User Instructions for JASCO Model 420 FTIR (located in YH1033)

1. INSTRUMENT START-UP. Make sure that the IR spectrometer has been turned on.


Start the spectra manager from the desktop screen on the computer. You will first have to use the spectra measurement program. Go to (Measure-parameter) and read in the default file ( The preset parameters are 16 scans with 4 cm-1 resolution and a measurement range of 250–4000 cm-1. This will be good enough for most standard measurements. A better resolution usually leads to very noisy spectra under those conditions.

Spectral range. Note that unless the instrument purge is quite rigorous, there will be considerable spectral interference from water vapor below 400 cm-1. For most of the applications, the suitable range is thus 400 to 4000 cm-1. To change the range, go to Settings-measurement range.

Number of scans and resolution. In measurement program: go to Measure-Parameters-Standard. The menu pops up with scan times: 16 (default). This can be changed in increments 2n. The resolution is set to 4 cm-1 as default. It can be set from 1 to 16 cm-1.

Y-axis. You can choose whether your spectra are plotted with the y-axis as absorbance or as % transmittance (%T). In the measurement program, go to Measurement-Parameter-Standard. The bottom half of the window is for selecting the vertical axis (%T is default). It can be changed to absorbance units by clicking the mouse.

Background spectrum. Make sure that the lid of the sample compartment is closed. Allow the sample compartment to purge for some time. Obtain a background IR spectrum by clicking the icon B in the upper left corner of the screen. The spectrum should show weak bands from water vapor (3000-3500 cm-1, 1600–1750 cm-1 and below 400 cm-1) and CO2 (twinned peak around 2350 cm-1). If the bands have significant intensity (i.e. strong enough to potentially interfere with the analysis of your sample), run it again to see if these peaks get smaller. If this doesn't happen, please inform the person in charge about the problem.

3. SAMPLING. To obtain an IR spectrum, you will have to either prepare a KBr-pellet (prepare the sample in the lab upstairs or in the hood in YH1033), a Nujol mull between CsI-plates or put your neat sample between IR plates if it is a liquid. Note that your the window material may be IR-opaque in some wavelength region(s). Be sure to choose a window material that will allow you to obtain spectral information in the region of interest. Both CsI and polyethylene are transparent throughout the spectral range of this instrument.

4. INSERTING SAMPLE AND ACQUIRING SPECTRUM. The instrument is a 'top-loader'. Open only the window on the top, insert your sample in the holder, and close the lid as quickly, but gently, as possible. Wait at least one minute to purge the air from the sample chamber. Then press the S button with the mouse to obtain the spectrum of your sample.

5. SPECTRAL ANALYSIS. After the spectrum is obtained, the spectrum analysis window will pop up with the recorded spectrum.

Here you will be able to do the following things:

a. Correct the baseline manually. (Processing-Correction-Baseline, short cut: icon with blue and red line). Use the cursor to move the line where you need it. The upper window is the work window, the bottom one shows the result after baseline correction.

b. Label peaks automatically and manually. (Processing-Peak Process-Peak find, short cut: spectrum with yellow tips).
The pre-set threshold (noise level) is 10%, which provides usually good results. However, sometimes the program does not identify certain peaks, e.g., shoulders not clearly resolved from main peaks, so you will have to label these manually. Use the cursor and move the line to whichever feature you want to label, and then press “Add” in the upper left corner. The peak will be labeled later on the printout. The label consists out of a number. A list of these labels will be on the bottom of the printout. Make sure that you print from this window, otherwise you will lose all the labels.

You should always type in some identifying information about the sample before you print your spectrum (Processing-Options-Comment). You may find it particularly helpful to type in your lab notebook page and spectrum number. This makes it easier to identify the spectrum later.

c. Save spectrum. (File-Save as) If you need to keep the data and want to process it later elsewhere, please save it on a disk. You have the option to save it as a JWS file (Jasco format) or as ASC (ASCII format). Please save your files in the Chem30CL (on desktop) folder. Spectra will be deleted in regular intervals to keep the hard drive on the spectrometer computer uncluttered. If you decide to store your files in JWS format, you need to ask the person in charge for assistance in installing the program disk on your own computer. Both ASCII and JASCO formats can be read and processed with a variety of software packages, including LabView, SpectraCalc, Kaleidegraph, and IGOR.