Thermo Scientific Nicolet iS50 AEM User manual

Nicolet iS50 FT-IR Spectrometers
iS50 AEM
User Guide
269-295900 Revision A February 2013

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Thermo Scientific iS50 AEM User Guide 1
1
iS50 AEM
This document describes the Thermo Scientific iS50 AEM (Auxiliary Experiment Module)
which is an optional sampling module for your Nicolet™ iS™50 spectrometer. The document
covers the following topics.
Contents
•About the AEM
•Important Features
•Operating Precautions
•Setting Up the AEM
•Checking Performance
•Collecting Spectra
•Maintenance
•Troubleshooting
NOTICE Be sure that all persons operating this system read the site and safety manual
first.

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Using this Manual or Help System
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Using this Manual or Help System
This manual or help system describes how to operate the AEM. It includes important safety
precautions; always read and follow these precautions.
Conventions Used
This manual uses these conventions for providing safety and other special information:
Other Documentation
The user guide and Help system for the Nicolet iS50 spectrometer describe spectrometer use
and maintenance. Since using the AEM is similar to using one of those spectrometers, we will
sometimes refer you to the on-line documentation or system manual for more information.
We provide complete instructions for using the software in the OMNIC Help system and in
Getting Started with OMNIC Software. Instructions for most accessories are included with the
particular accessory.
WARNING Indicates a hazardous situation which, if not avoided, could result in death or
serious injury.
CAUTION Indicates a hazardous situation which, if not avoided, could result in minor or
moderate injury.
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.

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About the AEM
Thermo Scientific iS50 AEM User Guide 3
About the AEM
The iS50 AEM provides you with an additional sample compartment for data collection.
Using OMNIC software or the AEM Touch Point, you can quickly redirect the infrared (IR)
beam path from the spectrometer to the AEM and start collecting spectra. This flexibility
eliminates the need to continually change accessories in the main sample compartment.
Many of the detectors and accessories that can be installed in the spectrometer can also be
installed in the AEM including:
• All Thermo Scientific Smart Accessories
•Otherbaseplate-mountedsample compartment accessories
• iS50 TGA interface, which can be connected to a compatible thermal gravimetric
analyzer
Figure 1. iS50 spectrometer with iS50 AEM
Note The iS50 AEM cannot be fitted with iS50 purge shutters, the IR beam polarizer, the
iS50 ABX (automatic beamsplitter exchanger) or the built-in iS50 ATR module. The
iS50 Raman module can only be used in the main spectrometer sample compartment; it
does not work with the iS50 AEM.
The AEM mounts on the right side of the spectrometer
Nicolet iS50
FT-IR spectrometer
iS50 AEM

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Important Features
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The iS50 AEM provides these enhanced features:
• Integrated iS50 design
• Push button configuration
• High efficiency optics (redirects the IR source from Nicolet iS50 spectrometer)
• Up to three dedicated IR detectors
•Optionalpurge
For information about additional sampling modules and accessories for your Nicolet iS50
spectrometer, contact our sales representative in your area.
Important Features
This section describes the major features of the iS50 AEM. These topics are included:
•From the Front
•Inside the Sample Compartment
•Back Panel Features
Before operating the AEM, you should be familiar with the fundamentals of FT-IR
spectroscopy and the operating characteristics of your FT-IR spectrometer.

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Important Features
Thermo Scientific iS50 AEM User Guide 5
From the Front
Figure 2. iS50 AEM front view
These features are visible from the front and sides of the AEM:
•Sample compartment. Place your accessories and samples here for analysis. When you
collect spectra, a focused IR beam will be reflected from the spectrometer to the sample in
the AEM sample compartment. The beam is focused at the center of the sample
compartment, at a height of approximately 9 cm (3.5 in) when measured from an
installed standard transmission baseplate.
•Detector compartment. Like the iS50 spectrometer, up to three detectors - two
interchangeable and one fixed DTGS - can be installed in the iS50 AEM at the same
time. For more information, see “Changing Detectors”.
•Detector fill port. Used to add liquid nitrogen to the dewar to cool an MCT detector.
before each use. For more information, see “Cooling the AEM Detector.”
•External beam port (left side). Light from the spectrometer passes through this port to
the AEM sample compartment input optics.
Touch Point
Sample compartment
Detector fill port
Detector compartment
Desiccant compartment
External beam port

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•Desiccant compartment. Contains desiccant when the AEM is shipped from the factory
to prevent excessive moisture from damaging the optics. If the AEM is purged, you can
remove the desiccant after the purge is installed and running. If the spectrometer and
AEM are not purged, then the desiccant must be installed and the system’s internal
atmosphere monitored for humidity. For more information, see “Connecting a Purge
Source” or “Checking the Desiccant.”
•Touch Point. Automatically configures the spectrometer for sampling with the AEM. The
Touch Point LED shows the status of the AEM. The LED has three states described
below.
Table 1. AEM status indicator states
Inside the Sample Compartment
There are two connectors inside the sample compartment of the AEM.
Figure 3. Inside the iS50 AEM sample compartment
•Purge Out Connector. Can be fitted with a purge exhaust to disperse purge gas into the
AEM sample compartment.
•Accessory Connector. If you have a photoacoustic or other accessory that has a detector
or motor, connect the cable from the accessory to this standard 25-pin connector.
LED status Meaning
On Ready for use
Off System is not configured for AEM sampling
Blinking Optics are reconfiguring
Note This is not a pass-through connector. If the accessory has a 15-pin connector,
use the sample compartment accessory adaptor cable that came with your
spectrometer to connect it.
Accessory connector Purge Out connector

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Thermo Scientific iS50 AEM User Guide 7
You can also use the Accessory connector to access power and ground for your own
detectors, accessory motors, and other custom hardware located in the AEM sample
compartment.
This table contains pinout information for the Accessory connector.
Table 2. Accessory connector pinout descriptions
CAUTION Avoid personal injury. Improper or unsafe cabling can cause damage to your
accessory and may create a safety hazard.
• Only qualified persons should connect custom hardware to the Accessory connector
inside the AEM sample compartment.
• Do not use this connector for signals that exceed a ±12 VDS. Limit the current to a
maximum of 500 mA.
Pin Number Description
3, 8 +5 VDC
23 +3.3 VDC
16, 21 +12 VDC (unfiltered for motors)
10, 22 Digital ground (for +5, +3, and +12 motors)
6 +12 VDC (filtered for detectors)
19 -12 VDC (filtered for detectors)
4, 17 Analog ground (for +12 detectors and -12 detectors)
2 Sample compartment motor +
15 Sample compartment motor -
18 Sample compartment detector +
5 Sample compartment detector -
20 SDA (for detector communication)
7 SCL (for detector communication)
1 SDA (for digital communication)
14 SCL (for digital communication)

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Figure 4. Sample Compartment Dimensions

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Back Panel Features
Figure 5. iS50 AEM back panel connectors
Table 3. Back panel connectors
Related Topics
•Connecting a Purge Source
Feature Description
Purge Input Connects to the purge gas supply if the spectrometer and AEM are
purged. For more information, see “Connecting a Purge Source.”
Accessory Transmits the detector signal from the AEM and allows
communication for controlling the AEM and its accessories from the
spectrometer. The cable from this connector attaches to the Accessory
port on the back of the spectrometer. (The spectrometer has a right
and left Accessory port. Use the one closest to the AEM.)
Purge Input
Accessory

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Operating Precautions
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Operating Precautions
• Use only dried air or nitrogen to purge the AEM. The purge gas must be free of oil and
other reactive materials. Heat from the source or from laser absorption may ignite
flammable gases or reactive materials in purge gas.
• Some detectors that can be used with the iS50 AEM must be cooled with liquid nitrogen
before use. Follow your organization’s Personal Protective Equipment (PPE) and handling
guidelines when working with liquid nitrogen.
For more information, refer to the site and safety guide that came with your Nicolet iS50
spectrometer and the iS50 AEM Site and Safety Supplement.
Setting Up the AEM
After the AEM has been installed by our representative, you are ready to connect a purge
source. This section explains how to connect purge and also describes how to make other
adjustments to the AEM to accommodate specific accessories, detectors and experiments.
•Connecting a Purge Source
•Cooling the AEM Detector
Connecting a Purge Source
Your AEM might be purged with a source of dry air or nitrogen to prevent excessive moisture
or chlorinated and fluorinated solvents from damaging the optics. The purge gas requirements
for the AEM are the same as for the spectrometer. We recommend using dry air supplied by a
purge gas generator or pure air generator (available from us), or nitrogen. Please refer to your
Site and Safety Information guide for specific purge gas requirements.
WARNING Avoid explosion hazard. Never use a flammable, combustible, or toxic gas to
purge this instrument. The purge gas must be free of oil and other reactive materials. Heat
from the source or from laser absorption may ignite flammable gases or reactive materials
in purge gas. Use only dried air or nitrogen to purge your instrument.
NOTICE Do not use argon as a purge gas. Argon is an insulator and prevents the system
from cooling properly.
NOTICE When chlorinated or fluorinated solvents are present, purge is required. Failure
to purge could cause accelerated corrosion of optical components and void the system
warranty.

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Setting Up the AEM
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Use a splitter or gas manifold to add a second supply line from your purge source. Attach the
second supply line to the purge input connector on the back of the AEM (see the illustration
in “Back Panel Features”). For information on how to install the purge equipment, set the
controls for the first time, and inspect and clean the purge filter, find “Installing a Purge Kit”
in Spectrometer Help Topics.
Adjust the AEM purge gas pressure and flow rate as described below.
If you need to adjust the flow rate, or if your application requires a different flow rate, follow
the instructions in “Setting the purge gas controls” in Spectrometer Help Topics.
We recommend that you leave the purge on at all times. This keeps the AEM free of
undesirable gases, protects the optics and improves the system’s thermal stability.
Related Topics
•Back Panel Features
•Setting Up the AEM
Installing Sidewall Adapters
If you plan to use an accessory that is purged through the sample compartment windows, such
as a gas cell, before you install the accessory, first remove the windows and install sidewall
adapters to provide a flat surface for the purge tube to tighten against. For more information,
refer to “Replacing the Sample Compartment Windows” and “Installing a Sidewall Adapter”
in Spectrometer Help Topics, available from the Help menu in OMNIC software.
Sidewall adapters are also used to secure the optical filter holder. Sidewall adapters are
included with many optical filter kits. They may also be purchased separately.
Note The Purge Out connector on the rear wall of the sample compartment is used for
purging the sample compartment and special accessories. See “Inside the Sample
Compartment” for more information.
Table 4.
Purge Pressure Purge Flow
20 psig 20 SCFH

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Setting Up the AEM
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Changing Detectors
The AEM can have up to three detectors installed - two interchangeable and one fixed DTGS.
The interchangeable detectors are optional and are installed in the front and back positions of
the detector compartment. The front detector position holds a room-temperature detector
only. The back detector position holds either a room-temperature or a cryo-cooled detector.
The fixed DTGS detector is a standard component and located in the middle position of the
detector compartment. The fixed DTGS detector is not user replaceable. Contact us if you
suspect the fixed detector must be replaced.
Changing the detector in the front or back detector position of the AEM is not difficult using
the Snap-In™ detector design. For more information, refer to “Changing a Detector” in
Spectrometer Help Topics.
Once you have changed a detector, you must turn on the spectrometer power switch and
select the new detector by choosing Collect > Experiment Setup in the OMNIC software and
setting the Detector option, or by opening the Touch Point Setup dialog box for the AEM
and setting the Region option. See “Configuring Your AEM Workflow” for more
information.
Cooling the AEM Detector
Some applications require a highly sensitive mercury-cadmium telluride (MCT) detector.
This detector is sensitive to infrared radiation between 5000 cm-1 and 600 cm-1.
An MCT detector must be cooled with liquid nitrogen before you collect data. The MCT
detector dewar is located in the back detector position under the dewar cover on the AEM.
Note If you are installing a detector that you bought separately from the rest of the
system, the procedure may differ slightly from the one provided in the user
documentation that came with your spectrometer. Use the instructions that came with the
new detector.
WARNING Avoid shock hazards. Before changing an installed detector, turn off the
spectrometer power and disconnect the power cord. Disconnect any accessory cables from
the AEM sample compartment connectors and close the sample compartment cover
tightly.

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Figure 6. AEM detector dewar cover
Equipment needed:
• small plastic laboratory funnel
• one-liter, glass lined or stainless-steel lined laboratory vacuum bottle
• a supply of liquid nitrogen
To cool the AEM detector
1. Open the detector dewar cover and remove the plastic stopper.
2. Insert a funnel into the liquid nitrogen fill port of the detector dewar.
3. Slowly fill the detector dewar with liquid nitrogen through the funnel.
Cool the funnel and funnel stem first: fill the funnel and let it drain completely into the
detector two or three times. Always let the liquid nitrogen flow into the detector before
adding more liquid nitrogen.
A small amount of liquid nitrogen spillage will not harm the instrument, but do not
overfill the detector or pour too quickly. Cooling the detector too quickly may cause the
dewar to rapidly boil off or spill out excess amounts of liquid nitrogen.
Dewar cover
WARNING Avoid freeze burns. Liquid nitrogen is extremely cold and therefore potentially
hazardous.
• Wear protective equipment and follow standard laboratory safety practices.
• To avoid hazardous contact with liquid nitrogen, make sure any dewar or container
used to hold liquid nitrogen can do so safely without breaking.
• When filling the dewar, be careful not to contact the liquid nitrogen with your skin.
Fill the dewar slowly. Cooling the detector too quickly may cause the dewar to rapidly
boil off liquid nitrogen.

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When the detector is nearly full, a small amount of liquid nitrogen will boil off.
Approximately one liter of liquid nitrogen will be consumed in this process.
4. Let the vapor plume dissipate, replace the plastic stopper, and close the dewar cover.
Allow at least 20 minutes for the detector to cool before use.
Related Topics
•Setting Up the AEM
Checking Performance
You should periodically check the performance of the AEM by using the advanced diagnostics
performance test. Keep a log of the date each test is run and the test result. You should also
record the number of scans collected and the resolution setting.
To run the performance test
1. Open OMNIC software.
2. Choose Collect > Advanced Diagnostics.
3. Choose Performance Test.
The Nicolet iS50 Diagnostics window lists the available performance tests for each
beamsplitter available for the spectrometer.
4. Select the type of beamsplitter installed in the spectrometer.
5. Select an available AEM detector.
6. Make sure the check boxes for all the other tests are cleared.
NOTICE Do not spill liquid nitrogen onto or near the detector window. Rapid
cooling of the window’s o-ring seal can cause the dewar to lose vacuum. Prolonged
exposure to atmospheric pressure can damage the detector element. Always fill the
dewar with the instrument cover in place.

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Figure 7. Nicolet iS50 Advanced Diagnostics window
7. Choose Run Selected Test.
The software collects background and sample scans to generate a 100% transmission
spectrum and calculates the spectrum’s signal to noise ratio. The numerical result is added
to the Actual column in the diagnostics window and a Pass or Fail result appears in the
Status column. If the Actual noise value is less than the Expected (or maximum allowable)
value, the test will report a pass result.
8. Close the Bench Diagnostics window.
Related Topics
•Troubleshooting
Collecting Spectra
This section explains how to configure your AEM workflow and collect spectra. These topics
are covered:
•Preparing the AEM for Sampling
•Configuring Your AEM Workflow
•Measuring a Sample with the AEM
Note If the AEM fails the performance test, consult the troubleshooting information or
contact our local service representative for assistance.

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Preparing the AEM for Sampling
Follow these steps to prepare the AEM to collect spectra.
To prepare the AEM
1. Power on the spectrometer.
2. Install a sample holder or other sampling accessory in the AEM sample compartment.
3. Remove any sample from the sample holder or accessory and make sure there is nothing
else blocking the beam in the AEM sample compartment
4. If you are using a liquid nitrogen cooled (MCT) detector, add the liquid nitrogen to the
detector dewar. See “Cooling the AEM Detector” for details.
5. Open OMNIC software.
6. Press the Touch Point on the AEM to configure the instrument optics for AEM sampling
and load the associated workflow.
7. Choose the Touch Point Setup button in the software and adjust the Touch Point settings
as needed. See “Configuring Your AEM Workflow” for more information.
8. Wait for the system to stabilize for at least an hour (if the spectrometer had been powered
off for more than 20 minutes).
Related Topics
•Configuring Your AEM Workflow
•Measuring a Sample with the AEM
Configuring Your AEM Workflow
The AEM Touch Point has an associated user-configurable workflow that can define
everything from background and sample collection to quantitative analysis and spectral
search. After the workflow is configured, you simply press the Touch Point to start the
workflow.
To configure your AEM workflow
1. Start OMNIC software.
Note If you are using certain accessories, you may need to modify your AEM to
accept them. For example, if you are using an accessory that is purged through the
sample compartment windows, you will need to remove the sample compartment
windows and install sidewall adapters. See “Replacing Sample Compartment
Windows” and “Installing Sidewall Adapters” for more information.

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Thermo Scientific iS50 AEM User Guide 17
The OMNIC window is displayed. For information about the OMNIC window, choose
Help > OMNIC Help Topics.
2. Choose the AEM Touch Point button in the software to configure the instrument for
AME sampling.
Figure 8. AEM Touch Point buttons
3. Choose the Touch Point Setup button in the software.
A dialog box is displayed.
Figure 9. Touch Point Setup for iS50 AEM
Notice that Sample Compartment (upper left pane) is set to AEM, and below that pane is
a list of iS50 experiments for the AEM. The selected experiment is highlighted and its
associated settings are visible in the dialog box.
Touch Point Setup button
AEM Touch Point button

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The Touch Point dialog box provides commonly used settings that define how your data
will be collected, displayed, measured and reported. Brief descriptions are provided below.
Table 5. iS50 AEM Touch Point settings
Option Description
Measurement time Determines the duration of scanning for each collected spectrum.
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
8cm
-1 or 4 cm-1 is a good starting point for most 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 Absorbance for most 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 you start collecting the spectrum. This option is
typically off for most applications but can be useful when running
experiments where sample position is important such as ATR.
Region Determines the spectral range of the spectrometer that will be
used to collect the data. The spectral range is defined by the type
of source, beamsplitter and detector used. One or 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 measuring 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 - Useful for identifying raw materials and for rapid
analysis through containers such as bottles or plastic bags.
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 current detector’s spectral range.
The Max/Min limits can be reduced to eliminate spectral regions
that provide no additional information about the sample.