Simple operation of the Nicolet FTIR in the OMNIC Program

 

STEP 1:

 

From the top menu row, select:

 

COLLECT

Then choose

COLLECT SAMPLE

 

STEP 2:

 

Unless the instrument has already collected one, a dialog box appears telling you that the instrument is ready to collect the background spectrum.  Remove the sample and click OK.

 

The background will be collected automatically.

 

For most routine operations, air will be your background.  If your instructions call for another material, place it in the sample holder before collecting the background.  

 

After the background is collected, a second dialog box may appear asking if you want the background added to the main window.  Select NO.  If this dialog box does not appear, proceed to step 3.

 

STEP 3:

 

When prompted by the "collect sample" dialog box, place the sample into the instrument.

 

Click on OK.

 

STEP 4:

 

After the sample spectrum is collected, a final dialog box appears asking if you want the spectrum added to the window, select YES.

 

STEP 5:

 

Print your spectrum by clicking on the appropriate icon.

 

Click on the CLEAR icon to prepare the instrument for the next user.

 

Sign and date your printout.

 

Sign and date the logbook.

 

 

How To Use the ZnSe Crystal Sample Holders With a Solid Sample.

 

How To Use the Concave ZnSe Crystal Sample Holders With a Liquid Sample.

Advanced user operation of the Nicolet FTIR in the OMNIC Program

 

 

You must have your instructor's permission before using the advanced procedure

 

Review:

 

Infrared (IR) spectroscopy is a chemical analytical technique, which measures the infrared intensity versus wavelength of light. Light in the infrared region of the spectrum is basically heat energy. The infrared radiation is generated by a heat source, so you can think of this IR as a 100,000$ toaster! 

 

When working in the infrared region, chemists describe the frequency as the wavenumber instead of the more familiar wavelength.  Wavenumbers are measured in "reciprocal centimeters" or fractions of a centimeter.  Infrared light is categorized as:

 

Far infrared (4 ~ 400 cm-1)

Mid infrared (400 ~ 4,000 cm-1)

Near infrared (4,000 ~ 14,000cm-1).

 

Another unique convention in IR spectroscopy is the use of "percent transmission" (%T) instead of absorption as the measure of signal intensity.  In this convention we set our zero point at 100% of the infrared radiation passing through the molecule.  Then we say that no radiation passing through the molecule (0% T) is our maximum absorbance.  

 

Yes, it is confusing, but you will quickly get used to it.

 

When an infrared light interacts with the matter, chemical bonds will stretch, wiggle, contract and bend.  As a result, chemical functional groups adsorb infrared radiation in a specific wavenumber range regardless of the structure of the rest of the molecule.

 

For example, the C=O stretch of a carbonyl group appears at around 1700cm-1. Hence, the correlation of the band wavenumber position with the chemical structure is used to identify a functional group in a sample. The wavenember positions where functional groups adsorb are consistent, despite the effect of temperature, pressure, sampling, or change in the molecule structure in other parts of the molecules.

 

In the lower wavenumber regions, another type of vibration is found.  Here the entire molecule vibrates as it absorbs infrared energy.  Since no two organic compounds are the same, no two of them will vibrate in exactly the same way and therefore each will have an unique pattern of infrared light absorption.  For this reason, the lower part of the spectrum is called the fingerprint region.

 

Think about musical instruments, each may play the same notes, but no two will ever vibrate in exactly the same way.

 

Introduction to FTIR:

 

A Fourier Transform Infrared (FTIR) spectrometer obtains spectra by first collecting an interferogram of a sample signal.  Where in most types of spectroscopy, the instrument measures energy absorbed (or transmitted) at a discreet wavelength, the interferometer measures all frequencies simultaneously.

 

An FTIR spectrometer acquires and digitizes the interferogram, performs the Fourier Transform, and outputs the spectrum.  (Pretty slick, eh?)

 

The process starts with a beamsplitter that splits the incoming infrared beam into two optical beams.  One beam reflects off of a fixed position mirror.  The other reflects off of a moving mirror (typically it travels only a few millimeters.)  The two beams reflect off of their respective mirrors and are recombined.

 

The re-combined signal results from the beams "interfering" with each other, hence the name interferogram.  The interferogram signal is then transmitted through or reflected off of the sample surface.  The specific frequencies of energy are adsorbed by the sample. 

 

The infrared signal after interaction with the sample is uniquely characteristic of the sample. The beam finally arrives at the detector and is measured. The detected interferogram can not be directly interpreted. It has to be "decoded" with a well known mathematical technique, the Fourier Transformation. The computer can perform the Fourier Transformation calculation and present an infrared spectrum, which plots transmittance  (or if you prefer, absorbance ) versus wavenumber.

 

When an interferogram is Fourier transformed, a single beam spectrum is generated which is nothing more than a plot of raw detector response versus wavenumber.

 

OK, so what does all this have to do running my samples?

 

Because the FTIR uses only a single beam, there is no reference signal that can be used to subtract out atmospheric moisture and carbon dioxide.

 

A typical background spectrum will contain:

 

3500 cm-1 and 1630 cm-1 Atmospheric water vapor.

2350 cm-1 and 667 cm-1 Carbon dioxide.

 

A background spectrum must always be run when analyzing samples by FTIR. The sample single beam spectrum must be normalized against the background spectrum.

 

The final transmittance/absorbance spectrum should be devoid of all instrumental and environmental contributions. If the concentrations of gases such as water vapor and carbon dioxide in the instrument are the same when the background and sample spectra are obtained, their contributions to the spectrum will subtract out and their bands will not occur. If the concentrations of these gases are different when the background and sample spectra are obtained, their bands will appear in the sample spectrum.

 

Reference:

Brian C. Smith, Fundamentals of Fourier Transform Infrared Spectroscopy, CRC Press, Boca Raton, 1996.

 

Step 1:

 

Turn on the power for the optical bench
Open the Omnic icon on the computer desktop

Step 2:

Select the experimental method you intend to use.  There is a drop down menu at the top of the screen.  If you plan to use an existing method, proceed to step 6.

 

Step 3:

 

To create a new method, open an existing method and modify it for your particular needs.  When finished you will save it as a new method.

Under the Collect menu choice, select Experiment Setup.

Step 4:

An experiment setup menu appears with the following tabs:

Collect
Bench
Quality
Advanced
Diagnostic

Under Collect and Bench tabs you find the following parameters: 

Number of scans:  (DEFAULT is 16.)

The final spectra is an average of all of your sample's scans.  More scans reduces the noise level (increases the signal-to-noise ratio) but increases total collection time.  Be aware of diminishing returns, if you have already collected a sufficient number of scans, increasing the number of scans will not materially increase the your spectrum's quality.

Resolution:  (DEFAULT is 4.)

A higher resolution is expressed by a lower numerical value.  Resolution is the ability of the instrument to resolve closely spaced peaks.  A spectrum with a 1 wavenumber resolution has a better peak differentiation than one run at a higher resolution.   The trade-off is that lower resolution settings require the mirror to travel a greater distance and this increases the analysis time.

Correction:  (DEFAULT is NONE)

Well, why not correct the spectrum???

There are several correction modes available to the user including those for erasing the effects of water and carbon dioxide.  The ATR correct allows the user to compensate for the fact that different wavelengths of infrared radiation penetrate into the sample to different depths.  This phenomena may skew peak intensities.

The problem with applying a correction is that the resulting spectra may not match those collected using a different correction or without a correction.  

Background Handling:

(DEFAULT is BEFORE EVERY SAMPLE)

When running multiple samples, it is inconvenient to stop and collect a background before or after each one.  Setting the number of minutes between the background spectra will cause the instrument to prompt you when it is time to collect a new background.  You will, however, be prompted to collect a background the first time you run a method.

Using a stored background file will disable the collect background option except when the new method's parameters are different from those used to collect the background.  In this case, you will be prompted to collect a new background, which you can store as a background file.

Velocity:  (DEFAULT is 1.5825)

This parameter controls the speed of the moving mirror.  Faster movement allows more scans to be collected in a shorter time but at the cost of a noisier signal.  Some sampling accessories will require a slower velocity in order to increase the signal strength.  

Gain:  (DEFAULT is 2)  

The gain determines how much the detector signal is electronically amplified so that it is larger relative to the electronic noise.  Increasing the gain is useful for weak signals.  An AUTOGAIN routine is available to help set the correct amplification level.

Aperture:  (DEFAULT is 25)

Aperture refers to the size of the opening through which the infrared beam passes.  Reducing its size reduces the amount of light reaching the sample and allows the use of higher resolutions or more sensitive detectors.  Smaller apertures therefore improve stability and accuracy while larger ones improve the signal to noise ratio.

Spectral Range:  (DEFAULT is 4000 to 400)

This parameter sets the frequency range in wavenumbers for the spectra that will be stored on the hard disk.  Data outside this range will not be retained.  When using the ZnSe crystal ATR device, the lower range of the instrument should be set to 650.  

Under normal circumstances you do NOT need to alter the parameters under the QUALITY, ADVANCED, & DIAGNOSTIC tabs.

Quality:  (DEFAULT Setting = Leave the Spectrum Quality Checks box unchecked and the parameters will be grayed out.)  

The purpose of the selections under the quality tab is to reject peaks that do not meet certain criteria.  A good example is when using a special sample holder.  To determine that the sample is correctly positioned, it may be necessary to confirm that a certain peak is present.  There are also commands that check for baseline errors and extraneous signals that result from reflectance taking place
inside a sample.

Advanced:

Most of the options under the Advanced tab relate to how the Fourier Transform is performed and how the finished spectrum is presented.  Zero filling for instance allows peaks to be smoothed by inserting interpolated data points between actual data points.  Apodization (literally "cutting off the feet") addresses the errors resulting from the  process of converting a mathematically infinite Fourier Transform into a real world IR spectrum.  Phase correction takes negative signals from the detector and presents them as positive data.  A single sided interferogram results in faster data collection and is used when the instrument is operated as a GC detector or in kinetics experiments.

The remaining parameters refer to wavelengths that will be excluded from the spectrum and external control of the instrument.  Previewing data collection allows a spectrum to be displayed without being saved.  It is used to check experimental conditions before running actual samples.

Zero Filling (DEFAULT = NONE)

Apodization (DEFAULT = Happ Genzel)

Sample Spacing (DEFAULT = 2)

Phase Correction (DEFAULT = Mertz)

Low Pass and High Pass Filters (DEFAULT VALUES = 90,000 & 200.  Leaving the box unchecked will allow the filter values to be automatically calculated from the mirror velocity.)

Single - Sided Interferogram (DEFAULT = OFF)

Start Collection at External Trigger (DEFAULT = OFF)

Preview Data Collection (DEFAULT = OFF)

Consult your instructor before using the Diagnostics tab.

Step 5:

After setting up the experiment click on  SAVE AS and give your experiment a new name.  Click on CANCEL to discard your changes and start over.  

 

Step 6: