Thermo Scientific Nicolet iS50 GC-IR User manual

Nicolet iS50 Spectrometer
iS50 ATR Module
User Guide
269-277500 Revision A June 2012

© 2012 Thermo Fisher Scientific Inc. All rights reserved.
Windows is either a trademark or a registered trademark of Microsoft Corporation in the United States and/or
other countries. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
For U.S. Technical Support, please contact:
Thermo Fisher Scientific
5225 Verona Road
Madison WI 53711-4495 U.S.A.
Telephone: [phone]
E-mail: [e-mail]
World Wide Web: http://www.thermo.com/spectroscopy
For International Support, please contact:
Thermo Fisher Scientific
Telephone: [phone]
E-mail: [e-mail]
World Wide Web: http://www.thermo.com/spectroscopy
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
For Research Use Only. This instrument or accessory is not a medical device and is not intended to be used
for the prevention, diagnosis, treatment or cure of disease.
WARNING Avoid an explosion or fire hazard. This instrument or accessory is not
designed for use in an explosive atmosphere.

Thermo Scientific iS50 ATR Module User Guide 1
1
iS50 ATR Module
The optional iS™50 ATR module offers convenient, reproducible attenuated total reflection
(ATR) sampling with the Nicolet™ iS50 spectrometer.
Figure 1. Nicolet iS50 spectrometer with optional iS50 ATR module
The iS50 ATR module provides these enhanced features:
•Built-indesign
• Push button configuration
• All-reflective diamond optics
• Dedicated broad-band detector
• Extended spectral range
The iS50 ATR module mounts in the main cover of the spectrometer.
iS50 ATR module

1iS50 ATR Module
2iS50 ATR Module User Guide Thermo Scientific
For information about additional sampling modules and accessories for your Nicolet iS50
spectrometer, contact our sales representative in your area.
For general information about the ATR technique including processing, searching and
analyzing ATR spectra, refer to the document or help topic titled “Tips for ATR Sampling.”
Conventions Used in this Document or Help System
This manual uses these conventions for providing safety and other special information:
Contents
•Important Features
•Specifications
•Compatible Software
•Operating Precautions
•Operation
•Compatible Samples
•Your First Experiment
•Sampling Accessories for the ATR Module
•Maintenance
•Troubleshooting
NOTICE Be sure that all persons operating this system read the site and safety manual
first.
NOTICE Follow instructions with this label to avoid damaging the system hardware or
losing data.
Note Contains helpful supplementary information.
Tip Provides helpful information that can make a task easier.

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 3
Important Features
Figure 2. iS50 ATR module features
The iS50 ATR module features include:
•Diamond crystal. A robust, durable material for ATR sampling. The crystal is brazed to
the crystal plate to maximize strength and chemical resistance.
• Crystal plate. The stainless-steel mount for the diamond crystal. The crystal plate is
permanently sealed to protect internal mirrors and optimize purge performance.
•Sampling plate. This plate can be removed for cleaning or sterilizing.
•Pressure tower. The pressure tower is a mechanical press used to achieve uniform contact
between a solid or powder sample and the ATR crystal (up to 267 N or 60 lbs of force).
The arm swings out of the way for easy access to the sampling area. The pressure tower
can be removed when analyzing only liquids.
•Pressure tip. The ATR module comes with two stainless-steel tip styles that can be used
to optimize contact between the sample and the diamond crystal. The extra tip can be
stored on the pressure arm.
•ATR Touch Point. This button automatically configures the spectrometer for ATR
sampling. The Touch Point LED shows the status of the ATR module. The LED has
three states described below.
Diamond crystal
Crystal plate
Sampling plate
Pressure tower
Pressure tip
Extra Pressure tip
and tip storage
ATR Touch Point

1iS50 ATR Module
4iS50 ATR Module User Guide Thermo Scientific
Table 1. iS50 ATR status indicator states
The ATR module spectral range options are the same as for the spectrometer and are
dependent upon the spectrometer configuration. Refer to the spectrometer help topics or user
guide for more information.
Specifications
Table 2. iS50 ATR module specifications
LED status Meaning
On Ready for use
Off System is not configured for ATR sampling
Blinking Optics are reconfiguring
Feature Specification
Crystal material Diamond, Type IIa
Crystal shape, size Round, 2.8 mm (0.11 in) diameter
Sampling zone 2 mm (0.08 in)
Refractive index 2.4 @ 1000 cm-1
Angle of incidence 45 degrees (single bounce)
Depth of penetration 2.0 micrometers at 1000 cm-1 for a sample material that
has refractive index of 1.5
Maximum sample thickness 12.7 mm (0.5 in)
Useful pH range 1 to 14
Pressure arm maximum force 267 Newtons (60 lbs)
Detector Dedicated broad-band DTGS (deuterated triglycine
sulfate)

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 5
Compatible Software
Table 3. Software compatible with the iS50 ATR module
Operating Precautions
To maximize the life of your ATR accessory or module, heed these precautions:
• Do not apply pressure to the bare crystal (the pressure tower should not be used for the
background collection).
• Do not use the pressure device to crush a sample.
• Do not apply pressure to the crystal for extended periods.
• Make sure your sample will not react with the ATR crystal or crystal plate. Each material
has unique characteristics. Please refer to the “Specifications” section for details.
• Do not scrape the crystal with extremely hard materials such as corundum, or with a knife
to remove particles.
Software Use for...
OMNIC™ Configuring the ATR workflow, including quantitative analysis and
spectral search, and collecting and analyzing ATR spectra. For more
information, see “Your First Experiment.”
To improve search results using a transmission reference library, use
the Advanced ATR Correction feature in OMNIC software. For more
information, refer to the “About the Advanced ATR Correction tool”
topic in “Tips for ATR Sampling,” or open OMNIC Help Topics and
find the “Using Advanced ATR Correction” topic.
OMNIC Specta™ Analyzing unknowns. This software includes enhanced algorithms, a
spectral database and features for using your computer’s hard drive as a
library. OMNIC Specta also offers a unique multi-component search
feature that makes it easy to identify the spectra of mixtures.
TQ Analyst™ Creating quantitative and classification methods that can be used with
OMNIC software. For more information, see the help system in your
TQ Analyst software.
NOTICE
• The diamond crystal, while very robust, can be broken if small, very hard materials
(like cement or metal beads) are compressed against it at maximum pressure, or if the
pressure tip is not centered on the crystal.
• Do not use the ATR module with concentrated sulfuric acid (H2SO4) or potassium
dichromate (K2Cr2O7); they will react with the diamond crystal.

1iS50 ATR Module
6iS50 ATR Module User Guide Thermo Scientific
• Do not use abrasive cleaning agents, pads or strongly acidic or basic solutions to clean
metallic surfaces of the accessory as these will damage the finish.
Operation
This section covers the following topics:
•Using the Pressure Tower
•Changing the Pressure Tip
•Removing and Installing the Sampling Plate
Using the Pressure Tower
Figure 3. Pressure tower features
Use the large knob to raise and lower the pressure arm. When using the arm to apply pressure
to a sample, rotate the control knob clockwise until you feel and hear a click. At this point the
maximum force (267 N or 60 lbs) is achieved and additional rotation of the control knob has
no effect. This mechanism is designed to protect the crystal from damage.
To raise the pressure arm, turn the control knob counterclockwise.
NOTICE Be certain the pressure is fully released before you move the pressure arm
horizontally.
To use the pressure tower ( watch video)
Pressure control knob
Pressure arm in sampling position
Pressure arm in
resting position

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 7
The pressure arm rotates to the side for sampling liquids or changing the tip. The pressure
tower can be removed if necessary. See “Installing and Removing the Pressure Arm” for more
information.
Changing the Pressure Tip
Figure 4. Pressure tip features
The tip can be screwed on and off while the pressure arm is raised. Move the arm to the
resting position for easy access. The following tip styles are available.
NOTICE
• Move the pressure arm away from the sampling area before you change the tip.
• Make sure the tip is properly threaded. The base of the tip should press against the
pressure arm when fully installed.
• Do not use tools to loosen or tighten a pressure tip. Using tools may damage the tip.
• Do not overtighten the tips.
To change the pressure tip ( watch video)
Pressure tip (installed)
Extra tip

1iS50 ATR Module
8iS50 ATR Module User Guide Thermo Scientific
The extra tip can be stored on the pressure arm.
Removing and Installing the Sampling Plate
Figure 5. Sampling plate features
Move the pressure arm to the sampling position (shown above) before you remove the
sampling plate.
To release the sampling plate, lift the back edge. To reinstall it, gently press down on the plate
until it seals against the O-ring around the crystal plate.
Table 4. Tip styles
Tip style Use with...
Flat The end of this tip is flat, which makes it ideal for measuring films
and flat plastics as well as tiny shavings and fibers. This is a general
purpose tip style.
Concave The end of this tip is slightly concave to allow good contact with
powders and curved solids such as a tablet or polymer bead.
NOTICE
• Make sure the sampling plate is installed before you place a sample on the ATR
crystal.
• Avoid damaging or contaminating the ATR internal optics. Keep samples and other
lab materials away from the ATR module when the sampling plate has been removed.
Sampling plate

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 9
Compatible Samples
The ATR module can be used to analyze any sample that allows good contact with the surface
of the crystal and has an index of refraction less than 2.0 (most organic materials range
between 1.3 and 1.7).
ATR is an excellent technique for measuring the composition of liquids, powders and bulk
solids or the surface properties of a layered solid. Because the effective pathlength is short,
ATR is especially useful for analyzing strongly absorbing or thick samples which often
produce large unreadable peaks when measured directly by infrared transmission. The ATR
technique also eliminates the sample preparation required to run these types of samples by
transmission.
For a detailed list of materials that are easy to measure by ATR, refer to the document or help
topic titled “Tips for ATR Sampling.”
Your First Experiment
This section explains how to configure your ATR workflow and demonstrates how to use the
ATR module to analyze a solid and a liquid sample. These topics are covered:
•Configuring Your ATR Workflow
•Measuring a Solid Sample by ATR
•Measuring a Liquid Sample by ATR
Configuring Your ATR Workflow
The ATR Touch Point has an associated user-configurable workflow that can define
everything from background and sample collection to quantitative analysis and spectral
search. You simply press the Touch Point to start the workflow. The Touch Point can also be
used to respond to prompts in the software while the workflow is running.
To configure your ATR workflow
1. Start OMNIC software.
The OMNIC window is displayed. For information about the OMNIC window, choose
Help > OMNIC Help Topics.
2. Choose the ATR Touch Point button in the software to configure the instrument for ATR
sampling.
NOTICE Do not use the ATR module to analyze concentrated sulfuric acid (H2SO4) or
potassium dichromate (K2Cr2O7); they will react with the diamond crystal.

1iS50 ATR Module
10 iS50 ATR Module User Guide Thermo Scientific
Figure 6. Touch Point Setup button location
3. Choose the Touch Point Setup button in the software.
A dialog box is displayed.
Notice that Sample Location (upper left pane) is set to ATR, and below that pane is a list
of iS50 ATR experiments. The selected experiment is highlighted and its associated
settings are visible in the dialog box.
The Touch Point Setup dialog box provides commonly used settings that define how your
ATR data will be collected, displayed, measured and reported. Brief descriptions are
provided below.
Touch Point Setup button
ATR Touch Point button

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 11
Table 5. iS50 ATR Touch Point Settings
Option Description
Measurement time Determines the duration of scanning for a sample data
collection.
Number of scans Shows the scans collected for the selected measurement time.
Multiple scans are averaged.
Resolution Sets the spectral resolution of the data you collect. Typically
4cm
-1 or occasionally 2 cm-1 are appropriate for most ATR
applications. The smaller the resolution value, the higher
(better) is the resolution. The resolution value, along with the
measurement time, affects the number of scans.
Final format Determines the Y-axis unit used for the collected data.
Typically set to log(1/R) or %Reflectance for ATR
applications.
Preview data
collection
Select this option if you want to collect and view (but not save)
preliminary data before the start of a sample or background
data collection. This lets you verify that your experimental
conditions are correct before collecting the spectrum.
Region Determines the spectral range of the spectrometer that will be
used to collect the ATR data. The spectral range is defined by
the type of source, beamsplitter and detector used. One of
more of the following options may be available:
•Mid-IR - useful for measuring organic materials,
polymers, plastics, rubbers and many other materials.
•Far-IR - ideal for inorganic materials that are blended in
plastics or paints including fillers, flame retardants and
structural composites such as glass fibers. To maximize the
signal for the far-IR beam path, use Collect > Experiment
Setup > Bench to set Gain to 8.
•NIR - The NIR region is generally not useful for ATR
sampling because, in most cases, the depth of penetration
is too shallow to produce a usable spectrum.
Note: Collecting data in multiple regions (must be done
sequentially) can be useful for finding differences between
compounded materials that contain fillers and other inorganic
compounds.
Max/Min Shows the default limits of the selected detector’s spectral
range. The Max/Min limits can be reduced to eliminate
spectral regions that provide no additional information about
the sample.

1iS50 ATR Module
12 iS50 ATR Module User Guide Thermo Scientific
Background handling Lets you specify when to collect a background spectrum to be
used for ratioing sample spectra you collect. Collecting a
background after a specified number of minutes is a good
choice for many applications. You will be prompted to collect a
background the very first time you collect a sample spectrum.
Analyze Measured
Sample
Allows you to select and run analyses on the collected sample
spectrum. The analysis results are attached to the spectrum
and saved in the spectral (.spa or .spg) file. The following
analyses are available:
•Quantify. Finds the concentrations of components in a
sample spectrum. For more information, open OMNIC
Help Topics and find the “Quantifying a Spectrum” topic.
To select the quantitative analysis method you want to use
to quantify a spectrum, choose Analyze > Quant Setup.
•Search. Identifies an unknown material by comparing the
unknown sample spectrum with each reference spectrum
in the selected libraries to find the spectra that most closely
match the unknown. For more information, open
OMNIC Help Topics and find the “Searching a Spectral
Library” topic.
Use Analyze > Library Setup to select the reference
libraries to be searched.
• QCheck. Compares spectra to determine their degree of
similarity, expressed as a correlation value from 0.0 (no
similarity) to 1.0 (the spectra are identical). For more
information, open OMNIC Help Topics and search for
the “Comparing Spectra with QCheck” topic.
Use Analyze > QCheck Setup to set up the comparison.
•Find Peaks. Identifies peak locations in a spectrum by
finding peaks whose Y values exceed a specified threshold
value. The peaks are labeled with their X values. For more
information, open OMNIC Help Topics and search for
the “Finding Peaks Above a Specified Height” topic.
•Threshold. The Y value above which peaks can be
found.
•Sensitivity. Determines how readily shoulders on
peaks and small peaks in the baseline will be found.
Table 5. iS50 ATR Touch Point Settings
Option Description

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 13
4. Select an appropriate experiment in the “Experiments Using: ATR” pane.
5. Set the Touch Point Setup options as desired.
6. If you want to overwrite the default settings without overwriting the default experiment,
choose Set Default.
7. Choose Save.
8. If you need to specify other experiment settings, choose Experiment Setup, set the
options as desired, choose Save and then choose OK to close Experiment Setup. For more
information, choose Help from Experiment Setup.
9. Choose OK to close the Touch Point Setup dialog box.
Measuring a Solid Sample by ATR
Before You Begin
• Power on the spectrometer and allow the instrument to stabilize. If your spectrometer has
been powered off for more than 20 minutes, this will take at least an hour.
• Select an appropriate film or other solid for your sample (we use a yellow sticky note for
this experiment).
•Makesurethesampling plate,pressure tower and appropriate tip are installed.
• Remove any previous sample from the sampling area and raise the pressure arm.
Auto Report Can be used to automatically display, print or save a basic
report of your analysis results. For more information, open
OMNIC Help Topics and find “Working with Auto Reports.”
•Preview. Displays the auto report after the analysis is
completed.
•Print. Prints the auto report after the analysis is
completed.
•Add to current notebook. Adds the report to the current
report notebook. For more information, open OMNIC
Help Topics and find “Adding a Report to a Notebook.”
Default experiment Shows the file name of the default experiment for the selected
sample location. The default experiments are write protected
to prevent them from being overwritten accidentally.
Note Some settings appear in Experiment Setup and in Touch Point Setup. Setting
these options in one location automatically changes them in the other.
Table 5. iS50 ATR Touch Point Settings
Option Description

1iS50 ATR Module
14 iS50 ATR Module User Guide Thermo Scientific
• Make sure the crystal and pressure point are clean. For cleaning instructions and
recommended solvents, see “Cleaning the Crystal.”
Figure 7. iS50 ATR module ready for a background measurement
1. Press the ATR Touch Point to select the ATR beam path and load its default workflow.
A message may be displayed while the instrument collects scans to determine stability
with the new configuration.
Note Nothing should be touching the crystal during the background measurement. If you
plan to use the pressure arm to take sample measurements, make sure the pressure point is
raised or move the pressure arm to the side.
To measure a solid sample by ATR ( watch video)
Make sure the pressure point is
not touching the crystal during
the background measurement

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 15
2. Wait until the stability test is completed, or choose OK to skip that test or Cancel to stop
all instrument tests. When the stability test is completed, another message may be
displayed while the instrument runs a performance test.
3. Wait until the performance test is completed. If the system passed the performance test,
choose OK. If the system failed the test, see “Troubleshooting.”
4. If your ATR workflow is not configured, follow the steps in the “Configuring Your ATR
Workflow” section to configure it.
5. Press the ATR Touch Point again to start the workflow.
A message asks you to enter a spectrum title.
6. Enter a title for your sample spectrum and choose OK (or press the ATR Touch Point to
accept the default title). If the software has no appropriate background spectrum in
memory, a message tells you to prepare for the background collection.

1iS50 ATR Module
16 iS50 ATR Module User Guide Thermo Scientific
7. Make sure there is no sample on the crystal and the pressure arm is raised and then press
the ATR Touch Point to start the background collection.
As the collection proceeds, the background data appear in the OMNIC main window.
When the background collection is complete, a message tells you to prepare for the
sample collection.
8. Prepare the sample.
a. Place the sample in the center of the crystal directly under the pressure point. See
“Compatible Samples” for more information. For best results the sample should
cover the crystal completely.
b. Make sure the pressure arm is in the sampling position.
c. Lower the pressure arm by rotating the pressure control knob clockwise until you feel
and hear it click. The tip should be pressed firmly against the sample.
9. Press the ATR Touch Point to collect the sample spectrum.
When the spectrum is completed, a message asks whether to add it to a window.
10. Choose Yes to add the spectrum to the selected window and complete the workflow.
If your workflow specifies an analysis such as quantify or search, those steps occur
automatically. To see the analysis results, choose the “r” button to the left of the title box
above the OMNIC spectral window.
Pressure arm
Crystal

1 iS50 ATR Module
Thermo Scientific iS50 ATR Module User Guide 17
The sample spectrum and its associated analysis results are stored in a virtual auto report.
If your workflow is set up to preview or print auto reports, the report is displayed or
printed using the default printer. Below is an example report showing an ATR spectrum
of a yellow sticky note taken with the iS50 ATR module, follow by the results from a
spectral search.
Figure 8. Auto report showing an ATR spectrum of a yellow sticky note taken with the
iS50 ATR module and the results from a spectral search
11. Raise the pressure arm and remove the sample.
12. Clean the sampling plate, crystal and pressure tip.
For cleaning instructions and recommended solvents, see “Cleaning the Crystal.”
Measuring a Liquid Sample by ATR
Before You Begin
• Select appropriate liquid, paste or gel sample (we use isopropyl alcohol for this
experiment).
•Makesurethesampling plate is installed.
•Raise the pressure arm and move it to the resting position or install the liquid sampling
kit.
• Make sure the crystal is clean. For cleaning instructions and recommended solvents, see
“Cleaning the Crystal.”

1iS50 ATR Module
18 iS50 ATR Module User Guide Thermo Scientific
Figure 9. iS50 ATR module with liquid sampling accessory ready for a background measurement
1. Press the ATR Touch Point to select the ATR beam path and load its default workflow.
A message may be displayed while the instrument collects scans to determine stability
with the new configuration.
Note Nothing should be touching the crystal during the background measurement.
To measure a liquid sample by ATR ( watch video)