate of reaction of OH + trimethylbenzene?
Q2. Compare the concentration vs. time profiles for trans-but-2-ene and acetaldehyde (CH3CHO) from the model runs with and without 1,3,5-trimethylbenzene present. Comment on the differences