ThermoFisher Scientific Nicolet AEM User manual

Nicolet AEM
with OMNIC Paradigm software
User Guide
269-361900 Revision A March 2023

© 2023 Thermo Fisher Scientific Inc. All rights reserved.
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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.

Auxiliary Experiment Module
This document describes how to safely operate the Thermo Scientific Auxiliary Experiment Module
(AEM), an optional sampling module for your Nicolet™ iS™50 spectrometer.
NOTICE
Be sure that all persons operating this system read the Site and Safety
manual first.
Auxiliary Experiment Module 3
Conventions used 5
Other documentation 6
About the AEM 7
Important features 9
From the front 10
Inside the sample compartment 11
Back panel features 15
Thermo Scientific Nicolet AEM User Guide 3
Chapter 1

Auxiliary Experiment Module
Operating precautions 17
Setting up the AEM 19
Connecting a purge source 19
Installing sidewall adapters 20
Changing detectors 20
Cooling a detector 21
Checking performance 25
Performance verification and qualification workflows 25
System status 26
Collecting spectra 29
Preparing the AEM for sampling 29
Measuring data 30
Maintenance 33
Checking the desiccant 33
Replacing sample compartment windows 35
Troubleshooting 37
AEM does not respond (loss of communication) 37
Spectroscopic signal is reduced 37
No IR beam present in AEM sample compartment 38
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Conventions used
This document uses these conventions for providing safety and other special information:
DANGER
Avoid hazard. Indicates a hazardous situation which, if not avoided, will
result in serious injury or death.
WARNING
Avoid hazard. Indicates a hazardous situation which, if not avoided,
could result in serious injury or death.
CAUTION
Avoid hazard. 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.
Thermo Scientific Nicolet AEM User Guide 5
Conventions used

Other documentation
Other documentation
The AEM User Guide and the Site and Safety supplement describe spectrometer use and
maintenance. Since using the AEM is similar to using one of those spectrometers, we will sometimes
refer you to online documentation for more information.
We provide basic instructions for using the accompanying OMNIC Paradigm software. In-depth
instructions for most accessories are included with the particular accessory. Further information on
how to operate the software can be found in the OMNIC Paradigm User Guide.
6 Nicolet AEM User Guide Thermo Scientific

About the AEM
The NicoletAEM provides you with an additional sample compartment for data collection. Using
either OMNIC Paradigm software or the AEM Touch Point, you can quickly redirect the infrared (IR)
beam path from the spectrometer to the AEM and begin 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:
lAll Thermo Scientific Smart Accessories
lOther baseplate-mounted sample compartment accessories
lThe TGA interface, which can be connected to a compatible thermal gravimetric analyzer
Note The AEM cannot be fitted with iS50 purge shutters, the IR beam polarizer, the ABX
(automatic beamsplitter exchanger), or the built-in ATR Module. The Raman Module can only be
used in the main spectrometer sample compartment and does not work with the Nicolet AEM.
Figure 1-1: An iS50 spectrometer with the AEM
Thermo Scientific Nicolet AEM User Guide 7
About the AEM

About the AEM
ANicolet iS50 FTIR Spectrometer
BAEM
TheNicolet AEM provides these enhanced features:
lIntegrated iS50 design
lPush button configuration
lHigh efficiency optics (redirects the IR source from the spectrometer)
lUp to three dedicated IR detectors
lOptional purge
For information about additional sampling modules and accessories for your NicoletiS50
spectrometer, contact our sales representative in your area.
8 Nicolet AEM User Guide Thermo Scientific

Important features
This section describes the major features of the Nicolet AEM. Before operating the AEM, you should
be familiar with the fundamentals of FTIR spectroscopy and the operating characteristics of your
FTIR spectrometer.
Thermo Scientific Nicolet AEM User Guide 9
Chapter 2

Important features
From the front
Figure 2-1: AEM front view
AExternal beam port
BDetector compartment
CDesiccant compartment
DDetector fill port
ESample compartment
FTouch Point
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These features are visible from the front and sides of the AEM:
lSample 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.
lDetector compartment. Like the iS50spectrometer, up to three detectors (two interchangeable
and one fixed DTGS) can be installed in the AEM at the same time. For more information, see
"Changing detectors".
lDetector fill port. Used to add liquid nitrogen to the dewar to cool an MCT detector before each
use. For more information, see "Cooling a detector".
lExternal beam port (left side). Light from the spectrometer passes through this port to the AEM
sample compartment input optics.
lDesiccant 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".
lTouch 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.
LED status Meaning
On Ready for use
Off System is not configured for AEM sampling
Blinking Optics are reconfiguring
Table 2-1: AEM status indicator states
Inside the sample compartment
There are two connectors inside the sample compartment of the AEM.
Thermo Scientific Nicolet AEM User Guide 11
Important features

Important features
Figure 2-2: Inside the AEM sample compartment
lPurge Out connector. Can be fitted with a purge exhaust to disperse purge gas into the AEM
sample compartment.
lAccessory 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.
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.
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.
CAUTION
Avoid personal injury. Improper or unsafe cabling can cause damage to your
accessory and may create a safety hazard.
lOnly qualified persons should connect custom hardware to the Accessory
connector inside the AEM sample compartment.
lDo not use this connector for signals that exceed a ±12 VDS. Limit the
current to a maximum of 500 mA.
This table contains pinout information for the Accessory connector.
Pin Number Description
3, 8 +5 VDC
Table 2-2: Accessory connector pinout descriptions
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Pin Number Description
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)
2Sample compartment motor +
15 Sample compartment motor -
18 Sample compartment detector +
5Sample compartment detector -
20 SDA (for detector communication)
7SCL (for detector communication)
1SDA (for digital communication)
14 SCL (for digital communication)
Thermo Scientific Nicolet AEM User Guide 13
Important features

Important features
Figure 2-3: Sample compartment dimensions
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Back panel features
Figure 2-4: AEM back panel connectors
AAccessory
BPurge input
Thermo Scientific Nicolet AEM User Guide 15
Important features

Important features
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.
Table 2-3: Back panel connectors
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Operating precautions
lUse only dry 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.
lSome detectors that can be used with the Nicolet 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 spectrometer and the
AEM Site and Safety supplement.
Thermo Scientific Nicolet AEM User Guide 17
Chapter 3

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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
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 either nitrogen or dry air supplied
by a purge gas generator or pure air generator (available from us). Please refer to your Site and
Safety 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 dry 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
A purge is required when chlorinated or fluorinated solvents are present, purge. Failure to purge
could cause accelerated corrosion of optical components and void the system warranty.
Thermo Scientific Nicolet AEM User Guide 19
Chapter 4

Setting up the AEM
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").
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.
Adjust the AEM purge gas pressure and flow rate as described below.
Purge Pressure Purge Flow
20 psig 20 SCFH
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.
Installing sidewall adapters
If you plan to use an accessory that is purged through the sample compartment windows (such as a
gas cell), remove the windows and install sidewall adapters to provide a flat surface for the purge
tube to tighten against before you install the accessory.
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.
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 cryo-cooled detector. The fixed DTGS detector is a
standard component 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.
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