Thermo Scientific Nicolet iS5 FTIR Spectrometer

Overview

The Thermo Scientific Nicolet iS5 Fourier-transform infrared (FTIR) spectrometer measures how a sample absorbs infrared light. The resulting spectrum is useful for identifying or comparing many organic, polymeric, biological, and other molecular materials.

Most Breakerspace FTIR work uses the iD7 attenuated total reflectance (ATR) accessory, which is left on the instrument by default. ATR makes it straightforward to collect spectra from many solids, semi-solids, powders, pastes, and liquids with minimal sample preparation. The lab also has an iD1 transmission accessory and a Pike Technologies EasiDiff diffuse reflection accessory for less common workflows.

This page is the operating page for the FTIR. It combines the quick reference for trained users, detailed training notes, reservation link, manuals, and exercises.

Quick Actions

Two-page Quick Guide For trained users. Print on Letter paper at 100%, two-sided, flipping on the long edge.

Full instrument page Print front and back

DMSE Breakerspace · Trained-user reference

Nicolet iS5 FTIR Spectrometer

Collect a clean ATR spectrum, preserve the data, and leave the crystal ready for the next user.

What FTIR shows

FTIR records how a sample absorbs infrared light as its molecular bonds vibrate. The spectrum is a pattern of bands that can support material identification or comparison. With ATR, the signal comes mainly from the material touching the diamond crystal, so clean surfaces and good contact matter.

Choose the routine ATR approach

Sample	Starting approach
Flat solid	Clean face; self-leveling tip; firm contact
Powder	Small, finely ground amount; concave or self-leveling tip
Non-volatile liquid	Small droplet; no pressure tip
Volatile liquid	Volatiles cover; ask if odor or exposure is uncertain

Compatible samples

• Use only non-hazardous materials and approved cleaning solvents.
• Use powders sparingly and clean the entire crystal plate afterward.
• Samples must not spill, crumble into the instrument, stain the plate, persistently smell, or damage the diamond.
• Ask first about sharp, sticky, abrasive, very hard, reactive, odorous, unknown, staining, or difficult-to-clean materials.

Read the spectrum carefully

• Compare the full pattern with a known reference, database match, control, or related sample.
• Weak signal often means poor ATR contact.
• Negative bands can indicate a dirty crystal during background collection.
• Water vapor, carbon dioxide, solvent, and residue can add features.
• Complex mixtures such as coffee give combined fingerprints, not a direct concentration of each ingredient.

DMSE Breakerspace · Nicolet iS5 FTIR Spectrometer

Routine ATR trained-user workflow

1 Start and collect a background

1. Leave the FTIR powered on unless staff have instructed otherwise.
2. Log on to Windows with your MIT Kerberos and open OMNIC.
3. Confirm that the instrument is connected in system status.
4. Wear nitrile gloves. Remove the ATR cover and inspect the crystal and plate.
5. Clean the crystal with isopropyl alcohol and a Kimwipe; allow it to dry.
6. Remove gloves before using the workstation and collect a background with nothing on the crystal.

2 Load the sample

1. Wear gloves before handling the sample, pressure tower, tip, or crystal area.
2. Place the sample directly over the diamond using the appropriate approach from Side 1.
3. For solids or powders, center the pressure tower and tighten until the clutch slips.
4. For a liquid, use a small droplet; use the volatiles cover when appropriate.
5. Remove gloves before returning to the computer.

3 Collect and save

1. Preview the spectrum and check signal strength, baseline, and obvious contamination.
2. If needed, wear gloves and improve sample contact or clean and recollect the background.
3. Collect the sample spectrum with a descriptive name.
4. Select and save every spectrum you need individually. Preserve the native spectrum file before exporting plots or reports.
5. Repeat the clean/background/load/collect/save cycle when contamination or comparison quality requires it.

4 Clean and close

1. Save and copy all data you need.
2. Wear gloves, unload the sample, and remove all visible residue.
3. Clean the crystal and surrounding plate with isopropyl alcohol and a Kimwipe.
4. Replace the crystal cover and clamp it in place with the pressure tower.
5. Remove gloves, close OMNIC, and log out of Windows.
6. Leave the FTIR powered on and remove samples, wipes, and waste from the area.

What This Instrument Shows You

The Basic Idea

FTIR spectroscopy uses infrared light to probe molecular vibrations. Molecules are not still objects: their bonds stretch, bend, twist, and rock. When infrared light has the right energy to drive one of those motions, the sample absorbs some of that light. The FTIR records absorption across many infrared wavelengths and displays the result as a spectrum.

Different chemical bonds absorb infrared light in different regions. For example, O-H, N-H, C-H, C=O, and C-O bonds tend to produce recognizable features. The lower-wavenumber “fingerprint” region can be especially useful because many molecules have distinct combinations of peaks there.

The ATR accessory makes the measurement easier by pressing the sample against a diamond crystal. Infrared light reflects inside the crystal, and a very shallow evanescent field interacts with the sample touching the crystal surface. Good contact matters: if the sample does not touch the ATR window well, the spectrum may be weak or misleading.

What Scientists Use It For

• A chemist might compare an unknown powder with reference spectra to ask whether it is closer to a polymer, sugar, salt, oil, or other material class.
• A materials scientist might check whether a plastic, coating, adhesive, fiber, film, or residue has the expected chemical signature.
• A biologist or bioengineer might compare dried biological materials, gels, scaffolds, or treated surfaces to look for broad molecular differences.
• A conservator, artist, designer, or archaeologist might identify binders, coatings, paper additives, textile fibers, or surface contamination.
• A student might use FTIR after microscopy: first see that a residue, film, or fiber is present, then ask what kind of molecular material it may be.

What To Look For In The Results

Start with the main peaks. Ask where strong absorptions appear, whether they are broad or sharp, and whether expected regions are present or missing. A broad feature can suggest O-H or N-H stretching; strong peaks near the carbonyl region can point toward molecules with C=O bonds; clusters of peaks in the fingerprint region can help distinguish similar materials.

Then compare, rather than relying on one peak alone. FTIR is most useful when you compare a sample spectrum with a known reference, a database hit, a control sample, or before/after spectra from the same project. A good match usually means several major features line up, not just one peak.

Think about how complicated the sample is before interpreting the spectrum. FTIR can be very useful for pure samples, suspected contamination on a mostly known material, or mixtures with a limited number of likely components. In those cases, you may be able to ask focused questions such as “does this look like polyethylene?”, “is this residue oily?”, or “did this surface pick up a silicone-like contaminant?” The answer is usually based on matching a pattern of peaks to a reasonable comparison, not on reading a chemical name from the spectrum.

For chemically complex bulk mixtures, the interpretation changes. Coffee is a good example: brewed coffee, roasted beans, or coffee residues contain many different reactive compounds mixed in unknown ratios. The FTIR spectrum of the bulk material is a combined molecular fingerprint from everything the infrared beam samples. That fingerprint can still be useful for comparison, such as comparing green and roasted coffee, different extraction methods, or before/after treatment, but it usually cannot be deconvoluted into a reliable list of individual compounds or concentrations.

For ATR spectra, also look for practical problems. A weak spectrum may mean poor crystal contact. Negative absorbance features can mean the crystal was dirty during background collection. Water vapor, carbon dioxide, contamination, and leftover solvent can all add features that do not belong to the sample.

What This Instrument Cannot Tell You

• FTIR usually identifies molecular features or material classes, not a complete formulation by itself.
• It cannot turn a complex bulk mixture into a list of every chemical component. When many compounds contribute overlapping peaks, the combined spectrum may be useful for comparison but not for assigning each peak to one ingredient.
• It is much stronger for pure samples, known materials with possible contamination, or simple mixtures than for unknown mixtures with dozens, hundreds, or thousands of components in unknown ratios.
• It cannot reliably identify materials that do not absorb infrared light strongly.
• It is often less direct for metals, ceramics, salts, and inorganic materials than for polymers, organics, and molecular solids.
• A database match is evidence, not proof. Similar materials can have similar spectra, and mixtures can be difficult to interpret.
• ATR mostly samples the material in contact with the crystal. A coating, residue, or surface layer can dominate the spectrum even if the bulk material underneath is different.

Standard Operating Protocol

Instrument Startup

• Power on the instrument, if needed.
• Log on to the instrument workstation using your MIT Kerberos.
• Start OMNIC software.
• Verify instrument connection using system status.
• Remove the protective cover from the ATR crystal plate.
• Clean the ATR crystal.
• Collect a background before loading samples.

Operation

• Wear nitrile gloves when handling samples, ATR accessories, the pressure tower, pressure tips, Kimwipes, or cleaning solvent.
• Remove gloves before using the keyboard, mouse, or instrument workstation.
• Clean the ATR crystal before each sample or whenever contamination is possible.
• Choose the sampling method and pressure tip appropriate for the sample.
• Load the sample so it makes good contact with the ATR crystal or the selected accessory.
• Collect the sample spectrum.
• Save each spectrum you need. Spectra must be selected and saved individually.
• Wear gloves again before unloading the sample or cleaning the crystal.
• Repeat background, sample collection, cleaning, and saving as needed.

Instrument Shutdown

• Save all data you need.
• Close OMNIC.
• Log off the workstation.
• Clean the ATR crystal.
• Put the cover on the crystal plate and clamp it in place using the pressure tower.
• Leave the instrument powered on. The manufacturer recommends leaving the instrument powered when not in use.
• Leave the work area clean and remove all samples, wipes, and waste.

Compatible Materials And Quick Sample Prep

• Samples must be non-hazardous and safe to handle in the Breakerspace.
• Many solids, semi-solids, powders, pastes, and liquids can be measured by ATR.
• Cleaning solvents must also be non-hazardous. Isopropyl alcohol is the routine cleaning solvent for the ATR crystal.
• Samples should be dry enough, stable enough, and contained enough that they will not spill, crumble into the instrument, stain the crystal plate, or leave persistent odor.
• Volatile liquids may evaporate during collection and should be discussed with staff if containment or exposure is uncertain.
• Powders should be used sparingly and cleaned completely after collection.
• Sharp, sticky, abrasive, hard, reactive, odorous, unknown, staining, or difficult-to-clean samples should be discussed with staff before measurement.

If you have any questions about whether a material is appropriate to characterize in the Breakerspace, please ask before bringing it to the lab.

Quick Method Selection

Detailed Operating Instructions

The sections above are meant as a quick reference for trained users. The sections below are written as a training guide for new users and include the practical details, images, and troubleshooting cues that are easiest to understand at the instrument.

Most users should start with ATR. ATR is fast, tolerant of many sample forms, and easy to clean when only non-hazardous materials are used. The most common preventable FTIR problems are a dirty ATR crystal during background collection, weak sample contact, unsaved spectra, and residue left on the crystal after use.

ATR Sample Preparation And Loading

To maximize signal strength, the sample must make good contact with the ATR window. Collect a background before loading samples.

Solid Samples

• Select the self-leveling pressure tip.
• Use a solid sample with a smooth, clean face where possible.
• Cover the ATR crystal with the sample.
• Position the pressure tower over the window.
• Tighten the knob until the clutch slips to provide clamping pressure.

Although many solid samples will not contaminate the window, wipe the window with isopropyl alcohol and a Kimwipe between samples.

Powder Samples

It is especially important that powders contact the surface of the diamond window as completely as possible, so finely ground powders often work better. Preview mode can help verify that the pressure tip is pushing the powder into intimate contact with the ATR crystal before collecting a spectrum.

• Either the concave or self-leveling pressure tip can work. Try both if one does not give good contact.
• Use a spatula to place a small amount of powder sufficient to cover the ATR crystal.
• Position the pressure tower over the ATR crystal.
• Tighten the knob until the clutch slips.
• Clean the crystal and surrounding plate completely after measurement.

Liquid Samples

• Place a small droplet of sample on the ATR crystal.
• Non-volatile liquids can be run uncovered without the pressure tower.
• Volatile samples can be covered with the volatiles cover to reduce evaporation. Clamp the volatiles cover with the pressure tower.
• Clean the crystal and surrounding plate completely after measurement.

Cleaning The ATR Crystal

• Apply a few drops of isopropyl alcohol to a Kimwipe.
• Wipe with the wetted portion of the Kimwipe, starting in the center and working outward.
• Use a dry portion of the Kimwipe, or a new Kimwipe, to dry the crystal and surrounding area.
• Confirm that no residue, powder, fibers, or droplets remain before collecting a background or leaving the instrument.

Experiment Setup

Experiment setup allows you to change collection parameters to fit the measurement. For faster collections, reduce the number of scans or scan resolution and note how the estimated time changes. To improve the signal-to-noise ratio, increase the number of scans.

There are two ways to collect a spectrum, with preview on or off. If Preview data collection is selected, the instrument shows a live spectrum that refreshes during preview mode. Once you are satisfied with the sample setup, run the full scan by clicking start collection in the upper right. Deselect Preview data collection if you want to bypass preview and run the full scan immediately. This setting applies to both background and sample collection.

For a comprehensive explanation of the experiment setup parameters, select help in the lower left.

Preview Data Collection Enabled

Preview Data Collection Not Enabled

Background Collection

Before collecting spectra, collect a background spectrum.

A background spectrum is a single-beam spectrum obtained without a sample in place. The background spectrum is the result of the output of the source; the response of the beamsplitter, optics, sampling accessory or holder, and detector; and any atmospheric absorptions inside the spectrometer. A single-beam sample spectrum can be ratioed against the background spectrum to remove the effects of the background and produce a transmission spectrum. (Definition from the Thermo Scientific OMNIC Help Topics)

• iD7 ATR accessory background collection is run with the cleaned diamond crystal exposed to air and no pressure clamp.
• iD1 transmission accessory background collection is run with no sample in the compartment.
• EasiDiff diffuse reflectance background collection is run on a sample cup holding pure KBr powder.
• Set up the instrument for your experiment and click Collect Background.
• After the background is collected, you can choose to add it to the spectra window or not. In both cases, that background scan will automatically be used for subsequent sample collections.

Negative absorbance in an ATR spectrum can indicate the crystal was not clean during background collection.

Sample Collection

Once the background is collected, load the sample according to the instructions above and click Collect Sample. Follow the process based on your experiment setup.

If preview is enabled, use the live spectrum as a practical check. If the signal is weak, improve contact between the sample and ATR crystal, adjust the pressure tip, or ask staff whether the sample is appropriate for ATR.

Volatiles Cover

Pressure Tips

Data Processing And Analysis

Data processing is beyond the scope of this operating page, but useful next steps include baseline correction, labeling major peaks, exporting spectra, and comparing unknowns with reference spectra.

The Breakerspace recommends the Wiley KnowItAll Spectroscopy Software & Libraries available through the MIT Libraries for database searching and spectral comparison when users have MIT access.

When comparing spectra:

• Compare several major peaks, not just one.
• Note whether the spectrum came from ATR, transmission, or diffuse reflectance.
• Keep track of background collection conditions, sample preparation, and cleaning.
• Save raw spectra before exporting images, reports, or processed versions.

Common Failure Modes

Manufacturer Manuals

• iS5 spectrometer user guide
• iD7 ATR user guide
• OMNIC software getting started guide
• Complete set of manufacturer manuals

Links

• Thermo Scientific FTIR sampling techniques
• Pike Technologies tips of the week

Exercises

• Level 1 - General training: Collect ATR spectra from a known plastic, a paper product, and a non-volatile liquid. Save each spectrum and note which handling step affected signal strength most.
• Level 1 - Cleaning check: Collect a background on a clean crystal, collect a sample, clean the crystal, then collect a second background. Compare whether any negative features or residue-related peaks appear.
• Level 2 - Sample-contact comparison: Collect the same solid sample with weak contact and with proper pressure. Compare signal strength and peak quality.
• Level 2 - Unknown comparison: Collect an unknown non-hazardous polymer or residue and compare it with a known reference or database result. Report the evidence for and against the proposed identification.
• Level 3 - Accessory comparison: With staff guidance, compare ATR with transmission or diffuse reflectance for a sample where the method choice changes the spectrum.