Thermo Scientific Nicolet iS50 GC-IR User manual

Nicolet iS50 FT-IR Spectrometers
iS50 Raman Module
User Guide
269-278000 Revision A July 2012

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Thermo Scientific iS50 Raman Module User Guide 1
1
iS50 Raman Module
This section describes the optional Thermo Scientific iS50 Raman module which allows you
to collect FT-Raman spectra with your Nicolet™ iS™50 spectrometer.
Figure 1. Nicolet iS50 spectrometer with iS50 Raman module installed
iS50 Raman module
The iS50 Raman module mounts in the spectrometer sample compartment.

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2iS50 Raman Module User Guide Thermo Scientific
Conventions Used in this Document
This manual uses these conventions for providing safety and other special information:
Contents
•About the iS50 Raman module
•Important Features
•Specifications
•Compatible Software
•Safety Considerations
•Operating Precautions
•FT-Raman Sampling
•Compatible Samples
•Configuring the Raman Module
•Installing the Raman Module
•Operation
•Preparing Samples
•Sampling Options
•Your First Experiment
•Removing the Raman Module
•Doing Experiments with Macros
•Maintenance
•Troubleshooting
NOTICE Be sure that all persons operating this system read the site and safety manual
first.
WARNING Indicates a hazardous situation which, if not avoided, could result in death or
serious injury.

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Thermo Scientific iS50 Raman Module User Guide 3
About the iS50 Raman module
The iS50 Raman module provides these enhanced features:
• Compact, integrated design
• Push button configuration with the optional ABX (Automatic Beamsplitter eXchanger)
• Long wavelength (low energy) excitation laser
• Dedicated detector
• Motorized sample stage
•Built-invideocamera
• Superior Raman sensitivity
• Small beam spot size
• Sample screening capabilities using our sampling templates and cluster analysis software.
The Raman module works with our ValPro™ qualification package and security
administration software and allows digital signatures and IQ-OQ-PQ-DQ certification.
Please refer to your ValPro and OMNIC™ DS documentation for more information. For
information about additional sampling modules for the Nicolet iS50 spectrometer, contact
our sales representative in your area.
Related Topics
•Important Features
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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Important Features
Figure 2. iS50 Raman module features
The iS50 Raman module features include:
•Raman sample compartment. Allows access to the Raman sampling area and sample
stage. The stage accommodates a variety of sample holders that can be quickly
interchanged.
A laser emission indicator (see below) tells you when the laser beam is present in the
sample compartment. Two independent safety interlocks ensure the laser beam is blocked
when the sample compartment door is open.
•Motorized sample stage. Used to mount a sample or sample tray in the Raman module
and to position the area of interest under the laser for analysis. Fine motor control in all
directions and built-in video camera allow precise positioning for very small samples.
•Sample compartment Touch Point. Configures the spectrometer for Raman sampling
and shows the status of the Raman module. The Touch Point LED has three states
described below.
Table 1. Sample compartment Touch Point indicator states
LED status Meaning
Off Raman module is not installed or connected properly
Blinking Optics are configuring for Raman sampling
On Raman module is ready for use
Raman sample compartment
Motorized sample stage
Laser emission indicator
Sample compartment
Touch Point
Sample holder

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Thermo Scientific iS50 Raman Module User Guide 5
•Laser emission indicator. Shows the status of the excitation laser inside the Raman
module. When this LED is lit, the laser is on. For more information, see “Tu r n i n g o n t h e
Laser and Adjusting the Laser Power.”
•Video USB cable. Allows the software to communicate with the video camera in the
Raman module. One end of the cable plugs into the Sample Compartment Accessory
port on the back of the spectrometer. The other end connects to any type A USB port on
the system computer.
•Electrical connector. Provides power to the Raman module and communication with the
spectrometer. For more information, see “Installing the Raman Module.”
Figure 3. iS50 Raman module back panel
Related Topics
•About the iS50 Raman module
•Installing the Raman Module
•Turning on the Laser and Adjusting the Laser Power
Note Two independent safety interlocks ensure the laser beam is blocked when the
sample compartment door is open.
NOTICE Do not leave samples inside the sample compartment for extended periods
when the laser is on.
Electrical connector

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Specifications
Table 2. iS50 Raman module specifications
Related Topics
•About the iS50 Raman module
•FT-Raman Sampling
•Turning on the Laser and Adjusting the Laser Power
Compatible Software
Feature Specification
Excitation source 1064 nm laser
Maximum power: 0.5 W
Reference interferogram source White light
Beamsplitter Calcium fluoride (CaF2)
or extended range potassium bromide (XT-KBr),
(located in the spectrometer)
Detector Dedicated Indium Gallium Arsenide (InGaAs),
(located in the spectrometer)
Table 3. Software used to run the iS50 Raman module
Software Use for...
OMNIC Configuring the Raman workflow, including quantitative analysis and
spectral search. Also, selecting sampling templates and processing
Raman spectra. For more information, see “Your First Expe riment” or
open OMNIC Help Topics from the Help menu in OMNIC
software.
OMNIC Raman Collecting and processing Raman data. For more information, open
the Raman menu in OMNIC software and select Raman Help Topics.
View™ Enhanced sample viewing and capturing and annotating video images.
The software works with a microscope video system and video image
to allow the image from the camera to be displayed on the computer
monitor and recorded.
TQ Analyst
Professional
Edition
Creating quantitative and classification methods that can be used with
OMNIC software. This software provides an extensive suite of
chemometrics features including Partial Least Squares and other
advanced algorithms for quantitative analysis and material
identification. For more information, open the Help menu in
TQ Analyst software and select TQ Analyst Help Topics.

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Related Topics
•Your First Experiment
Safety Considerations
The use of redundant safety interlocks on the main cover of the Raman module and on the
Raman sample compartment cover prevent accidental exposure to invisible laser radiation.
The presence of a strong magnetic field in the area may interfere with or defeat the safety
interlocks.
Related Topics
•Turning on the Laser and Adjusting the Laser Power
•Your First Experiment
Table 4. Optional Software for the iS50 Raman module
Software Use for...
Atls™ Performing automated data collection and spectral mapping
experiments as well as image analysis with the iS50 Raman module.
You can automatically collect different types of compositional maps
and display the collected data in a variety of formats. You can also
create reports containing map data and print contour maps, 3-D
displays, and comprehensive video images of the sample. For more
information, open the Atls menu in OMNIC software and select
Atls Help Topics.
Array Automation Collecting and processing data from groups of samples that are
arranged in an ordered array. The array may be rectangular as provided
by a micro-titer well plate or linear if capillary tubes are being used.
For more information, open the Array menu in OMNIC software and
select Array Help Topics.
OMNIC Specta™ Analyzing unknowns. OMNIC Specta software includes our unique
multi-component search feature for identifying the spectra of
mixtures, a 9,000 compound spectral database, and features for using
your computer’s hard drive as a spectral library. For more information,
open the Help menu in OMNIC Specta software and select the
Software Help Topics item.
WARNING Avoid laser hazard. Keep all magnets and strong magnetic fields (such as those
produced by mass spectrometers and some kinds of medical equipment) away from the
Raman module, and do not attempt to defeat the safety interlocks on the module housing
and sample compartment cover—hazardous exposure to laser radiation could occur.

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Operating Precautions
• Do not pour liquids directly onto the Raman module.
• Do not use harsh detergents, chemicals or abrasives to clean the surface of the Raman
module; these can damage the finish. For cleaning instructions and recommended
solvents, see “Maintenance.”
• Always place samples on a sample holder and then load the holder on the sample stage.
Do not place a sample directly on the stage.
• Before you install a sample holder on the sample stage, ensure the height of the holder
plus the sample (or the sample container) does not exceed 2.5 cm (1.0 in). Materials
above the maximum height may break inside the module or damage delicate mirrors and
motors located behind or above the stage. If those components appear soiled or damaged,
contact our local sales or service representative for assistance.
• Avoid spilling samples or solvents in the Raman sample compartment. Clean the residue
tray regularly; see “Cleaning the Residue Tray” for instructions.
• Do not allow moisture or cleaning products to come into contact with any part of the
interior of your sample stage. Do not attempt to clean any internal components, and do
not touch any optical surface inside the Raman sample compartment.
• Store the Raman module right side up.
Related Topics
•Raman Sample Holders
•Installing a Sample Holder
•Cleaning the Raman Module Housing
•Cleaning the Sample Stage
•Cleaning the Residue Tray
•Storing the Raman Module
FT-Raman Sampling
Monochromatic light from the excitation laser in the iS50 Raman module is directed to the
sample. When the light strikes the sample, the sample emits Raman radiation; in effect, the
sample becomes the “source” of radiation. This radiation travels through the Raman module
and spectrometer optics to a dedicated detector located in the spectrometer. The laser light,
on the other hand, does not travel past the Raman sample compartment.

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Thermo Scientific iS50 Raman Module User Guide 9
Raman Spectrum
The Raman spectrum shows the sample emission at all the frequencies measured and thus can
be used to identify the sample. Intensity is expressed in emittance units, which measure the
amount of light emitted by the sample. Frequency is expressed in terms of wavenumber,
which is a measurement of number of waves per centimeter (cm-1). In Raman spectroscopy
the X-axis is converted to Raman shift, which is a measure of the difference between the
observed spectral bands and the wavelength of the excitation laser.
The Raman Effect
When a laser beam strikes a sample, a very small portion of the laser light, less than 0.0001%,
is scattered by the sample at a frequency different from that of the excitation laser. This
shifting of the frequency is called the Raman effect, and the frequency-shifted light is called
Raman radiation. For more information, open Raman Help Topics from the Raman menu in
OMNIC software and find “Raman Shift.”
Related Topics
•Important Features
•Specifications
Compatible Samples
The Raman module can be used to measure a wide variety of samples types. Some examples
are provided below.
Table 5. Samples compatible with the Raman module
Types Characteristics Examples
Solidsa
aReduce the laser power for materials with dark inks or strong coloration such as printed tablets or carbon black
rubber. These materials may absorb the laser light, resulting in extreme heating or destruction of the sample.
Non-absorbing materials Minerals, crystals, sulfur
Tablets Non-absorbing materials Aspirin, other pharmaceuticals
Powders, granules,
pelletsb
bSprinkle a few grains or crystals onto a Raman sample holder or a standard microscope slide (metal is best but
glass works too) attached to a Raman slide holder. If a powder is loosely packed, you can improve the Raman signal
by pressing the powder into a pellet and then placing the pellet on a Raman sample holder. We offer an optional
powder press for this purpose. Contact our representative for details.
Granular or crystalline
powders
Active and inactive pharmaceutical
ingredients, polymer pellets
Liquids, gelsc
cPlace a few drops of liquid directly into one of the wells in the 9 or 48 well sample holder, or into a small cup or
pan that fits the sample holder recesses, or into a vial that fits the Raman vial holder.
Non-absorbing materials Clear solvents, sol-gels

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Several styles of sample holders are provided with the iS50 Raman module for fast,
reproducible sampling of solids, liquids, powders and gels. For more information, see
“Preparing Samples.”
Related Topics
•Raman Sample Holders
•Installing a Sample Holder
•Removing a Sample Holder
•Using the Defocusing Lens to Adjust the Beam Size
•Cleaning the Residue Tray
Configuring the Raman Module
This section explains how to configure the iS50 Raman module the first time it is installed on
a Nicolet iS50 spectrometer.
Before you begin, check that the following software is installed on the computer connected to
the Nicolet iS50 spectrometer:
• Thermo Scientific OMNIC, version 9, SP1 or higher
• Thermo Scientific View version 9, SP1 or higher, or
Thermo Scientific Atls, version 9, SP1 or higher
To configure the Raman module
1. Make sure the spectrometer and computer are powered on (allow at least 20 minutes for
the spectrometer to stabilize).
NOTICE
• Do not spill liquids directly onto the Raman module.
• Always place samples on a Raman sample holder and then load the holder on the
Raman sample stage. Do not place a sample directly on the stage.
• Before you install a sample holder on the sample stage, ensure that the height of the
holder plus the sample (or the sample container) does not exceed 2.5 cm (1.0 in).
Materials above the maximum height may break inside the module or damage delicate
mirrors and motors located above or behind the stage.
• Avoid spilling samples or solvents in the Raman sample compartment. Clean the
residue tray regularly; see “Cleaning the Residue Tray” for instructions.
Note You do not need to configure the iS50 Raman module each time you install
OMNIC software; only the first time OMNIC software is used with the Raman module.

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2. Close OMNIC, View and Atls software if they are open.
3. Install the Raman module in the spectrometer sample compartment.
4. Start OMNIC software.
The Microscope Configuration dialog box is displayed.
Figure 4. Microscope Configuration dialog box
5. Set Microscope to iS50 Raman Module and choose Save.
6. If beamsplitters must be installed manually for your spectrometer, install the CaF2or
XT-KBr beamsplitter in the spectrometer beamsplitter compartment. For more
information, find “Using Beamsplitters” in Spectrometer Help Topics.
7. Align the interferometer.
The system remembers the alignment settings for each beamsplitter. This means the next
time you use the Raman module, you won’t necessarily need to align the spectrometer. See
“Aligning the Interferometer” for instructions and information about how often to
perform this step.
Related Topics
•Installing the Raman Module
Note If the Microscope Configuration dialog box does not appear after you start
OMNIC software, the Raman module has already been configured.
Note If you have the optional ABX (automatic beamsplitter exchanger), the correct
beamsplitter installs automatically after you install the Raman module.
Note To see the iS50 Raman module configuration settings at any time, open View
software and choose Microscope > System Configuration.

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Installing the Raman Module
This section explains how to install the iS50 Raman module in the sample compartment of
your Nicolet iS50 spectrometer.
To install the Raman module
1. Remove the sample compartment cover from the spectrometer, any connectors at the
back of the sample compartment, and the Snap-In™ baseplate (if installed).
For more information, find “Using Your Spectrometer” in the Spectrometer Help Topics
or the Nicolet iS50 User Guide.
2. Remove any optional filters or energy screens that may be installed on the left or right side
of the spectrometer sample compartment.
For more information, find “Installing or Removing Optional Hardware” in the
Spectrometer Help Topics or the Nicolet iS50 User Guide.
3. Connect the Video USB cable that came with the Raman module.
Plug one end of the cable into the Sample Compartment Accessory port which is located
at the bottom of the spectrometer back panel near the purge connector.
Connect the other end of the cable to any type A USB port on the computer.
4. Grasp the hand holds at the front and back edges of the Raman module and carefully
place the module at the front of the sample compartment.
Figure 5. Installing the iS50 Raman module
Note You will need to configure the iS50 Raman module the first time it is used with
OMNIC software. See “Configuring the Raman Module” for more information.
NOTICE Avoid scraping the electrical connector on the Raman module back panel
against the back wall of the sample compartment as you lower the Raman module
into the sample compartment.

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5. Slide the Raman module back to secure the electrical connection.
The motors inside the Raman module will activate when the electrical connector is
secured.
6. Secure the front latch.
To do this, lift and rotate the handle 90 degrees counterclockwise and then firmly press
the handle toward the module.
Figure 6. Securing the iS50 Raman module front latch
7. If beamsplitters must be installed manually for your spectrometer, install the CaF2or
XT-KBr beamsplitter in the spectrometer beamsplitter compartment. For more
information, find “Using Beamsplitters” in Spectrometer Help Topics.
If you have the optional ABX (automatic beamsplitter exchanger), the correct
beamsplitter installs automatically after you install the Raman module.
Note If the Microscope Configuration dialog box is displayed, the Raman module is
not configured. See “Configuring the Raman Module” for more information.
Note If your spectrometer is equipped with optional purge shutters, for best results, open
the right purge shutter while the Raman module is collecting data. For more information,
find “Controlling the Purge Shutters” in OMNIC Help Topics. (If Shutter Mode is set to
Automatic on the Bench tab in Experiment Setup, the purge shutters will open
automatically for Raman data collection.)

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Related Topics
•Configuring the Raman Module
•Aligning the Interferometer
Operation
This section covers these topics:
•Configuring the System for Raman sampling
•Turning on the Laser and Adjusting the Laser Power
•Adjusting the Sample Position
•Setting a Timer to Turn Off the Laser
Configuring the System for Raman sampling
If your Nicolet iS50 spectrometer includes the iS50 ABX (Automatic Beamsplitter
eXchanger), after you install the Raman module, the spectrometer automatically configures its
optics for Raman sampling. (If you don’t have an ABX, the software will prompt you to install
the appropriate beamsplitter.)
To configure the spectrometer for Raman sampling when the Raman module is already
installed, for example after using the optional NIR or ATR module, press the sample
compartment Touch Point.
Related Topics
•Turning on the Laser and Adjusting the Laser Power
•Adjusting the Sample Position
•Setting a Timer to Turn Off the Laser

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Thermo Scientific iS50 Raman Module User Guide 15
Turning on the Laser and Adjusting the Laser Power
The Raman module has a 1064 nm excitation laser. The laser is located at the rear of the
module under the main cover, and emits continuous-wave laser energy that is invisible to the
eye. The laser has a nonaccessible maximum power level of 0.5 W at the sample. The laser
must be on when you are focusing a sample and collecting Raman data.
To access the features to control the laser, open OMNIC software, choose Collect >
Experiment Setup and select the Bench tab.
Figure 7. Bench tab settings for the iS50 Raman module
To turn on the laser, click the ON button in the Laser box. It takes a few seconds for the laser
to begin emitting radiation.
Neutral density filters are used to control the power of the laser that reaches the sample
compartment. Reducing the power at the sample can be useful when you have a heat-sensitive
(usually dark) sample.
Note You can leave the white light set to On except when you are focusing a sample. See
“Using the White Light Source” for details.

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To adjust the laser power
1. Set Power to 0.25 W.
2. Select Spectrum to show the spectral data in the display pane on the Bench tab.
3. Adjust the power up or down until you see adequate sample peaks in the spectral display.
While you adjust the power, monitor the video image of your sample for signs of
decomposition, especially if the sample is a dark color.
Related Topics
•Important Features
•Specifications
•Configuring the System for Raman sampling
•Adjusting the Sample Position
•Setting a Timer to Turn Off the Laser
•Using the White Light Source
Adjusting the Sample Position
You can adjust the sample position and focus using Template View, available from the Raman
menu in OMNIC software, along with the video pane in either View or Atls software. For
basic information about using OMNIC and View software to position and focus a sample
and collect Raman data, see “Your First Experiment.”
NOTICE
• If your sample starts to decompose, reduce the laser power and then turn off the
laser. Move the sample so that the laser beam will strike an area that is not
decomposed, and then turn the laser on. If the sample starts to decompose again,
repeat these steps, but be aware that some samples may be too sensitive to laser
energy to be suitable for analysis.
• To maximize the life of your laser, do not leave the laser on for extended periods
when not in active use. To set a timer for the laser, see “Setting a Timer to Turn
Off the Laser.”
Note The laser must be on and the white light off while you adjust the sample position
and focus. See “Turning on the Laser and Adjusting the Laser Power” and “Using the
White Light Source” for details.

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For complete information about controlling the sample stage with View, double-click the
View icon on your computer desktop and choose Help > View Help Topics.
Complete information about using Atls to control the sample stage is available by choosing
Atls Help Topics from the help menu in OMNIC software.
Related Topics
•Turning on the Laser and Adjusting the Laser Power
•Setting a Timer to Turn Off the Laser
Setting a Timer to Turn Off the Laser
You can set up the Raman laser to turn itself off after a specified period or after OMNIC
software closes. This will prevent the laser from being left on inadvertently and prolong its
life.
To set a timer for the laser
1. In OMNIC software, choose Collect > Experiment Setup.
2. Select the Advanced tab.
Figure 8. Advanced tab parameters in Experiment Setup
Note Position settings in OMNIC, Atls and View software are calibrated in
micrometers.

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3. Set one of these options:
•SelectTurn Laser Off When OMNIC Closes
•SelectTurn Laser Off After ___ Minutes Of Inactivity and then enter the number of
minutes.
4. Choose OK.
Related Topics
•Turning on the Laser and Adjusting the Laser Power
•Adjusting the Sample Position
•Your First Experiment
Preparing Samples
The Raman sample stage can be used with solids, liquids and powders (see “Compatible
Samples” for details). They can be held in metal, glass or transparent plastic containers or
metal or glass slides, and can also be placed in reusable or disposable sample cups or slides, or
directly in the recess of a Raman sample cup holder or other Raman sample holder.
These topics are covered:
•Raman Sample Holders
•Installing a Sample Holder
Raman Sample Holders
The following sample holders are included with the iS50 Raman module:
• 9 well. Contains nine 13 mm wells.
• Slide holder (on the reverse side of the 9 well sample holder). Accepts a standard
microscope slide (metal, clear plastic or glass).
• 48 well. Contains 48 7 mm wells.
• Vial holder. One side has three recesses to hold glass or clear plastic vials; the other side
has four.