Susan J. Kohler

November 5, 1998

The Nicolet FTIR is really pretty straightforward to use, and has excellent introductory tutorials on CD and good help files. Here is just a little bit of quick information to get you started.

Startup: Turn on the PC and monitor if they are powered off. When the PC has booted, double click on the "EZ OMNIC" icon to start the Nicolet software. You will be asked for a user name. You can use "pchem" or "organic" or another name if one has been set up for your course or project. The use of the proper login name gets you to the proper directory paths for data storage and retrieval.

Window Overview: When the program opens, the window will look like this:

OMNIC runs in a series of windows, and comes up by default in Window1 (see the title in the top bar of the window.) OMNIC will sometimes open other windows (i.e. the Subtract window) while it is working, and you will often have the option of adding spectra to either an existing window or a new window. You can navigate between the windows by using the pulldown Window menu at the top of the screen.

Near the top of the screen is a small white window labeled Experiment where the name of the experimental setup is located:

An arrow at the right side of this activates a pulldown menu which shows other available experimental setups. Below this is a row of buttons to perform various tasks, and then below the button bar is a white title bar which displays the title of the currently active spectrum:

If multiple spectra are displayed in the same pane (the window for the spectral display is the pane), then the pulldown menu activated by the arrow to the right of the title bar shows the titles of all available spectra. The blue button with the white "i" to the left of the title bar activates a display containing information about the spectrum including the title, date collected, acquisition parameters, and comments. Next comes the pane for the spectrum, and finally there is a row of buttons for spectral analysis.

Experiment Choice: In the Experiment window which is located near the top of the screen, you will see the name of an experimental setup (like "pchem default"). The name is that of the last setup in use; you can use the pull down menu to select the proper one for your experiment. You may also modify the experimental conditions by choosing the Experimental Setup option from the Collect pulldown menu.

Running an Experiment: If your experimental setup includes running a background scan either before or after your sample scan, it is sufficient to just click on the Collect Sample button to run both the sample and background scans. At the end you may be asked for a name for your spectrum. This will be a descriptive name (a title), not the filename under which it is stored. The storage filename is specified as part of the Experimental Setup (see above). You may also be asked if you would like to add the spectrum to the window; you should say yes to get the spectrum into the window so that you may manipulate it. Note the title which you gave the spectrum appears in a window just above the spectral display. You may display more than one spectrum at a time in the same window. The "active" one will be red. To make two spectra active at once (i.e. if you want to add or subtract them), hold down the Ctrl button while selecting them.

Expansion: Once a spectrum is displayed in the spectral pane, you may wish to expand a region to examine it in more detail. To do this, click with the left mouse button and (while holding down the button) drag a rectangle around the region of interest. Then release the button and click again while the cursor is in the expansion box. The region of interest will fill the pane. If you look at the small window at the bottom of the OMNIC window, you will now see a gray copy of your spectrum with a white region corresponding to the expansion region:

You may move the expansion region by dragging the white region, or change its size by dragging one of the edges. There are arrows on the left and right sides of the display which will also resize the expansion dimensions. To return to full display, simply double click on the expanded region.

Peak Picking and Annotation: You may find the peaks automatically by clicking on the Find Peaks button (the threshold is adjustable) or manually. To do it manually, click on the button at the bottom of the screen with the blue "T" on it:

Then place the cursor on a peak and click. The frequency in wavenumbers will appear with a line to the point on the spectrum. If you wish to change the text, just type in what you want it to say. If you hold down the mouse button, you can drag the writing to a different part of the spectrum. The lines which attach the numbers to the axes may be turned off and other annotation controlled through a setup menu under the Display Setup choice on the View menu.

Subtraction: Two spectra may be subtracted by displaying them in the same window, selecting both of them as active (Hold down Ctrl key while clicking with the mouse on the second spectrum), displaying them as Absorption spectra (click on the Absorb button), then clicking the Subtract button. You will get a new OMNIC window entitled Subtract and a display with three panes of spectra: the two originals and their difference.

The slide bar to the left allows you to scale one spectrum relative to the other for better subtraction. The title bar at the top of the panes gives you options for adding the spectrum to a new window, replacing the original spectrum with the results, or adding the spectrum to an existing window.

To Continue: There are many options for data manipulation, library searches, finding peak areas, baseline smoothing, etc., etc. You should look at the help menus and just try out various options, and watch the tutorials on the CD.

To End: Remove your sample and shut down the computer. DO NOT turn off the spectrometer itself.

This is just an introduction, and I will be happy to provide more instructions as you think necessary.

The tutorials are good, and the help files provide information about resolution, number of scans, etc. The tutorial disk should live in the computer. Also, the software is on a number of PCs in both room 230 and 215, so data can be saved (to a floppy?) and worked with in another location.

If the spectra look bad, you should run an alignment procedure. This is supposed to be done ‘every week or so" and is easy to do. First, check the interferogram pattern when there is no sample in the beam. This can be done by choosing Experimental Setup under the Collect pull down menu. From the Experimental Setup page, choose the Bench tab. The interferogram should be approximately 10 volts peak to peak (note Max and Min values are printed on the page above the display). If it is less than this, do the align. This is done by going to the Diagnostic tab (still within the Experimental Setup page) and clicking on the Align.. button.

There is an option for storing spectra automatically. If this is chosen, all the spectra will have the base name as indicated on the Collect page of the Experimental Setup. Doing this, of course, will generate vast quantities of data which can later be removed. As long as we set up the proper paths for different courses, this should not be a problem. I’ll be glad to help.