Journal of Chemical Education

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Advanced Chemistry Collection

GC Simulator
Windowscompatible computers

Users Guide

Getting Started User Directions Student Exercise

GC Simulator

Getting Started
Click the Start button, then select Programs. In the list of programs, select JCE Software. Click GC Simulator from the GC Simulator sub-menu. The opening screen is shown in Figure 1. Two gray buttons are located in the lower center of the window. The Exit button will exit the program with a request for confirmation of your action. The Go button Figure 1. The opening screen. continues the program. After clicking Go, a dialog is displayed to remind you that the program is only a simulator and not a development tool. Click OK to close the dialog and bring up the navigation menu bar shown in Figure 2. The buttons on the bar are used for navigation in the program.

Figure 2. The navigation menu bar.

The navigation menu bar consists of nine buttons. The first button (from the left) leads to the Make-up Standards and Unknowns window in which samples are prepared. The second button leads to the GC-Start-up window where the power and carrier gases are turned on; the column and detector are chosen; and injection volume is set. The third button brings up the GC Main Control Panel window where the detector and injector temperatures are set, and the choice between isothermal and programmed temperature operation is made with all subsequent settings. The fourth button leads to the Manual InjectIntegrator/Plotter window and the fifth to the Autosampler Loader window. The next two buttons lead to the autosampler output for the first five samples and the last five samples, respectively. The next button, Exit, allows you to exit the program after confirmation, and the last button, Cancel, hides the navigation menu bar. You can also hide the menu by clicking anywhere in the window other than a button in the menu. When first starting the simulator, it may be helpful to use the buttons from left to right, but this order is not required. No on-screen help is available. Follow the instructions in this manual to learn how to use the program. As with most modern Windows programs, allowing the cursor to remain over an object will identify or produce a short description of the use of that object.

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User Directions

Make-up Standards and Unknowns

Clicking the first button in the navigation menu bar brings up the Make-up Standards and Unknowns window (Figure 4), which is used for sample preparation. If you are just starting the program, you will first see the window shown in Figure 3. This window allows you to load a file containing the data for the compounds and unknowns you will use. Two files, Cmpdata.gcd and Cmpdata2.gcd are included with the program. The Make-up Standards and Unknowns window is shown in Figure 4. You can make up single samples for manual injection or multiple samples for either autosampler injection or manual injection. The Go button in the upper left corner is used to bring up the navigation menu. Figure 4 shows the window before any decision has been made concerning single or multiple samples. Single-Sample To make up a single sample, click the Single-Sample button. Under the SingleSample button, Pure and Mixture buttons and a slider, which is used to set the percentages of the components in a mixture, will appear as shown in Figure 5. The MultiSample button will be disabled. If you want a pure sample, click the Pure button and then click the name of a compound in the scrolling list.

Figure 3. Selecting a data file.

Figure 4. The Make-up Standards and Unknowns window is used for sample preparation.

Figure 5. Preparing a sample.

To create a mixture, click the Mixture button. Use the slider to select the percentage of the first component of the mixture, and then click the name of the compound in the scrolling list. If you do not set a percentage before clicking the name of compound, a reminder will be displayed. Select the percentage for the second component, and then the name of the compound. Continue until all of the components you want have been added to the mixture. A component may be removed by clicking its name in the list a second time. A mixture can contain up to 10 components. The counter below the list of compounds and the colored bar 2-6

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will help you keep track of the number of components you have selected and the relative amount of each in the sample. The maximum percentage of the slider always reflects the remaining percentage for the mixture. If the first component percentage is set to 35%, then the maximum on the slider will be 65%. Thus to set the last component percentage such that the percentages add to 100%, just set the slider to the extreme right and select the final component. If you are making up a single mixture, pointing at the Number of Components box will give the makeup of the sample.

Percentage of components of a sample must alw ays add up to 100%. This condition is enforced either by limiting the total to 100% or by increasing the final component percentage to a value suc h that the total is 100%.

To create an unknown sample, click the Unknown Setup button on the right side of the screen (Figure 5). If your instructor has assigned an unknown, click the radio button (small circle) in front of Assigned, and select the name of the unknown from the scrolling list, then click Finish. To have the program generate an unknown for you, click the radio button (small circle) in front of Random. The computer will select a random unknown that may have up to six components, or you can specify the number of components in your unknown by using the slider. Unknowns are created from information in the data file you selected when you started the program. To complete a single sample, click the large DONE button or the Go button. Multi-Sample To make up a set of samples (up to 10), click the Multi-Sample button. Under the Multi-Sample button, Pure and Mixture buttons and the slider, which is used to set the percentages of the components in a mixture, will appear. The Single-Sample button will be disabled. The Pure, Mixture, and Unknown buttons work as described above for the SingleSample. After the fist sample is specified, again click Pure, Mixture, or Unknown to create the next sample. Continue until all samples have been created. Only one unknown may be included in a set of samples.

It is not possible to edit samples in a series after the samples are completed. The whole series must be redone . (When you are making up real samples , it is very difficult to change the percentage of only one component of a mixture . At least,there is no chemical disposal problem here .) To redo a series of samples , just click New Sample , and all of the old samples will be discarded. Clicking the New File button will clear out the present data and allow you to load a new data file .

Figure 6a shows the sample window as it is being used to make up a fourcomponent sample that will be part of a series of samples. Figure 6b shows the selection of an unknown from the Assigned list. When you have completed a single sample or a series of samples, it is time to start the GC instrument.

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Figure 6a. Preparing a multicomponent sample.

Figure 6b. Choosing an unknown sample.

GC-Start-up
Click the Go button to bring up the navigation menu. Click the second button, and the GC-Start-up window will be presented as shown in Figure 7. First, choose a column for your separation by clicking a column type and its packing polarity in the Column Selections area. A Capillary column will give the fastest separation and the narrowest peaks but requires a very small sample Figure 7. The GC-Start-up window contains the main (no more than 0.1 l). The instrument controls. Megabore column is nearly as good at separations and can use a larger sample (up to 5 l). The Packed column can accommodate the largest sample (up to 10 l), but gives broad peaks and longer retention times. The packing polarity used depends on the sample. Polar packings tend to retain polar compounds and Nonpolar packings tend to retain nonpolar compounds. In a real situation, too much retention means a component may be permanently adsorbed to the column. This is a condition to be avoided because replacing a column can be expensive. Turn on the instrument by clicking the START button. The Main Power light should turn green and say On. Now choose the carrier gases to be used. You can select from helium, air, and hydrogen (labeled He, Air, H). In Figure 8, all gases are on because the flame ionization detector (FID) is in use. The pressure and flow settings are fixed and can not be changed. 2-8

Figure 8. FID detector in use.

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Choose a detector for the instrument by clicking on one of the DETECTORS graphics. The thermal conductivity detector (TCD) requires that the helium carrier gas be on. If the FID is chosen, all of the gases must be on (as shown in Figure 8). There are reminder messages if you forget. After clicking the FID, notice that a small button appears in the graphic labeled IGNITION. Click this button to ignite the flame necessary for operation of the detector. The FID detector is much more sensitive than the TCD detector. The last choice available on this window is the Injection Volume. The program defaults to a volume, depending on the column selected, but it is often necessary to experiment with the volume injected to get the best chromatogram. Capillary columns require very small samples. The FID must be used as the TCD is not sensitive enough. The packed column can be used with larger samples but may overload the FID, so the TCD must be used with the packed column. The megabore column may be used with either detector.

GC Main Control Panel

Choose Go and then click the third button in the navigation menu bar. This brings up the GC Main Control Panel, shown in Figures 9 and 10. You must decide whether to use Isothermal or Programmed temperature control of the gas chromatograph. For sample mixtures with distinct differences in boiling points or polarities of the components, isothermal control will probably work well. If the components boiling points are close together or very widely spread, however, temperature programming may be necessary to achieve a good separation. Isothermal Operation The GC Main Control Panel for isothermal operation is shown in Figure 9. Click the Isothermal button and then set the three sliders in the top half of the screen to the temperatures. The Injector and Detector must be set at least 50 C higher than the Column Oven. The column chosen determines the maximum temperature for the column oven. When Isothermal operation is chosen, all the programming controls located in the bottom half of the screen are disabled. Programmed Operation For programmed operation as is shown in Figure 10, click the Program button. The temperature controls in the bottom half of the screen become active and must be set. In Figure 10, the controls have been programmed. The top control, Initial Temp, is used to set the initial temperature of the column. The initial temperature User Reproducible

Figure 9. Isothermal operation of the GC.

Figure 10. Programmed operation of the GC.

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must be lower than the final temperature. The Initial Hold slider sets how long the program waits at the initial temperature before starting to increase the temperature. The Heating Rate slider is used to set the rate (C/min) at which the temperature rises to the final temperature setting, which is set using the Final Temp slider. The bottom slider, Hold, is used to set the time the temperature remains at the final temperature before it is reset to the initial temperature. When the temperature program has been set, click the Lock button and a graph of your program will be shown on the right, as in Figure 10. The Lock button must be clicked in order for the program to take effect. There is a reminder if you forget. You must also set the Injector and Detector temperatures located in the top half of the screen. These temperatures must be at least 50 C higher than the final temperature setting (Final Temp) in the programmed settings.

Manual Injection-Integrator/Plotter
Click Go and then click the Manual Injection-Integrator/Plotter button (fourth button in the navigation menu bar). The manual injection window is shown in Figures 11a and 11b. If you have only a single sample, it must be run using the manual injection window. If you have multiple samples you can use either manual injection or the autosampler.

Figure 11a. Manual injection with isothermal operation.

Figure 11b. Manual injection with programmed operation.

The ready light must be green before an injection can be made. The ready light turns from red to green when all temperatures reach their set values. If you click the Inject button while the ready light is red, an error message is displayed. If you are using a single sample click the Inject button to inject the sample. If you are using multiple samples, then you must first pick a sample to be injected. Click the Pick button. Figure 12 shows the window 2-10

Figure 12. Select a sample to inject.

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that displays the set of samples. Click the sample you wish to inject and then click the Inject button. If a message appears saying that the column temperature is so low that a component or components will remain on the column then you must increase the temperature of the column in order to get all the components off the column. A real GC instrument gives no such warning. Not getting all the components off a column leads to the peaks for these components showing up in the next chromatogram. It is a condition to avoid. Click OK and then return via the navigation menu bar to the GC Main Control Panel to set a higher temperature. You can move back and forth between windows as many times as necessary to get a complete chromatogram. The default run time for a manual inject chromatogram is 90 min., which produces a chromatogram the full width of the window. For programmed operation, the time is set by the length of a temperature program. You can click the reset button to stop a chromatogram at anytimebut remember that if you stop too soon all components may not be detected. There is no warning if you reset with more components to go! The Attenuator and Integrator buttons are described below.

Autosampler Loader
If you have multiple samples, it is probably best to inject them using the autosampler. However, it is a good practice to determine the best separation conditions using the single manual injection before you run the autosampler. To use the autosampler, click Go and the fifth button in the navigation menu bar. This brings up the Autosampler Loader window as shown in Figure 13a. To load samples into the autosampler tray, click a sample with the left mouse button. The cursor changes into a vial. Drag the vial to a numbered location on the autosampler tray and then release the mouse button. Figure 13b illustrates the window after six samples have been loaded into the sample tray.

Figure 13a. The Autosampler Loader for samples 15.

Figure 13a. The Autosampler Loader for samples 6 10.

If you forget which sample you have placed in a position in the autosampler tray, click and hold the left mouse button on the position. If the sample is a known mixture, click the right mouse button and the makeup of the mixture will be displayed, as shown in Figure 13a. Otherwise, the sample at that location will reappear in the list and remain visible until the right button is released.

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If you decide that you want to rearrange the samples in the tray, click Reload Tray and replace the samples in the new order. It is not necessary to place all samples in the tray, but only the samples in the tray will be injected. At the bottom of this window is the Run Time setting control. This control determines how long the chromatogram lasts after the injection. Setting this can save considerable time, but it is possible to end the chromatogram too soon and miss a peak. The system defaults to 33 minutes, which is the maximum time for any run. The run will stop at the end of a programmed temperature run, at the run time you set, or 33 minutes, which ever comes first. To set a time, click the Run Time button, then use the slider to set the desired time. Click the Ready button to switch directly to the first autosampler output window (Figure 14a). The autosampler output windows are shown in Figures 14a and 14b. Click the START button to start the autosampler. Samples will be injected one after another and the chromatograms will appear. The system will automatically switch to the next window (see Figure 14b) for the samples beyond five. Empty positions in the autosampler tray will be skipped. The autosampler will run until chromatograms of all samples are completed. If you need to stop the autosampler, click the Stop Turntable button. The autosampler will stop after the completing the chromatogram of the sample that is presently running. You cannot stop a chromatogram in progress. Figure 14b shows the window after the chromatogram of sixth sample has been completed. The Attenuator and Integrator buttons are described below.

Figure 14a. Autosampler output for samples 15.

Figure 14b. Autosampler output for samples 610.

The Attenuator and Integrator

Both the manual injection and autosampler output windows include Attenuator and Integrator buttons. Unless otherwise noted, the buttons behave the same way in both windows. Attenuator Button Click the Attenuator button to bring up a slider that allows you to attenuate (decrease) the signal so that the peaks of a chromatogram will not go off the top of the plot. The attenuator works in steps of powers of 2; thus the sample may be decreased by a factor of 2, 4, 8, etc. up to a factor of 1024. The attenuator button and setting are visible in Figures 11a, 11b, and 14b. The attenuation affects only the plotting and does not affect the area of a peak.

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Integrator Button The Integrator function is much more complex than the attenuator. There are two levels of operation for the integrator. The one referred to as dumb displays the retention time, area of a peak, and percentage area (see Figure 11a.) The other level is called smart because it can also identify the compund(s) in the sample (see Figure 16). Retention time is used to identify a compound from a chromatogram.

You must provide retention time data for the compounds , at the current operating conditions, to the integrator in order to identify compounds correctly .

To use the dumb integrator, click the Integrator button, then click the Dumb button. In the manual injection window, the integration results will automatically appear in the GC Simulator REPORT in the lower left corner as soon as the chromatogram is complete. In the autosampler window, click a finished chromatogram to display the GC Simulator REPORT for that chromatogram. To use the smart integrator, click the Integrator button, then click the Smart button. The program asks if you wish to make a list of known compounds and their retention times for the integrator to use in its identification routine. If you select Cancel you will be returned to whichever integrator was active prior to clicking the Smart button. If you click No then the smart integrator will be used, but it will not be able to identify compounds and the printout will show blanks where the names would have been printed. If you select Yes, you will be presented with the data entry window shown in Figure 15. Enter the name of each compound you wish to identify and its associated retention time. The cursor should be blinking in the top left open block. If not, then click there. Type the compounds name as you wish it to be displayed by the integrator. (You can type up to 18 characters, but only the first 12 will be displayed on the chromatogram. Subscripts and superscripts are not allowed. Press the Enter key, and the cursor will jump to the retention time box and enter the retention time. This box allows only numbers and a decimal to be entered. Only values between 1 and 95 minutes are allowed. Press the Enter key when you have finished. To place the compound into the list press the Enter key again or click the Add button. Continue to enter compound names and retention times in this manner until you have entered all of the compounds you wish to identify. Compounds may be entered in any order. The listed items cannot be edited, but individual entries may be removed from the list by clicking the entry and then clicking the Remove button. Click Clear List to remove all entries from the list. When the list is satisfactory, click the DONE button. The data you have entered will be used Figure 15. Enter compound name and by the smart integrator to identify retention time for the smart integrator. peaks in a chromatogram.

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Remember, if you c hange the chromatographic conditions suc h that the retention times of the components c hange, the integrator will still identify peaks according to your entered data and will probably identify all or some of the compounds incor rectly. You must update the data in this list after any suc h changes. The data entry box ma y be called bac k by clicking the Smart button and then clicking Yes .

The integrator is not really very smart. In practice, gas chromatography is not a good method of identifying unknowns unless the unknowns are closely related molecules. The peak identifier routine looks at a window around the retention time you enter, from shortest retention time to longest. If peaks are close together, the routine may incorrectly identify the compound with the longer retention time. In the manual injection window, the integration results will automatically appear in the GC Simulator REPORT in the lower left corner as soon as the chromatogram is complete. In the autosampler window, click a finished chromatogram to display the GC Simulator REPORT for that chromatogram. If you click a chromatogram before selecting an integrator, a reminder will appear. Figure 16 illustrates the result of clicking a chromatogram. The identification algorithm looks for a peak within a window of 10% of the retention time entered in the known list. If two peaks are found within the window, both are identified with the same name. This is normal operation and not a program bug. Switching between the two autosampler output windows may be done using the navigation menu or the 610 or 15 buttons.

Figure 16. The components are correctly identified.

Printing
It is not possible to print a copy of a chromatogram or report directly from the program. In order to obtain a printed copy, you must print screen captures. Press Print Screen to copy the entire viewable screen to the clipboard. Holding down the Alt key while pressing the Print Screen key copies only the active window. If you do this when an integrator report is visible, you can capture an image of the report. A captured screen can be pasted into a graphics program or word processor and then printed. Other screen capture programs are available.

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Student Exercise
The steps below illustrate the operation of GC Simulator and show how it can be used to identify the components of an unknown mixture. Refer to the Getting Started and User Directions sections of this manual for general operating instructions and the figures showing the program windows.
1. 2a. Start GC Simulator . Click Go at the opening window and then c lick OK in the reminder. Click the first button (Make-up Standar ds and Unknowns ) in the navigation menu bar. Select cmpdata.gcd in the data file selection window and c lick OK. You are now at the Make-up Standar ds and Unknowns window , whic h is used for sample preparation. You will prepare six samples: four samples containing pure known compounds , a mixture of the four known compounds , and unknown sample. b. c. Click the Multi-Sample button. To prepare a pure sample , click the Pure button, and then click the name of the compound in the scrolling list. Prepare pure samples of benzene , toluene , ethylbenzene , and o-xylene . Prepare a mixture containing equal amounts of the four compounds . Click the Mixtur e button and set the slider to 25% . Click benzene. Again set the slider to 25% and then click ethylbenzene . Again set the slider to 25% and click toluene . Now set the slider to the extreme right (note that this is 25%) and c lick o-xylene. To obtain an unknown sample , click the Unknown Setup button and then click the radio button (the small circle) in front of Assigned . Scroll down the list of available unknowns, and select the unknown labeled Student #2 . Click the Finish button. Click the DONE button to end the sample preparation. Click the Go button to display the navigation menu bar, and then click the second button, the GC-Star tup button. In the GC-Startup window , you will c hoose a column and pac king material, turn on the GC instrument, turn on carrier gases, choose a detector, and determine the volume of sample to be injected. b. c. d. e. 4a. Click the Meg abore column and Nonpolar packing. Click the Star t button. Click the button for each of the three gases ( He , H , and air ) and then select the FID by c licking its image. Click the IGNITION button on the FID. Check the Injection Volume to be sure it is set to less than one microliter ( 1 L). If necessary, adjust the volume using the slider. Click the Go button to display the navigation menu bar, and then click the third button, GC Main Contr ol Panel button. In the window that opens , you will program the temperature for your separations . Click the Program button and then set the temperature programming controls at the bottom of the screen as follows: Initial temp: 95 C Initial Hold: 3 min. Rate: 12 C/ min. Final Temp: 135 C Final Hold: 10 min. c. Click the Lock button.

d.

e.

f. 3a.

b.

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d. 5a. b. Set both the Injector and Detector temperature controls located in the top half of the screen to 200 C . Click the Go button. Click the Autosampler Loader button in the navigation menu bar. Click, hold, and drag the first sample to the 1 position on the autosampler tray then release the mouse button. Repeat this procedure until each of the samples has been placed in an empty position, 16. Click a position on the tray using the left mouse button to show the content of that position. Click the right mouse button on the position of the known mixture to display its components . Click the Run Time button and set the run time to 20 minutes. Click Ready . This will bring up the output window for samples 1 through 5. Click the Attenua tor button and use the slider to set the attenuator to8. Click the STAR T button. The autosampler will begin the process of obtaining a c hromatogram for eac h sample. Note that the autosampler will wait for the column to cool down between eac h run. When Sample 6 is reached, the window will automatically switch to the 610 output window . When the process is done you will be at the 610 output window . You can switc h back by clicking the Go button and then selecting the 15 output window button from the na vigation menu bar or by clicking the 1-5 button in the upper right corner of the screen. Click the Integra tor button and then click the Dumb button. Click each chromatogram to see its integrator report. Click on the Integra tor button and then click the Smart button. Click Yes in the message box. Enter the names and retention times of each of the four pure compounds from the c hromatograms . Click DONE when you are finished Click the chromatogram of eac h pure compound and the known mixture . The smart integrator now identifies their components . Notice that the percentages in the known mixture are not exactly what you entered originally (25% eac h). There is some variation in the response of the detector to eac h component. Click the unknown chromatogram. The integrator reports the identities of the components and their percentages . Use the information from the known mixture to correct the percentages of the compounds in the unknown. What is the composition of the unknown mixture? Click Go and then Exit . Answer OK to the confirmation question in order to exit the program.

c. d.

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