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Telephone: 800-642-6538 or 608-276-6373
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OMNI-Transmission, FiberPort, Ever-Glo, Passport, Import, SeaPort, Solid-Substrate, Talon,
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are trademarks of Thermo Electron Scientific Instruments Corporation, a subsidiary of Thermo
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269-155800
Contents
Welcome .............................................................................................1
About this manual ..........................................................................2
Questions or concerns ....................................................................3
System requirements ......................................................................4
Installing OMNIC...........................................................................5
Where to find the information you need ........................................6
Wizards and tutorials .................................................................6
On-line Help ..............................................................................7
Finding answers to your questions.............................................9
Before You Collect Spectra ..............................................................14
Checking the purge.......................................................................15
Smart Purge settings ................................................................16
Checking the desiccant.................................................................17
Turning on the system components..............................................18
Cooling the detector .....................................................................19
Starting OMNIC ...........................................................................20
Selecting an experiment ...............................................................21
Your First Experiment ......................................................................23
The OMNIC window....................................................................24
Spectral window ......................................................................24
Menu bar ..................................................................................25
Experiment drop-down list box ...............................................25
Bench Status indicator .............................................................26
Toolbar.....................................................................................26
Collecting a sample spectrum ......................................................27
Installing the standard sample holder ......................................28
Collecting the sample spectrum...............................................30
How do I know if my spectrum is good? .....................................37
Saving the spectrum .....................................................................37
Converting the spectrum’s units...................................................38
Labeling a peak with the annotation tool .....................................40
Verifying the composition of the sample .....................................43
Creating a user library ..................................................................47
Adding a spectrum to a user library .............................................47
Creating and printing a report ......................................................48
Spectrometer Basics..........................................................................51
Spectrometer components ............................................................51
Using the data collection buttons.............................................52
What’s inside?..........................................................................54
What is on the rear panel?........................................................55
Turning on the spectrometer power .............................................56
Using a light source......................................................................58
Using beamsplitters and detectors................................................60
Selecting the right beamsplitter and detector...........................60
Improving the quality of your spectral data.............................64
How to collect data in the visible spectral range..........................70
About the moving mirror velocity................................................71
Spectrometer Options .......................................................................72
Using the filter wheel ...................................................................72
Using the energy screen wheel.....................................................75
Using the internal polarizer ..........................................................78
Accessories .......................................................................................81
Smart Accessories ........................................................................81
Other sampling accessories for different applications .................85
System accessories .......................................................................90
How to cable an accessory ...........................................................91
Pass-through connectors ..........................................................91
Detector/Motors connector ......................................................95
Quick Answers to Your Questions About Using OMNIC ...............97
Collecting spectra.........................................................................97
Converting spectra to other units ...............................................101
Using spectral libraries...............................................................102
Opening, saving and deleting spectra.........................................106
Printing .......................................................................................109
Displaying spectra ......................................................................110
Correcting spectra.......................................................................116
Subtracting, adding, multiplying and dividing spectra ..............116
Customizing OMNIC .................................................................119
Other questions...........................................................................120
Quick Answers to Your Questions About
Using the Spectrometer
Maintenance and Service ................................................................128
Running diagnostic tests on spectrometer components..............129
Maintaining your spectrometer ..................................................130
Aligning the spectrometer......................................................130
Aligning an accessory............................................................132
Checking spectrometer performance .....................................132
Servicing your spectrometer.......................................................134
Troubleshooting Software Problems ..............................................135
Troubleshooting Hardware Problems .............................................137
Performing advanced diagnostic tests ........................................148
Troubleshooting Applications Problems ........................................150
Index ...............................................................................................155
.............................................................123
.
Welcome
Congratulations on your purchase of a Nicolet 4700 or Nicolet 6700
spectrometer from Thermo Electron! The spectrometer lets you
collect spectra in the mid-IR, far-IR and near-IR spectral ranges. The
system integrates advanced hardware features with the power and
flexibility of Thermo Electron’s OMNIC
software*.
If you have not used the spectrometer before, view the
“Spectrometer Tour” and “Getting Started With OMNIC” tutorial
available through Getting Started in the Help menu of OMNIC.
*
Some dedicated systems use other Thermo Electron software packages.
Nicolet FT-IR User’s Guide 1
About this manual
This manual explains how to use the system to collect and process
FT-IR spectra after a Nicolet 4700 or a Nicolet 6700 spectrometer is
installed. Included is information about using your OMNIC software
as well as chapters on how to operate, maintain and service the
spectrometer.
This manual describes some hardware features that are not available
on all Nicolet models. Use the instructions for the features on your
system.
Although the appearance of your spectrometer may vary from some
of the illustrations in this manual, the instructions are correct for
your system.
The following conventions are used in this manual to draw your
attention to the on-line documentation and other important
information.
This symbol tells you that you can find more information in the online tutorials. To access a tutorial, click the Help menu in OMNIC.
?
This symbol tells you that you can find more information in the online OMNIC Help system. Choose OMNIC Help Topics from the
Help menu.
This symbol tells you that you can find more information in this
manual.
2 Thermo Electron Corporation
Note Notes contain helpful supplementary information. S
Important Follow instructions labeled “Important” to avoid damaging the
Caution Indicates a potentially hazardous situation which, if not avoided,
Warning Indicates a potentially hazardous situation which, if not avoided,
Danger Indicates an imminently hazardous situation which, if not avoided,
Questions
or concerns
system hardware or losing data.
may result in minor or moderate injury. It may also be used to alert
against unsafe practices.
S
could result in death or serious injury.
will result in death or serious injury.
In case of emergency, follow the procedures established by your
facility. If you have questions or concerns about safety or need
assistance with operation, repairs or replacement parts, use the
information below to contact Thermo Electron. Outside the U.S.A.,
contact the local Thermo Electron sales or service representative.
Phone: 1-800-642-6538 (U.S.A.) or
+608-273-5015 (worldwide)
Fax: +608-273-6883 (worldwide)
E-mail: techsupport.analyze@thermo.com
World Wide Web: http://www.thermo.com/spectroscopy
S
S
S
Nicolet FT-IR User’s Guide 3
System requirements
If you are supplying your own computer, be sure that it meets the
following requirements for hardware and software.
● One of the following versions of Windows
®
software:
- Windows 2000 (latest Service Pack recommended)
- Windows XP Professional (latest Service Pack
recommended)
● Microprocessor:
Intel® Pentium® III, 1.0 GHz (recommend)
Intel Pentium II, 400 MHz (minimum)
● Random access memory (RAM):
256 megabytes (recommended)
128 megabytes (minimum)
If you plan to use a microscope,
1 gigabyte (recommended)
512 megabytes (minimum)
● Disk drives:
5.0 gigabytes (recommended) hard disk drive
2.0 gigabytes (minimum) hard disk drive
1.44-megabyte floppy disk drive for 3.5-inch floppy disks
Quad speed CD-ROM drive
● Video:
4 Thermo Electron Corporation
15-inch SVGA
4 megabytes of video RAM
16-bit video card capable of displaying at least 256 colors with
1024 by 768 resolution
● IO devices and card slots:
Sound card and speakers for listening to the audio portions of
tutorials
Keyboard and serial, USB or PS/2
Printer port (USB, parallel and/or serial) if you plan to print on a
local printer
One USB 2.0 connector (not a hub) for data transfer
Ethernet port if you plan to connect the system to a network
Internet connection if you plan to use the internet features of the
software
One additional serial port if you plan to use PLUS™ 2 Liquid
Analysis System, Centaurµs microscope with motorized stage, or
standard Continuµm microscope
Two additional serial ports if you plan to use a Continuµm
microscope with a motorized stage
Two additional serial ports and one additional USB 2.0
connection (not a hub) if you plan to use a Continuµm XL
microscope
One additional PCI slot if you plan to use a microscope with
video capability
®
-style mouse
Installing OMNIC
If you purchased your computer from Thermo Electron, your
software is already installed. If you provided your own computer,
you need to install OMNIC on your hard drive. See the instructions
that came with the software CD, or read “Installing OMNIC or EZ
OMNIC” in the document titled OMNIC Spectroscopy Software that
came with your software. You can use these same instructions if you
ever need to reinstall the software.
Nicolet FT-IR User’s Guide 5
Where to find the
information you need
Wizards and tutorials
The on-line and printed documentation included with your system is
designed to let you find the information you need quickly. We
recommend first using the on-line documentation provided with
OMNIC when you have a question. OMNIC includes several on-line
tutorials, a wizard and a complete Help system. See “Starting
OMNIC” in the “Before You Collect Spectra” chapter for
information about starting OMNIC.
The following wizards and tutorials are available on your system.
Getting Started With OMNIC – This tutorial, available through
Getting Started in the Help menu, introduces you to OMNIC. It
includes basic information about the OMNIC window, using the
toolbar and tool palette, creating and using spectral libraries,
creating your own experiment files, and using on-line laboratory
notebooks to create and save reports.
Spectrometer Tour – When you finish this tutorial, you will be
familiar with the major components in your spectrometer. The
tutorial is available through Getting Started in the Help menu.
Beginner’s Guide to FT-IR – Run this tutorial to learn how an FTIR spectrometer works and the theory behind FT-IR spectroscopy.
The tutorial is available through Getting Started in the Help menu.
Sampling Techniques – This item in the Help menu gives you
access to the “Choosing a Sample Technique” tutorial, which helps
you choose the best technique for your analysis. Also available are
tutorials describing how to install and use a number of sampling
accessories, including Smart Accessories.
6 Thermo Electron Corporation
Learning OMNIC – This item in the Help menu gives you access to
tutorials that explain how to use OMNIC to collect spectra and
perform a number of other software operations.
Spectrometer Help Topics – This tutorial, available in the Help
menu, contains step-by-step instructions for installing optional
hardware, changing replaceable parts, maintaining your
spectrometer, and setting up the system for a variety of experiments.
If you ever have a problem with your spectrometer, use this tutorial
to access troubleshooting information and get part number and
ordering information.
Technical Support – This tutorial, available in the Help menu,
outlines the many support, training, and custom application services
available from Thermo Electron. It includes Technical Support
telephone and fax numbers, as well as e-mail and web site addresses.
The Library Creation Wizard prompts you, step by step, through
creating a user library of spectra. The wizard appears when you click
the Create Library button in Library Manager, available in the
Analyze menu in OMNIC.
On-line Help
Choose the Help Topics that interest you from the Help menu to
display that Help system. It lets you quickly find answers to your
questions about using the software.
There are several other ways to enter a Help system:
• You can see information about many features in OMNIC (such
as a parameter in a dialog box) by clicking the feature using the
right mouse button. (If the active dialog box or window includes
a question mark button near the upper-right corner, you may
need to first click that button and then click the feature of interest
using the left mouse button.) A brief description of the item
appears, and in most cases one or more buttons that you can click
to display more detailed information. Here is an example:
Nicolet FT-IR User’s Guide 7
Click the Discussion button to display a complete discussion of
the item (or the dialog box or window that contains the feature).
Click the How To button to display a step-by-step procedure for
using the item (or the dialog box or window that contains the
item).
• The left pane in each help window lists the topics available in
that help system.
Here is an example of a help window showing the contents of
some of the books in the system:
8 Thermo Electron Corporation
Finding answers
to your questions
The basics
?
Use the following sections to help you locate the information you
need in the on-line and printed documentation. The on-line
documentation is available in the Help menu of OMNIC.
How do I turn on the system?
Spectrometer Tour (available through Getting Started)...
“Powering up”
“Before You Collect Spectra” chapter...
“Turning on the system components”
How do I start the software?
“Before You Collect Spectra” chapter...
“Starting OMNIC”
How do I prepare the software for data collection?
Collecting a Spectrum (available through Learning OMNIC)...
“Preparing the Software”
How can I learn how to use the software?
View the tutorials listed when you point to Getting Started or
Learning OMNIC.
OMNIC Help Topics includes complete instructions for all the
OMNIC features. Use the Index tab or Contents tab to find the
information you need.
Nicolet FT-IR User’s Guide 9
Using the spectrometer
and changing parts
What’s inside the spectrometer?
Spectrometer Tour (available through Getting Started)...
“Inside the spectrometer”
How does the spectrometer work?
Beginner’s Guide to FT-IR (available through Getting Started)
How do I purge the system?
Spectrometer Help Topics...
“Installing purge controls” in “Installing optional hardware”
How do I use Smart Purge
Spectrometer Help Topics...
“Setting the Smart Purge controls” in “Installing optional
hardware”
How do I change beamsplitters?
Spectrometer Help Topics...
“Changing beamsplitters” in “Setting up experiments”
“Selecting a beamsplitter, detector, and source” in
“Setting up experiments”
?
10 Thermo Electron Corporation
How do I change detectors?
Spectrometer Help Topics...
Collecting spectra
“Selecting a beamsplitter, detector, and source” and
“Changing detectors” in “Setting up experiments”
How do I install a source?
Spectrometer Help Topics...
“Selecting a beamsplitter, detector, and source” and
“Installing a new source” in “Setting up experiments”
Which beamsplitter and detector should I use?
Spectrometer Help Topics...
“Selecting a beamsplitter, detector, and source” in “Setting up
experiments” (See the tables showing the compatibility of
sources, beamsplitters and detectors.)
“Spectrometer Basics” chapter...
“Selecting the right beamsplitter and detector” in “Using
beamsplitters and detectors”
How do I install a sample?
Spectrometer Tour (available through Getting Started)...
“Installing samples”
Nicolet FT-IR User’s Guide 11
How do I collect a spectrum?
Collecting a Spectrum (available through Learning OMNIC)
“Your First Experiment” chapter
Accessories
What accessories are available?
Spectrometer Tour (available through Getting Started)...
“Accessories”
“Accessories” chapter
How do I install an accessory?
Spectrometer Help Topics...
“Installing optional hardware” (Step-by-step instructions and, in
many cases, on-line videos help you install accessories. If your
accessory is not covered on-line, use the printed instructions.)
12 Thermo Electron Corporation
Maintenance and service
How should I maintain my spectrometer?
Spectrometer Tour (available through Getting Started)...
“Service and maintenance”
Spectrometer Help Topics...
“Maintaining your spectrometer”
“Maintenance and Service” chapter
What should I do if there is a problem with the system?
Contact Thermo Electron technical support. Outside the U.S.A.,
contact the local Thermo Electron sales or service representative.
Phone: 1-800-642-6538 (U.S.A.) or
+608-273-5015 (worldwide)
Fax: +608-273-6883 (worldwide)
E-mail: Techsupport.analyze@thermo.com
World Wide Web: http://www.thermo.com/spectroscopy
Nicolet FT-IR User’s Guide 13
Before You Collect Spectra
Warning The Spectrometer Safety Guide that came with your system contains
important safety information. This guide is available in several
languages. Contact your local Thermo Electron office for
information about the languages that are available. Before you use
the system, read the entire guide. To prevent personal injury and
damage to equipment, follow the safety precautions contained in the
guide whenever you use the system.
It’s easy to collect spectra with your spectrometer. By leaving the
system turned on at all times—with the needed components already
installed—you can keep it ready to use with a minimum of
preparation. Keeping the system on also improves its stability and
gives you more consistent results.
All the things you need to check before collecting spectra are listed
below; each of these items is discussed in a section of this chapter. By
the time you have run through these items once or twice in the course
of your work, you will know how to check the system and start
collecting spectra quickly.
S
• Check the purge or desiccant.
• Make sure the system components are powered on.
• Cool the detector (if you are using an MCT, InSb or other
detector that requires cooling with liquid nitrogen).
• Start OMNIC and select an experiment.
14 Thermo Electron Corporation
Checking the purge
Skip this section if you purchased
the “Sealed and Desiccated” option.
If your spectrometer is purged but you don’t have the Smart Purge
option, make sure the pressure regulator is set between 20 and
40 pounds per square inch (psi) and the flowmeter reads
approximately 30 standard cubic feet per hour (scfh). The settings for
systems equipped with Smart Purge are given in the next section; read
this section first.
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 the “Setting up experiments” book in Spectrometer Help
Topics.
Warning Never use a flammable gas to purge the spectrometer. The purge gas
must be free of moisture, oil, carbon dioxide and other reactive or
infrared-absorbing materials. Use dried air or nitrogen to purge the
spectrometer. Other gases, even inert gases such as argon, can
damage the spectrometer and should never be used for this purpose.
S
50
40
30
20
10
80
100
60
40
20
0
160
SCFH AIR
120
140
We recommend that you leave the purge on at all times. This keeps the
spectrometer free of undesirable gases, protects the optics and
improves the system’s thermal stability.
Nicolet FT-IR User’s Guide 15
In Spectrometer Help Topics view “Installing optional hardware” for
information about installing purge equipment and setting the
controls for the first time. “Maintaining your spectrometer” contains
information about inspecting and replacing the purge filter. In the
Spectrometer Tour (available through Getting Started) view “Sample
compartment” for information about using Smart Purge.
Smart Purge settings
The Smart Purge option increases the purge gas flow rate when you
install or remove samples. If you have this option, set the pressure
regulator to 80 psi. The auxiliary tank may be required depending on
the flow rate supplied by your purge gas source. See the following
table for details.
Flow Rate* Tank Required? Comments
less than
50 scfh
50-99 scfh optional Using the tank will improve
100 scfh or
greater
* Flow rates greater than 50 scfh cannot be measured with the flowmeter installed by
Thermo Electron. See your air dryer manual or contact the department that maintains your
purge equipment if you don’t know the flow rate of the purge gas source.
yes Some purge gas and pure air
generators provide a flow rate of
less than 50 scfh.
performance.
no A flow rate of 100 scfh gives the
best results.
?
16 Thermo Electron Corporation
You can use OMNIC to set the duration of increased purge flow. In
OMNIC Help Topics find “purge” in the Index and go to “Setting
Smart Purge.”
Checking
the desiccant
Note The Check Desiccant button measures humidity more accurately
If your spectrometer is sealed and desiccated, a bag of desiccant is
located under the beamsplitter compartment cover. The desiccant
protects the beamsplitter and other optical components by reducing
the amount of water vapor inside spectrometer. See “Checking and
changing desiccant” in the “Maintaining your spectrometer” book in
Spectrometer Help Topics if you need to change the desiccant.
If your spectrometer is in use, check the humidity level inside it
monthly (more often in very humid climates) by clicking the Check
Desiccant button on the Diagnostic tab of the Experiment Setup
dialog box. If the level exceeds the factory-specified limit, a
message informs you. Be sure to change the desiccant so that the
optics will be protected.
If your spectrometer is in storage, check the round, blue indicator on
the desiccant holder under the beamsplitter compartment cover
monthly. Change the desiccant if the indicator has turned pink. Keep
all covers closed tightly while the spectrometer is in storage.
than the indicator. For this reason you should rely on the button to
monitor the performance of the desiccant when the spectrometer is
in use. Rely on the indicator only when the spectrometer is in
storage.
See “Ordering parts” in Spectrometer Help Topics to find the part
number for ordering desiccant bags.
S
Nicolet FT-IR User’s Guide 17
Turning on the
system components
Warning Always follow the safety precautions described in this manual and in
We recommend that you keep your spectrometer on at all times,
unless the building is subject to power outages or you need to
perform a service or maintenance procedure. Leaving the system on
keeps it stable and gives you the most consistent results. If you must
turn the spectrometer off, allow it to stabilize for at least 15 minutes
(one hour for best results) before collecting spectra.
Follow these steps to turn on the system components:
1. If the external power supply is not already connected,
connect it.
In the Spectrometer Tour (available through Getting Started)
view “Connecting to AC power” in the “Powering up” unit for
information about connecting the power supply.
2. Turn on any accessories you plan to use.
This includes accessories such as a gas chromatograph, a GC
interface or an infrared microscope.
the Spectrometer Safety Guide that came with your system.
3. Turn on the spectrometer by pressing the power switch (I/O)
on the external power supply to I.
When you turn on the spectrometer, the four status indicators—
Power, Scan, Laser and Source—flash in various sequences as the
system runs through its diagnostic routines. When the routines are
finished, the Power, Laser and Source indicators stay lighted. The
Scan indicator flashes with each scan of the interferometer.
S
18 Thermo Electron Corporation
Cooling the detector
After you turn on the spectrometer, let it stabilize for at least
15 minutes (one hour for best results) before collecting spectra.
See “Turning on the spectrometer power” in the “Spectrometer
Basics” chapter if you need more information.
4. Turn on the printer and then the computer.
Turn on the printer and computer as explained in the
documentation that came with those components.
Reverse the order given in the preceding procedure when you turn
off system components:
1. Turn off the computer.
2. Turn off the printer.
3. Turn off the spectrometer.
4. Turn off the accessories.
Some detectors, such as an MCT or InSb detector, require cooling
with liquid nitrogen. In Spectrometer Help Topics view “Cooling a
detector” in “Setting up experiments” for instructions.
Warning Liquid nitrogen is extremely cold and therefore potentially
hazardous. Avoid contact with skin. Wear protective clothing and
follow standard laboratory safety practices to prevent injury. Liquid
nitrogen can be hazardous if handled in an insufficiently ventilated
room.
After you fill the detector dewar with liquid nitrogen (the dewar
holds about 750 mL), allow the detector to cool at least 20 minutes
before collecting spectra.
S
Nicolet FT-IR User’s Guide 19
Starting OMNIC
Follow these steps to start OMNIC:
1. Start your Windows software.
Depending on the version of Windows you are using, you may
be required to enter your user name and password. Enter the
information when you are prompted.
2. Double-click the OMNIC shortcut on the Windows desktop.
Alternatively, you can click the Start button on the Windows
Depending on how the program has been configured, dialog
taskbar, point to Programs (All Programs in Windows XP), point
to the Thermo Nicolet folder, and then click the OMNIC
program.
boxes may appear asking for a user name and password. Type
the requested information and then choose OK.
The OMNIC window appears. This window is described in the
next chapter and in the “Getting Started With OMNIC” tutorial
available through Getting Started in the Help menu.
20 Thermo Electron Corporation
Selecting
an experiment
The parameter settings for collecting spectra are stored in
experiment files. You load the settings you wish to use when you
select an experiment from the Experiment drop-down list box below
the OMNIC menu bar (see the example below).
A number of experiments are included with OMNIC for performing
a wide variety of data collections. You can open these experiments
by choosing Open in the Experiment Setup dialog box. Experiment
Setup is available in the toolbar and in the Collect menu. You can
also use Experiment Setup to set up and save your own experiments,
or to check or change the parameter settings after you select an
experiment.
If you install a Smart Accessory
automatically (or a list of appropriate experiments is made available
for your selection).
In the tutorial in the next chapter the Default - Transmission (or
Transmission E.S.P.) experiment is used. You will probably find that
this experiment is suitable for most of your applications.
If you want to check or change the parameters after selecting an
experiment, use Experiment Setup in the Collect menu.
, the correct experiment is selected
Nicolet FT-IR User’s Guide 21
You are now ready to collect spectra.
If you have not used the system before, you can learn how to
perform an experiment by viewing the “Collecting a Spectrum”
tutorial (available through Learning OMNIC in the Help menu) or
by using the tutorial in the next chapter of this manual. If you need
to change a source or detector, view “Replacing the source” or
“Replacing the detector” in the “Servicing your spectrometer” book
in Spectrometer Help Topics.
Note The most commonly used hardware configuration for mid-IR
experiments includes a KBr beamsplitter, an ETC source and a
DTGS detector. You may need to change the settings of the example
experiment if your hardware configuration is different.
S
22 Thermo Electron Corporation
Your First Experiment
This chapter will get you started collecting spectra with your
spectrometer and working with the data using OMNIC. You will
learn how to do the following things:
• Open a configuration.
• Select an experiment.
• Collect a sample spectrum.
• Save the spectrum.
• Convert the spectrum to other units.
• Label a peak in the spectrum.
• Verify the composition of the sample by comparing the spectrum
with spectra in a QC library.
• Create a user library.
• Add the spectrum to a user library.
• Create and print a report containing the spectrum.
You can learn all these things and more by running the on-line
tutorials provided with OMNIC. Start with the Spectrometer Tour
and Getting Started With OMNIC (available through Getting
Started).
Follow the instructions in the preceding chapter to prepare the
system and start OMNIC before using this chapter.
Note If you have a dedicated system (such as an ECO/RS) that normally
uses a software package other than OMNIC, skip this chapter. See
the special documentation that came with your system for
instructions for using that software. If you need information about
using the spectrometer, see the chapters that follow this one.
S
Nicolet FT-IR User’s Guide 23
The OMNIC window
Spectral window
The large window that appears on the screen when you start OMNIC
is called the OMNIC window.
Within the OMNIC window is a spectral window, which you can use
to display and manipulate spectra. When a spectrum is displayed in a
spectral window, you can use OMNIC commands to perform
operations on it. For example, you can change the spectrum’s format
or search it against a spectral library to identify it.
24 Thermo Electron Corporation
Menu bar
Experiment
drop-down list box
Below the title bar is the menu bar, which contains all of the
OMNIC menu names. (Depending on which optional software you
purchased, the menu names in your menu bar may be somewhat
different from those shown.) The menus are arranged in an order that
you’ll find convenient as you use the software. All of the menu
commands are explained in detail in the on-line tutorials or the
OMNIC Help system.
Below the menu bar is the Experiment drop-down list box. It lists all
of the experiment files you have opened, plus the default experiment
file and an experiment file for any Smart Accessory module you
have installed. By selecting an experiment with this feature, you can
quickly set the software parameters for the type of experiment you
want to perform. You can see the parameter settings for the selected
experiment by using Experiment Setup, available in the toolbar or in
the Collect menu.
Nicolet FT-IR User’s Guide 25
Bench Status indicator
Note If you want to view the on-line videos to help troubleshoot a
Toolbar
?
To the right of the Experiment drop-down list box is the Bench
Status indicator.
If the indicator is a green check mark, the spectrometer has passed
all of its diagnostic tests.
If the indicator is a yellow circle, a cooled detector in the
spectrometer has become warm. A message appears explaining the
problem and allowing you to access information about correcting it.
If the indicator is a red X, the spectrometer has failed a diagnostic
test and requires corrective action. A message appears explaining the
problem and allowing you to access information about correcting it.
problem, put the spectrometer’s Tutorial CD into the computer’s
CD-ROM drive.
At the left side of the window is the toolbar. (You can use Edit
Toolbar in the Edit menu to position the toolbar at the top or right
side of the OMNIC window as well. Each button in the toolbar
represents a command or other feature. To see the name of the
command or feature, point to the button and wait a moment. To
initiate the command or feature, click the button with the left mouse
button.
In OMNIC Help Topics find “toolbar” in the Index and go to
“Displaying and using a toolbar” for information about using and
customizing the toolbar buttons.
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26 Thermo Electron Corporation
Collecting a
sample spectrum
A sample spectrum is usually ratioed against a background
spectrum. The background spectrum measures the response of the
spectrometer without a sample in place. Dividing the sample
spectrum by the background—called “ratioing”—removes the
effects caused by the instrument and atmospheric conditions so that
the peaks in the final spectrum are due solely to the sample.
Here is a typical mid-IR background spectrum:
For most applications you don’t need to collect a new background
spectrum for each sample spectrum if you haven’t changed the
software parameters. To obtain good results, however, collect a new
background regularly, perhaps once every four hours. (You can
obtain the best results by collecting a new background for each
sample, but this is usually necessary only if you are running
quantitative experiments.)
Nicolet FT-IR User’s Guide 27
Installing the
standard sample holder
If the standard sample holder is not already installed, install it now.
The following illustration shows the sample holder in place.
Accessory
support
Sample
holder
If you are using separate Snap-In™ sample compartment baseplates
for different accessories and sample holders, you can quickly switch
baseplates to install the sample holder. For information about using
Snap-In baseplates, view “Removing the Snap-In baseplate” in
“Setting up experiments” in Spectrometer Help Topics.
If your sample holder is mounted on a Smart baseplate, the
Transmission E.S.P. experiment is automatically selected when you
install the baseplate in the sample compartment.
28 Thermo Electron Corporation
Height
adjustment
screw
If your sample holder is not installed on a baseplate, use a flat-blade
screwdriver and the slotted screws to attach the holder to a baseplate
as shown below. Then install the baseplate in the sample
compartment.
If there is a sample in the
holder, remove the sample.
To install a sample or filter, slide the sample or filter into one pair of
slots. If the accessory support is currently installed in the slot you
want to use, remove the support before installing the sample or filter
(see the first illustration in this section). Replace the support when
you are finished using the slot. Do not discard the support; it is
needed for installing slide-mounted accessories.
Nicolet FT-IR User’s Guide 29
Collecting the
sample spectrum
In the data collection procedure that follows, you will collect a
background spectrum and then a spectrum of the secondary
polystyrene standard that came with your spectrometer. Before
collecting the spectra, you will open a configuration that sets a
number of software options for this procedure.
You can also learn how to collect spectra by viewing Collecting a
Spectrum (available through Learning OMNIC).
Follow these steps:
1. Choose Open Configuration from the File menu.
The Open Configuration dialog box appears listing the available
configuration files. Opening one of these files lets you quickly
set a number of software options.
2. Select the DEFAULT.CON file and then choose OK.
This file was provided with your OMNIC software for setting the
options for this procedure.
3. If it is not already selected, select the Default - Transmission
experiment (or the Transmission E.S.P. experiment).
Both of these experiments set the parameters correctly for
collecting a polystyrene sample spectrum. The currently selected
experiment is shown in the Experiment box near the top of the
OMNIC window.
To select the Default - Transmission (or Transmission E.S.P.)
experiment, first click the arrow button at the right end of the
Experiment drop-down list box. The Default - Transmission (or
Transmission E.S.P.) experiment appears in the list.
30 Thermo Electron Corporation
Select the Default -
Transmission experiment by clicking it.
A number of other experiments are provided with OMNIC for
performing a wide variety of data collections. You can select
these experiments by using the Open button in the Experiment
Setup dialog box. After you have selected one of them the first
time, the experiment will appear in the Experiment drop-down
list for future selection. You can also set up and save your own
experiments.
4. Press the Sample button on top of the spectrometer to start
sample data collection.
You can also click the Collect Sample button in the toolbar or
choose Collect Sample from the Collect menu.
The Collect Sample window appears and then a dialog box
showing the default title for the sample spectrum:
Nicolet FT-IR User’s Guide 31
5. Type a title in the text box and choose OK, or just press the
OK/Enter button on top of the spectrometer to accept the
default.
Since the experiment you are using specifies that a background
be collected before every sample, a message appears asking you
to prepare to collect a background spectrum:
This means that you need to remove any sample from the sample
32 Thermo Electron Corporation
holder so that the beam path is clear. When you then collect a
background spectrum, the result is a measurement of the
response of the spectrometer alone; that is, without absorptions
due to a sample.
6. Look through the sliding door to make sure there is no
sample in the sample holder and then press the OK/Enter
button to start data collection.
If there is a sample in the sample holder, remove it before
pressing the button:
If your spectrometer is purged but does not have the Smart
Purge option...
Open the sliding door, remove the sample, close the sliding
door and then wait 1 minute before choosing OK.
If your spectrometer has the Smart Purge option...
Open the sliding door, remove the sample and then slide the
door until it is open about 1 cm. When you hear the purge
flow rate return to normal, close the door all the way and
choose OK.
If your spectrometer is sealed and desiccated...
Open the sliding door, remove the sample, close the sliding
door and then choose OK.
A background spectrum appears in the Collect Sample
window. The spectrum is updated as more data are collected.
When all the data have been collected, a message appears
asking you to prepare to collect the sample spectrum:
Nicolet FT-IR User’s Guide 33
7. Install the thin film polystyrene sample labeled “Secondary
Polystyrene Standard: 1.5 mil Polystyrene” through the
sliding door, wait if necessary (see the instructions below)
and then press the OK/Enter button.
34 Thermo Electron Corporation
If your spectrometer is purged but does not have the Smart
Purge option...
Open the sliding door, install the sample, close the sliding
door and then wait 1 minute before choosing OK.
If your spectrometer has the Smart Purge option...
Open the sliding door, install the sample and then slide the
door until it is open about 1 cm. When you hear the purge
flow rate return to normal, close the door all the way and
choose OK.
If your spectrometer is sealed and desiccated...
Open the sliding door, install the sample, close the sliding
door and then choose OK.
For more information about installing samples, view “Installing
samples” in the Spectrometer Tour (available through Getting
Started).
As data are collected, the sample spectrum in the Collect Sample
window is updated. Here is an example:
The progress of the collection is indicated by the gauge below
the spectrum.
The number of scans collected so far and the total number of
scans for the collection are displayed to the right of the gauge.
Nicolet FT-IR User’s Guide 35
When data collection is finished, a message may appear, asking
whether to add the spectrum to a spectral window.
Note If Collect To A New Window is selected in the Collect options
(available through Edit Options in the Edit menu), this message does
not appear since the spectrum is placed into a new spectral window
automatically.
8. Press the OK/Enter button to add the sample spectrum to the
spectral window.
Choosing No would end the procedure without saving the
spectrum. Choosing More Scans would return you to the Collect
Sample window, allowing you to collect more scans with the
More button. Choosing View Collect Status would display
information about the collection, including any problems that
occurred (see the next section).
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36 Thermo Electron Corporation
How do I know if
my spectrum is good?
Saving the spectrum
The Collect Status indicator near the bottom of the Collect Sample
window shows the status of the collection. When the indicator is a
green check mark, it shows that the spectrum has passed all of the
selected spectral quality checks made so far. After the collection is
finished and the indicator is a green check mark, you can add the
spectrum to a spectral window (if it is not added automatically).
If you ever have a problem with data collection while one or more
quality checks are turned on, the Collect Status indicator may
change. If the indicator is a yellow circle, the spectrum has failed a
spectral quality check (a measured value was not within the allowed
range), but it is not serious enough to stop the collection. If the
indicator is a red X, there is a problem with the quality of the
spectrum. After correcting the problem, collect the spectrum again.
To view information about the collection, including a list of any
problems that have occurred, click the Collect Status indicator
during or after the collection. You can also click the View Collect
Status button in the message that may appear when the collection is
finished (see step 7 of the procedure in the preceding section). For
each listed problem, an Explain button is provided to let you access
troubleshooting information.
You can save your spectrum on the hard disk by using either of two
commands in the File menu: Use Save when you want to save a
spectrum using the current filename and path. Use Save As when
you want to save a spectrum using a new filename or path.
Follow these steps to save the spectrum you just collected:
1. Select the polystyrene spectrum by clicking it.
2. Choose Save As from the File menu.
The Save As dialog box appears.
Nicolet FT-IR User’s Guide 37
3. Type a descriptive name (such as POLY.SPA) following the
directory path in the File Name box.
Here is an example:
C:\My Documents\OMNIC\Spectra\POLY.SPA
The text can be either upper or lower case. The default directory
path for saving files is determined by the settings on the File tab
of the Options dialog box, available through Options in the Edit
menu.
4. Choose OK.
If you typed a filename that already exists in the directory, a
message appears asking whether to replace the existing file.
Choose No and then use a different filename to save the
spectrum.
Converting the
spectrum’s units
You can also
choose % Transmittance
from the Process menu.
The sample spectrum you collected is in absorbance units. Since many
of OMNIC’s data manipulation commands work best on spectra in
absorbance units, it is often useful to convert a spectrum to absorbance
by using the Absorbance command. In this example you will convert
the spectrum to % transmittance and then back to absorbance.
1. Select the spectrum by clicking it.
2. Click the % Transmittance button in the toolbar.
38 Thermo Electron Corporation
The spectrum is converted to % transmittance units:
The Process menu allows you to convert spectra to several other
units as well. These units are discussed in detail in the OMNIC on-
?
line Help system. In OMNIC Help Topics find “converting
spectrum” in the Index and go to the topic that deals with the units
you are interested in.
Nicolet FT-IR User’s Guide 39
You can also choose
Absorbance from the Process menu.
Labeling a peak with
the annotation tool
3. Click the Absorbance button in the toolbar to return the
spectrum to absorbance units.
In the next section, you will label a peak in the absorbance
spectrum using the annotation tool.
The palette contains six tools that let you select a spectrum or
spectral region, change how spectra are displayed in a spectral
window, find the height or area of a peak, or label a peak. The names
and appearance of the palette tools indicate their functions.
Region
Peak height
Annotation
Only one tool can be used at a time. To use a tool, first select it by
clicking it. A tool remains selected until you select another tool.
40 Thermo Electron Corporation
Selection
Spectral cursor Peak area
When you use a tool, the readout above the palette may display
information for the tool operation, such as the X and Y values of the
pointer location or the limits of the selected spectral region. Here is
an example of X and Y values displayed in the readout when the
selection tool is selected and the pointer is within the spectral
display:
Follow these steps to label a peak in the polystyrene spectrum:
1. Select the annotation tool by clicking it.
The annotation tool lets you label peaks with their frequency
locations (X values) or other information.
When the annotation tool is selected and you move the pointer
into the spectral display, the pointer looks like this:
You can label a peak by clicking above it with the annotation
tool. This displays the label text above the peak with a line
connecting the label to the peak. The text is selected so that you
can immediately edit it. When you press Enter, the label appears
in its final form.
Nicolet FT-IR User’s Guide 41
You can more accurately locate the top of a peak by holding
down the Shift key when you click near the peak.
2. Label a prominent peak by holding down the Shift key and
clicking a little above the peak.
The label appears. Here is an example:
3. Press Enter to accept the label text.
You could also perform other operations on the label using the
annotation tool. To modify a newly created label, edit the
selected text before pressing Enter. To modify an existing label,
click it and then type a new label and press Enter. To delete an
existing label, click it and then press the Delete key.
?
In OMNIC Help Topics find “tool, annotation” in the Index and go
to “Annotation tool” for more information about the annotation tool.
In the next section, you will compare the spectrum with the
spectra in a QC library to verify the composition of the sample.
42 Thermo Electron Corporation
Verifying the
composition
of the sample
Note If you were unsure of the composition of the sample, you could
You can verify the composition of your polystyrene sample by
automatically comparing the collected spectrum with the spectra in a
QC (Quality Control) library. The software compares the sample
spectrum with reference spectra in the appropriate category in the
library and then tells you whether the sample matches a library
spectrum.
perform a “spectral search” using a search library. In that case, the
software would search the library and then display a list of the
library spectra that best matched the unknown spectrum.
Follow these steps to perform a QC comparison:
1. Select the spectrum by clicking it.
2. Choose Library Setup from the Analyze menu.
The Library Setup dialog box appears with the Search Libraries
tab displayed.
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Nicolet FT-IR User’s Guide 43
The Library Directories box lists the directories that are currently
being used for spectral searches and QC comparisons. All the
libraries in the listed directories are available for your QC
comparison.
3. Add the LIBS directory (within the OMNIC directory) to the
list of directories if it is not already in the list.
This is the directory that contains the provided Polystyrene
Quality Control Sample library. To add the directory to the list,
choose Add Directory. In the dialog box that appears, locate and
select the LIBS directory, and then choose OK.
4. Click the QC Libraries tab to display the available QC
libraries.
The available QC libraries appear in the Available QC Libraries
And Groups box.
44 Thermo Electron Corporation
The libraries listed in the QC Libraries And Groups box are the
libraries with which your spectrum will be compared.
5. Add the Polystyrene Quality Control Sample library to the
comparison list.
To do this, click the appropriate library name in the Available
QC Libraries And Groups box, and then click the Add button.
6. Choose QC Compare in the Library Setup dialog box to start
the comparison.
You can also close the Library Setup dialog box and begin a QC
comparison at any time by choosing QC Compare from the
Analyze menu.
When you begin a comparison, the QC Compare window
appears. At the bottom of the window a gauge shows the
progress of the comparison.
When the comparison is finished, the sample spectrum and the
library spectrum that best matches it are displayed in panes in the
upper portion of the window. Comments about the comparison
appear in the lower portion of the window. Here is an example:
Nicolet FT-IR User’s Guide 45
7. Close the QC Compare window by choosing Close.
?
In OMNIC Help Topics find “QC comparison” in the Index and go
to “Performing a QC comparison” if you want more information
about comparing sample spectra with QC libraries.
46 Thermo Electron Corporation
Creating a
user library
?
Adding a spectrum
to a user library
Note You cannot add spectra to a commercial library, nor can you move
?
OMNIC’s Library Creation Wizard makes it easy to create your own
spectral libraries. Creating your own library lets you customize the
information in the library depending on your needs. You set the
library parameters (including the resolution and spectral range) and
specify which checks and corrections to perform. The wizard leads
you step by step through the process.
If you are using OMNIC, start the Library Creation Wizard by
choosing Library Manager from the Analyze menu and then clicking
the Create Library button on the Library Names tab.
In OMNIC Help Topics find “library, creating” in the Index and go
to the “Creating a user library” topic for more information.
Once you have created a user library, you can use the library to store
spectra you have collected. To do this, select the spectrum and then
choose Add To Library from the Analyze menu. To move a copy of
a spectrum you have collected from one user library into another,
use Library Manager in the Analyze menu.
copies of commercially collected reference spectra into libraries you
create.
In OMNIC Help Topics find “adding, spectrum to user library” in
the Index and go to the “Adding a spectrum to a user library” topic
or the “Adding user library spectra to another user library” topic for
more information.
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Nicolet FT-IR User’s Guide 47
Creating and
printing a report
?
OMNIC makes it easy to create and print a report containing the
results of your work. Follow the steps below.
You can also view the “Creating Reports” tutorial (available through
Learning OMNIC in the Help menu) to learn how to create and print
reports and add them to report notebooks.
1. Choose Template from the Report menu.
A dialog box appears allowing you to select a report template for
the report.
2. Select the report template file named QCCOMP.RPT.
This file contains a report template specially set up for this
procedure. The template has items for the spectral window,
spectrum time, title and comments, and QC comparison results.
When you select the template file, a preview image of the
template appears at the right. This feature allows you to see what
different templates look like so that you can pick one with the
items you need for your report. You can view the image as a
graphical layout by selecting the Layout option. This shows you
how the printed report will look on paper. You can also view the
image with template items labeled by selecting the Description
option. This lets you identify items that are too small to be seen
clearly.
3. Choose Select to make the example template the current
template for printing reports.
When you print your report, OMNIC will automatically fill in
the items in the template with the appropriate information and
images. For example, if an item in the template is linked to the
active spectral window, the contents of that window are included
when you print the report.
48 Thermo Electron Corporation
You can click the Zoom button to
see an enlarged image of the report.
You can create your own report templates by using the Create
button, or you can modify one of the existing templates
whenever you want to design a new template. Save the template
with a new name after you make your changes.
?
In OMNIC Help Topics find “report template, selecting” in the
Index and go to “Selecting, editing or creating a report template” for
more information about using reports.
4. Choose Preview/Print Report from the Report menu.
A preview of the report appears showing the report items filled
in with information about your spectrum. Your report should
look similar to this:
Collection time:
The preview lets you check the content of the report before
printing it.
Nicolet FT-IR User’s Guide 49
5. If you have a printer connected to the computer, choose Print
to print the report.
The Print dialog box appears allowing you to set some
parameters that affect printing.
6. Choose OK.
The report is printed on your system printer.
50 Thermo Electron Corporation
Spectrometer Basics
This chapter describes the major components of your Nicolet 4700
or Nicolet 6700 spectrometer, including the light source,
beamsplitter and detector. It then explains what you will need to
know before collecting data in various spectral ranges.
In the Spectrometer Tour (available through Getting Started) view
“From the front,” “The back panel” and “Inside the spectrometer”
for complete descriptions of your spectrometer’s internal and
external components.
Spectrometer
components
The following illustration identifies some major components visible
on the outside of a typical Nicolet 6700 spectrometer. (Some
components may not be present on your spectrometer.)
Sliding door
Detector fill ports
Status indicators
Data collection
buttons
Beamsplitter
and desiccant
compartment
Detector
compartment
Sample
compartment
Emission port for
external source
External beam port
Nicolet FT-IR User’s Guide 51
Using the
data collection buttons
For more information about the Auxiliary pass-through connectors,
see the “How to cable an accessory” section of the “Accessories”
chapter.
The buttons on the top of the spectrometer let you quickly perform
some basic operations with the spectrometer without using your
keyboard or mouse. (OMNIC must be running.)
52 Thermo Electron Corporation
Press the Sample button to collect a sample spectrum. This has the
same effect as choosing Collect Sample from the Collect menu. In
OMNIC Help Topics find “spectrum” in the Index and go to
“Collecting a sample spectrum” for more information.
Press the Background button to collect a background. This has the
same effect as choosing Collect Background from the Collect menu.
In OMNIC Help Topics find “background spectrum” in the Index
and go to “Collecting a background spectrum” for more information.
Press the OK/Enter button to respond affirmatively—for example, to
a software prompt—during data collection. This has the same effect
as choosing OK (or other affirmative response, such as Yes) within
the software.
Press the Stop button to respond “Cancel” or “No” to a software
prompt during data collection. This has the same effect as choosing
Cancel or No within the prompt.
Press the Macro button to start a macro you have specified with the
Macro for Macro button field on the Advanced tab in Experiment
Setup. In OMNIC Help Topics find “macro” in the Index and go to
“Specifying a macro for the Macro button” for more information.
Nicolet FT-IR User’s Guide 53
What’s inside?
Electronics
Passport optics
(optional)
Sample
compartment
External
beam port
Back
detector
Detector
mirror
Front detector
The illustration below shows a top view of the optical layout of a
typical Nicolet 6700 spectrometer with covers removed to reveal
components. (Some components may not be present in your
spectrometer.)
Interferometer BeamsplitterLaser
Beamsplitter
storage
Fixed mirror
or optional
emission optics
External
emission port
Filter wheel
(optional)
External
beam port
Aperture
Energy screen
wheel (optional)
Infrared source
Source select
optics (optional)
Near-IR source
Sample holder
Polarizer
(optional)
SabIR port
Fixed mirror or optional
SeaPort optics
In the Spectrometer Tour (available through Getting Started) view
“Inside the spectrometer” for complete descriptions of your
spectrometer components.
(optional)
54 Thermo Electron Corporation
What is on
the rear panel?
The rear panel includes a power connector, right-and left-side
accessory connectors, computer connector (USB 2.0, not a hub),
auxilliary signals connector, and purge gas input. You may also find
optional Auxilliary and/or dual channel connectors on the rear panel.
Danger Avoid shock hazard. Always power off the spectrometer and
disconnect the power supply from the wall outlet or power strip
before disconnecting the power supply from the back of the
spectrometer.
In the Spectrometer Tour (available through Getting Started) view
“The back panel” for complete descriptions of the rear panel
components.
Nicolet FT-IR User’s Guide 55
Turning on the
spectrometer power
Warning Always follow the safety precautions in this manual and in the
Note After you turn on the spectrometer, let it stabilize for 15 minutes
Follow these steps to turn on the spectrometer power:
1. If the external power supply is not already connected,
connect it.
In the Spectrometer Tour (available through Getting Started)
view “Connecting to AC power” in the “Powering up” unit for
information about connecting the power supply.
2. Turn on any accessories you plan to use.
This includes accessories such as a gas chromatograph, a GC
interface or an infrared microscope.
Spectrometer Safety Guide that came with your system whenever
you use the spectrometer.
3. Turn on the spectrometer by pressing the power switch (I/O)
on the external power supply.
When you turn on the spectrometer, the four status indicators—
Power, Scan, Laser and Source—flash in various sequences as
the system runs through its diagnostic routines. When the
routines are finished, the Power, Laser and Source indicators stay
lighted. The Scan indicator flashes with each scan of the
interferometer.
(one hour for best results) before collecting data. Leave the
spectrometer on at all times, unless the building is subject to power
outages or you need to perform a service or maintenance procedure.
Leaving the spectrometer on increases stability and consistency of
performance.
4. Turn on the printer and then the computer.
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56 Thermo Electron Corporation
Reverse the order given in the preceding procedure when you turn
off system components:
1. Turn off the computer.
2. Turn off the printer.
3. Turn off the spectrometer. (Press the power switch on the
external power supply to
4. Turn off the accessories.
In the Spectrometer Tour (available through Getting Started) view
“Powering up” for complete instructions for turning on your system.
Note The spectrometer enters “stand-by” mode 10 minutes after data
collection activity has ceased. This mode continues for 1 hour. After
1 hour, the interferometer stops scanning and the spectrometer enters
“sleep” mode. The Scan light stays on continuously. Any data
collection activity will cause the interferometer to begin scanning.
Exiting OMNIC also activates stand-by mode.
Note If the Power, Laser or Source indicators flash or will not light at all,
or if the Scan indicator will not light, the Bench Status indicator will
show a red X and troubleshooting tips will appear on the screen. If
you cannot resolve the problem by following these tips or by turning
the spectrometer power off and then on, contact Thermo Electron at
one of the numbers below. Outside the U.S.A. call your local sales
or service representative.
Phone: 1-800-642-6538 (U.S.A.) or
+608-273-5015 (worldwide)
Fax: +608-273-6883 (worldwide)
E-mail: techsupport.analyze@thermo.com
World Wide Web: http://www.thermo.com/spectroscopy S
O.)
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Nicolet FT-IR User’s Guide 57
Using a light source
Caution Even after the spectrometer is turned off, the external housings of
The Nicolet 4700 comes with a single infrared light source. The
Nicolet 6700 is available with a single internal source or with
optional dual sources. If your spectrometer does not have the dualsource option, you will need to change sources in order to use a
different internal source.
In Spectrometer Help Topics view “Installing a new source” in
“Setting up experiments” if you need to install or change a source.
working IR sources remain hot for up to 15 minutes. To avoid being
burned, allow the source to cool before touching it.
The ETC infrared source can be operated in the three modes of
operation described below.
Normal mode – In this mode the temperature of the source is
maintained at an optimal level for normal spectral data collection.
This improves the consistency of your spectral data by ensuring that
the infrared energy level reaching your samples is constant. The
source operates in Normal mode unless you configure it to enter
Turbo or Rest mode at specific times or the spectrometer is in sleep
mode.
Turbo mode – Use this mode if you are analyzing a sample, such as
a thick film, that requires greater infrared energy. This increases the
output of the source, especially in the frequency range around 2,500
wavenumbers. To turn Turbo mode on or off, use the Source
parameter on the Bench tab of the Experiment Setup dialog box,
available through Experiment Setup in the Collect menu. So long as
you are collecting data, the source remains in Turbo until you turn
that mode off. Whenever the spectrometer is in stand-by mode, the
source returns to Normal mode. When the spectrometer enters sleep
mode, the source shifts into Rest mode. This extends the life of your
source. In OMNIC Help Topics find “source” in the Index and go to
“Specifying the source type” for details.
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58 Thermo Electron Corporation
Rest mode – Rest mode lowers the temperature of the source so that
its life is extended. The source automatically shifts into Rest mode
when the spectrometer moves into sleep mode. You can configure
the source to enter Rest mode at specific times.
When you resume data collection activity, the source automatically
re-enters Normal mode. In OMNIC Help Topics find “source” in the
Index and go to “Extending the life of the source with rest mode” for
details.
You can switch between different internal sources simply by
changing the Source setting on the Bench tab of the Experiment
Setup dialog box. This option lets you collect spectra in the mid-IR
to far-IR range or in the visible to near-IR range. The spectral range
is determined by the source, beamsplitter and detector you are using.
Nicolet 6700 spectrometers with the emission accessory can use an
external source, if one is available. The beam from the external
source passes through the emission port on the right side of the
spectrometer.
?
In OMNIC Help Topics find “source” in the Index and go to
“Specifying the source type” for instructions for using different
sources in your spectrometer.
Nicolet FT-IR User’s Guide 59
Using
beamsplitters
and detectors
Selecting the right
beamsplitter and detector
A number of beamsplitters and detectors are available for use in the
Nicolet 4700 and Nicolet 6700 spectrometers. You can change the
detector type in either model, but the beamsplitter type can be
changed only in the Nicolet 6700. Not all beamsplitters and detectors
can be used together. Some detectors can accommodate only a
portion of the energy from the source and require changing the
aperture size (on a Nicolet 6700) or installing an energy filter. This
section explains how to select and optimize the performance of
beamsplitters and detectors.
In Spectrometer Help Topics view the appropriate lesson in “Setting
up experiments” if you need to install or change a beamsplitter or
detector.
There are two considerations when selecting a beamsplitter-detector
combination: compatibility and spectral range. Combinations are
considered compatible if they provide a detector signal that is large
enough to allow the beamsplitter to be aligned. This does not
necessarily mean a particular combination will provide the
maximum capable sensitivity range of each component.
The following table shows which beamsplitter-detector
combinations perform best and which are compatible.
60 Thermo Electron Corporation
BEAMSPLITTER
Near-IR Mid-IR* Far-IR
DETECTOR
Quartz
CaF
XT-KBr KBr Csl Solid Substrate
2
DTGS
(KBr window)**
DTGS
(Csl window)
DTGS
(PE window)
MCT-A
MCT-B
InSb
PbSe
Si
PbS
InGaAs
Best = Optimum beamsplitter-detector combination.
OK = Compatible beamsplitter-detector combination.
X = Incompatible beamsplitter-detector combination.
* A ZnSe beamsplitter may also be used as a mid-IR beamsplitter in extremely
humid environments.
** Valid for room temperature and thermoelectrically cooled versions.
OK
OK
OK OK
OK
Best
OK
OK OK
OK
X Best Best OK X
X
X
X
X
OK
OK
Best
Best
OK
Best
Best
OK OK Best X
X X OK Best
Best
Best
OK
X
X
Best
Best
X
X
X
X
OK
OK
X
X
X
X
X
X
X
X
X
X
XXX
Nicolet FT-IR User’s Guide 61
The next table lists the spectral ranges of compatible beamsplitterdetector combinations.
Light Range Beamsplitter Detector Spectral Range (cm-1) Source
visible quartz PbSe 13,000 - 2,800* ETC, white light
CaF
2
near-IR quartz MCT-A
PbS TEC (with SabIR
InGaAs 12,000 - 3,800 ETC, white light
CaF
MCT-A‡ 11,700 - 1,200* ETC, white light
2
InGaAs 12,000 - 3,800 ETC, white light
PbSe 11,000 - 2,000* ETC, white light
DTGS-KBr 11,000 - 375* ETC, white light
XT-KBr MCT-A
InGaAs 12,000 - 3,800 ETC, white light
Continued on next page...
†
Si
25,000 - 8,600 White light
PbSe 13,000 - 2,000* ETC, white light
†
Si
14,500 - 8,600 White light
‡
11,700 - 2,800* ETC, white light
MCT-B
InSb
‡
11,700 - 2,800* ETC, white light
‡,§
11,500 - 2,800* ETC, white light
PbSe 13,000 - 2,800* ETC, white light
) 10,000 - 4,200* ETC, white light
MCT-B
InSb
‡
11,700 - 1,200* ETC, white light
‡,§
11,500 - 1,850* ETC, white light
PbSe 13,000 - 2,000* ETC, white light
PbS TEC (with SabIR) 10,000 - 4,200* ETC, white light
‡
11,000 - 600* ETC, white light
MCT-B
InSb
‡
11,000 - 400* ETC, white light
‡,§
11,000 - 1,850* ETC, white light
DTGS TEC 11,000 - 375* ETC, white light
62 Thermo Electron Corporation
Light Range Beamsplitter Detector Spectral Range (cm-1) Source
mid-IR KBr DTGS-KBr 7,400 - 350 ETC
MCT-A‡ 7,400 - 600 ETC
DTGS TEC 7,100 - 350 ETC
MCT-B
DTGS-CsI 6,400 - 350 ETC
CsI
¶
DTGS-CsI 6,400 - 225 ETC
MCT-A
MCT-B
ZnSe DTGS-KBr 4,000 - 650 ETC
MCT-A‡ 4,000 - 650 ETC
MCT-B‡ 4,000 - 650 ETC
DTGS TEC 4,000 - 650 ETC
DTGS-CsI 4,000 - 650 ETC
far-IR Solid-Substrate
DTGS-PE 700 - 50 ETC
Si bolometer 700 - 20 ETC
Notes:
* This spectral range reflects the combination of the ranges of the ETC and white light sources, as well as the limits of the beamsplitter-
detector combination. The range achieved using one of these sources will not be as broad as the total range shown.
†
Si detectors can be used only with a white light (tungsten-halogen) source.
‡
These detectors must be cooled with liquid nitrogen before use.
§
InSb detectors will not produce a signal under intense light. During installation and alignment, start with the smallest aperture setting.
¶
CsI beamsplitters are extremely hygroscopic (sensitive to moisture).
‡
7,400 - 400 ETC
‡
6,400 - 600 ETC
‡
6,400 - 400 ETC
Nicolet FT-IR User’s Guide 63
Improving the quality
of your spectral data
Improving linearity
and photometric accuracy
If you are using the spectrometer for quantitative analysis or other
demanding applications, you are concerned with the precision and
accuracy of your spectra. For these types of applications it is important
that the spectra you collect have high wavelength precision. This
means that the frequency axis (X-axis) location of peaks in a spectrum
is consistently reproducible and within IUPAC (International Union of
Pure and Applied Chemistry) published specifications. You must also
be certain that your spectrometer responds linearly to the samples you
are studying. This means that absorption band intensity is directly
proportional to the number of molecules subjected to the light beam;
thus, as the number of molecules in the beam increases, the detected
absorbance signal also increases at a consistent rate.
If you are studying samples that produce tiny spectral peaks or have
weak spectral features, or if you are looking for small changes in
your samples, make sure the signal-to-noise ratio is high enough to
let you distinguish spectral features from the noise inherent in all
experimental data. This prevents the signals containing spectral
information from being lost among the signals generated by the
random movement of electrons, building vibrations, light source
fluctuations and other such sources.
The next sections explain several ways you can optimize Thermo
Electron detectors to improve the quality of your spectral data.
Some detectors (including PbSe, Si, MCT-A and InSb detectors) are
highly sensitive and can become saturated or produce a distorted
(non-linear and photometrically inaccurate) signal if the light energy
is not reduced before it reaches the detector element or if the
detector gain is set too high.
Look at a single-beam spectrum in the low-end region around 600 to
375 cm
As a rule of thumb, the distance from 0 to the baseline should be less
than 1% of the spectrum’s maximum intensity value. If the detector
is saturated, you will see false energy in the low-end region. The
baseline might be far above zero.
-1
. You should see a straight line very near 0 intensity units.
64 Thermo Electron Corporation
Note The maximum intensity of a mid-IR single-beam spectrum is
typically found near 2,000 cm
Note If the distance from the baseline to 0 is greater than 20% of the
spectrum’s maximum intensity value, your detector electronics may
be overloaded. Contact technical support for assistance.
The distorted signal may cause problems with photometric accuracy.
For good quantitative data, the sample and background
interferograms should be about the same size. Scattering samples
and very dense samples produce very small signals that, when
compared with much larger background signals, can distort
quantitative data.
Check the background and sample interferograms. If you see a
substantial difference in their sizes, photometric accuracy could be a
problem.
To solve these problems, you can use the following options to
modify the infrared beam:
-1
. S
S
• Use a bandwidth-limiting filter.
• Use an energy screen.
• Adjust the aperture (on a Nicolet 6700).
In Spectrometer Help Topics view “Setting up experiments” for
instructions for using filters and energy screens.
In some cases, system performance improves if you use a filter or
screen. The filter or screen that you should use for your application
depends on the samples being measured and other experimental
conditions. Try using various filters or screens to determine which
give the best results.
Nicolet FT-IR User’s Guide 65
When to use
bandwidth-limiting filters
When to use energy screens
Use bandwidth-limiting filters to improve the signal-to-noise ratio of
the data and also prevent detector saturation by allowing only energy
in your particular area of interest to pass to the detector element.
An optional filter wheel (available for the Nicolet 6700 only) lets
you automatically move a filter into the beam path before collecting
data. See “Using the filter wheel” in the “Spectrometer Options”
chapter for more information.
In Spectrometer Help Topics view “Setting up experiments” for
instructions for installing filters in the sample compartment or
optional filter wheel.
Depending on the types of detectors you use, your system may include
a set of four energy screens. These metal screens help prevent detector
saturation and signal distortion by blocking out a portion of the energy
at all frequencies of the infrared beam. If your experiments deal with
information from a broad range of frequencies, these screens may be
the most effective means of reducing the light level.
The energy screens are labeled A, B, C and D. The following table
shows the percentage of the infrared energy that each screen passes.
It also lists the detectors typically used with each screen, as a
starting point for correcting linearity problems.
Screen % Transmitted* Detectors Typically Used With Screen
* These are nominal values that may vary due to diffraction and detector variations.
66 Thermo Electron Corporation
None 100 DTGS
A 30 MCT-A
B 10
C 3
D 1
To correct for photometric accuracy, you may need to add a “heavier”
screen (one that transmits less infrared energy). With corrections for
photometric accuracy you will notice some reduction in the signal-tonoise ratio but will obtain more reliable quantitative data. Generally,
the signal-to-noise ratio is reduced less than is the signal intensity.
In Spectrometer Help Topics view “Setting up experiments” for
instructions for installing energy screens in the sample compartment.
An optional energy screen wheel lets you automatically move a
screen into the beam path before collecting data. See “Using the
energy screen wheel” in the “Spectrometer Options” chapter for
more information.
What aperture size
to use for your detector
The aperture in a Nicolet 6700 is a variable-diameter opening that
controls the angular size of the infrared beam and, thus, the amount of
radiation that reaches the sample. Using an aperture has these
advantages:
• It lets you use more sensitive detectors.
• It helps prevent infrared energy saturation, so the response of the
detector is more linear.
• It improves wavenumber accuracy and resolution by acting as a
point source of infrared radiation.
In general you will find that the larger the aperture, the better is the
signal-to-noise ratio of the collected data. The smaller the aperture,
the better the stability and accuracy will be. Small apertures are
needed for high-resolution experiments.
DTGS detectors can accommodate most of the energy from the
source, which means you should use a large aperture size. Detectors
that require cooling with liquid nitrogen are very sensitive and
require a small aperture size or the use of an energy screen (see the
preceding section for more information).
Nicolet FT-IR User’s Guide 67
Note On a Nicolet 6700, the setting of the Aperture parameter determines
the
area of the aperture opening. Doubling the setting approximately
doubles the area. The light energy is proportional to the aperture
area. A setting of 100 gives a nominal aperture diameter of 8 mm
and an approximate area of 0.50 cm
2
. S
The following table lists recommended aperture settings for different
detectors with the appropriate energy screen installed. (See the
preceding section for information about the correct energy screen to
use for each detector type.) The settings in the table are based on the
physical size of the detector elements and maximize the amount of
infrared energy that reaches the sample. To correct linearity and
photometric accuracy problems, you can reduce the setting, but you
will pay a price in terms of the signal-to-noise ratio.
Detector Aperture Setting
DTGS 100
MCT-A, MCT-B, InSb, PbSe, Si, InGaAs 32
?
In OMNIC Help Topics find “aperture” in the Index and go to
“Setting the aperture size” for information about changing the
aperture setting.
68 Thermo Electron Corporation
How to improve the
signal-to-noise ratio
Note If the distance from the baseline to 0 is greater than 20% of the
If you primarily analyze qualitative data, you may wish to optimize
the system for a better signal-to-noise ratio. This can be particularly
important when you are working with scattering samples and
samples that absorb more infrared energy. These samples produce
smaller signals that can be “lost” in the noise.
There are several ways to improve the signal-to-noise ratio. The
most commonly used method is to increase the number of scans.
This both reduces the noise level and makes small absorptions easier
to distinguish. You can also improve the ratio by reducing the
resolution (that is, using a higher Resolution setting).
Another method is to use an energy screen that transmits more light
(or no screen at all). In this case, the resulting spectrum might be
distorted and accuracy and stability could be reduced. Checking the
single-beam baseline in the region below the low-end cutoff will
give you a rough idea of how much distortion is occurring. If the
distance from the baseline to 0 is more than 15% of the spectrum’s
maximum intensity value, you may have difficulty reproducing the
results.
spectrum’s maximum intensity value, your detector electronics may
be overloaded. Contact technical support for assistance.
In Spectrometer Help Topics view “Setting up experiments” for
instructions for installing filters and energy screens.
S
Nicolet FT-IR User’s Guide 69
How to improve
the resolution
?
How to collect
data in the visible
spectral range
If you want to achieve higher resolution, you may need to use a
smaller aperture setting (on a Nicolet 6700) and an energy screen that
transmits more light (or no screen at all). Your spectroscopy software
will automatically change the aperture setting if a smaller beam size is
required. Be aware that the smaller beam size will reduce the signal-tonoise ratio.
In OMNIC Help Topics find “aperture” in the Index and go to
“Setting the aperture size” for information about changing the
aperture setting.
The ability of the spectrometer to collect data is affected by the
detector-beamsplitter combination and any energy screens or optical
filters that are installed in the spectrometer. For example, if you use an
optional quartz beamsplitter, a silicon detector and a white-light
source, the sampling range is extended to 25,000 cm
Since silicon detectors are very sensitive, you will also need to
install an energy screen or bandwidth-limiting filter to prevent the
detector from being saturated during the experiment. The following
table lists a variety of spectral bands in the extended spectral range
and lists the filter or energy screen that should be used to obtain data
in each range. It also lists typical aperture and gain settings for
experiments in each range. (Only the Nicolet 6700 has an aperture.)
-1
.
Spectral Range Filter or Screen Aperture Gain
16,000 - 9,000 cm-1 red filter 32 1
16,000 - 9,000 cm
23,000 - 16,000 cm
26,000 - 21,000 cm
70 Thermo Electron Corporation
-1
energy screen A 32 1
-1
broad-band blue filter 100 8
-1
narrow-band blue filter 100 8
You can use these filters and settings as a starting point and vary
them as required by your experimental conditions. To set the
aperture and gain, set the Aperture and Gain parameters on the
Bench tab in the Experiment Setup dialog box.
In Spectrometer Help Topics view “Setting up experiments” for
instructions for installing filters and energy screens.
The optional filter wheel (available for the Nicolet 6700 only) and
energy screen wheel let you automatically move a filter and energy
screen into the beam path before collecting data. See “Using the
filter wheel” and “Using the energy screen wheel” in the
“Spectrometer Options” chapter for more information.
About the moving
mirror velocity
Important When you switch to a different detector (on either model
While a wide range of moving mirror velocities are available on
Nicolet 4700 and Nicolet 6700 spectrometers, some velocity settings
cannot be used for collecting data at certain combinations of spectral
range and resolution:
If you are collecting data over a spectral range above 7899 cm
velocity settings faster than 2.53 cm/s are not available.
To specify the velocity and spectral range, set Velocity and Spectral
Range on the Bench tab of the Experiment Setup dialog box. To
specify the resolution, set Resolution on the Collect tab.
spectrometer) or beamsplitter (on a Nicolet 6700 only), OMNIC
automatically resets the default spectral range in the Experiment
Setup dialog box. Be sure to check the range and set the velocity to a
value that is appropriate.
S
-1
,
Nicolet FT-IR User’s Guide 71
Using the filter wheel
Spectrometer Options
This chapter explains how to use these optional spectrometer
features:
• The automated filter wheel (available for the Nicolet 6700
only) moves optical filters (supplied by you) into the beam path.
• The energy screen wheel moves an energy screen into the beam
path to reduce the energy reaching the detector.
• The polarizer allows you to control the orientation of the
electric field vector of the infrared beam entering the sample
compartment.
The optional filter wheel accessory (available for the Nicolet 6700
only) lets you automatically insert optical filters (band-pass, lowpass or high-pass) into the beam path. This lets you reduce the
amount infrared light that reaches the detector in a spectrally
selective way. This is particularly useful for studies of small spectral
regions or for blocking noisy spectral regions that contain no data of
interest. Energy from other regions does not reach the detector, thus
improving the signal-to-noise ratio in the region of interest.
72 Thermo Electron Corporation
The accessory has two wheels: wheel A is closest to the source.
Each wheel can be moved to one of four positions. Both wheel A
and wheel B have an open position for collecting spectra without a
filter in the beam path. Positions 1, 2 and 3 are available for filters
that you provide. Each position accepts one 1 mm thick or one 4 mm
thick filter that is 1-inch in diameter. Spacers are provided to secure
1-mm filters in position.
In Spectrometer Help Topics view “Installing an optical filter in the
automated filter wheel” in the “Setting up experiments” book for
instructions for installing filters in the wheel.
Once you have installed your filters, enter their descriptions into
OMNIC using the Filter Wheel table on the Configure tab of the
Experiment Setup dialog box. Be descriptive.
?
In OMNIC Help Topics find “filter wheel” in the Index and go to
“Entering descriptions of the filters in the filter wheel” for more
detailed instructions.
Nicolet FT-IR User’s Guide 73
Your filter descriptions will be saved in the experiment file and are
available for selection through the Filter Wheel A and Filter Wheel
B parameters on the Bench tab of Experiment Setup. Your
descriptions of the filters used during data collection also are saved
in the collection and processing information for the spectra you
collect.
By controlling which position of each wheel is in the beam path, you
can collect spectra with no filter, just one filter or a combination of
two filters. For example, you could install and select a band-pass
filter to block out frequencies in both the high and low ends of the
spectral range, resulting in a spectrum with absorptions only in the
middle of the range. You also could accomplish mid-range data
collection using a high-pass filter installed in one wheel and a lowpass filter installed in the other.
To specify the filter(s) to use for an experiment, set Filter Wheel A
and Filter Wheel B on the Bench tab of the Experiment Setup dialog
box (available through Experiment Setup in the Collect menu).
74 Thermo Electron Corporation
Using the
energy screen wheel
?
In OMNIC Help Topics find “filter wheel” in the Index and go to
“Controlling the filter wheel” for more detailed instructions.
The optional energy screen wheel lets you automatically insert an
energy screen into the beam path to block out a portion of the energy
at all frequencies of the infrared beam. This is useful for preventing
detector saturation and signal distortion. For more information about
using energy screens, see “When to use energy screens” in the
“Spectrometer Basics” chapter.
The wheel can be moved to any of four positions: an open position
(for collecting spectra without a screen in the beam path) and 3
screen positions. As shipped from the factory, the screen positions
are populated with 30%, 10%, and 3% screens. The Screen Wheel
parameters in Experiment Setup to describe the percentage of light
transmitted by each screen installed in the wheel. Simply select one
to move the screen into the beam path.
Nicolet FT-IR User’s Guide 75
To specify the screen to use for an experiment, set Screen Wheel on
the Bench tab of the Experiment Setup dialog box (available through
Experiment Setup in the Collect menu).
?
In OMNIC Help Topics find “energy screen wheel” in the Index and
go to “Controlling the energy screen wheel” for complete
instructions.
After you have moved a screen into the beam path, you can see its
effect on the signal intensity in the live display on the Bench tab.
This helps you select the optimum screen for a particular sample.
76 Thermo Electron Corporation
A 1% screen also is shipped with the wheel. Contact technical
support if you wish to use this or other screens that you provide in
the wheel. If you use the 1% screen or one of your own, be sure to
change the description of the screen position on the Configure tab.
?
In OMNIC Help Topics find “energy screen wheel” in the Index and
go to “Specifying the energy screens in the energy screen wheel” for
more detailed instructions.
Nicolet FT-IR User’s Guide 77
Using the
internal polarizer
An optional automated polarizer lets you automatically control the
orientation of the electric field vector of the IR beam entering the
sample compartment. The range of orientation is 0 to 180 degrees
in increments of 1 degree. At 0 degrees, the electric field vector is
oriented vertically, perpendicular to the sample compartment base
plate. This option is useful for performing polarization studies of
thin films and other sample types.
78 Thermo Electron Corporation
Note The polarizer cannot be installed on spectrometers with sample
compartment windows.
In Spectrometer Help Topics view “Installing optional hardware” for
detailed information about installing the polarizer.
In these experiments, a unique background is required for each
polarization position used. For example, if you are going to collect
spectra at 0 and 90 degrees, corresponding background spectra are
required at 0 and 90 degrees.
S
To set the polarization angle, type any number from 0 to 180 in the
Polarizer Angle text box on the Bench tab of the Experiment Setup
dialog box (available through Experiment Setup in the Collect
menu). Use the up and down arrows to step the polarizer one degree
at a time to optimize your signal.
?
In OMNIC Help Topics find “polarizer” in the Index and go to
“Controlling the polarizer” for more detailed instructions.
Begin you experiment by collecting backgrounds (as single beam
spectra) at each polarizer angle required by your experiment. Save
each background spectrum with a unique, descriptive name, such as
Background 0, Background 90. Once the background spectra are
collected and saved, you can begin to collect sample spectra. Sample
data may be collected and saved as single beam spectra. Once data
collection is complete, use the appropriate background file to
reprocess the data into your final format. Sample data also may be
collected and saved as ratioed spectra (%T, A, %R etc.) using the
corresponding stored background. Use the Background Handling
parameter on the Collect tab in Experiment Setup to specify the
Nicolet FT-IR User’s Guide 79
background file name. Click the Use Specified Background File
checkbox and then enter the background spectrum filename.
If you have OMNIC Macros\Basic or OMNIC Macros\Pro, you can
create a macro that changes the angle incrementally with each
successive set of background and sample spectra.
Then use Experiment Setup to specify that the Macro button start the
experiment and run the macro. Use the Macro for Macro button field
on the Advanced tab in Experiment Setup dialog box (available
through Experiment Setup in the Collect menu) to specify the macro
to run. You may browse to locate the macro file or type the full path
and file name into the text field.
If you have OMNIC Series, you can display the series of spectra
collected in this way. To create a series (.SRS) file from your
spectra, follow the instructions in "Creating a series data set" in the
"Series Menu Commands" chapter of the OMNIC Series User's
Guide.
80 Thermo Electron Corporation
Accessories
This chapter briefly describes the types of sampling and system
accessories that are available for your spectrometer. Complete
descriptions and operating instructions are included with the
accessories.
Smart Accessories
In addition to traditional accessories, a variety of Smart Accessories
are available for your spectrometer. Nicolet FT-IR spectrometers
identify each Smart Accessory as it is installed and set the software
parameters for data collection. Also, a series of spectral quality
checks are performed to ensure that the accessory is installed and
operating correctly.
Detailed tutorials for installing, operating and maintaining each
Smart Accessory are provided on-line. To start a Smart Accessory
tutorial, click Sampling Techniques in the Help menu and then click
the accessory name.
Smart ARK
accessory with high stability, complete purge capabilities, tool-free
alignment and high performance specifications. It includes integral
purge tubes that seal the accessory from the atmosphere, and a cast
aluminum body for exceptional stability.
Smart Collector
light-scattering solids that are difficult to analyze using transmission
techniques. This method is also useful when the sample, usually a
powder, must be analyzed without modification.
– This is a horizontal ATR (attenuated total reflection)
– Diffuse reflection enables analysis of highly
Nicolet FT-IR User’s Guide 81
Smart Diffuse Reflectance – The diffuse reflection technique lets
you analyze highly light-scattering solids that are difficult to analyze
using transmission techniques. The technique is also useful when the
sample, usually a powder, must be analyzed without modification.
This accessory lets you analyze a wide variety of sample types and
features integral sample cups for convenient, fast sampling.
Smart DuraSamplIR
accessory has a viewing feature that makes it easy to position the
sample and monitor the applied pressure. The accessory is ideal for
small samples and can be used to measure liquids, powders and
pliable solids.
Smart DuraScope
of a diamond ATR element with video enhancement to create an
analysis tool for a wide range of sample types, from large, hard
materials to small inclusions and contaminants. You can position the
sample while looking through the diamond ATR element. This helps
you manipulate micro samples to achieve optimum contact with the
crystal, resulting in superior quality spectral data.
Smart Endurance
is rugged and versatile. It stands up to highly corrosive, caustic,
intractable or abrasive samples, making it a good choice for almost
any sample type.
Smart Golden Gate – This is a horizontal, single-reflection ATR
accessory that features an extremely durable diamond crystal. It
handles a wide range of sample types, including hard or brittle
solids, corrosive liquids and hard powders.
– This single-reflection horizontal ATR
– The Smart DuraScope combines the benefits
– This single-reflection diamond ATR accessory
82 Thermo Electron Corporation
Smart Mid-IR FiberPort – This high-throughput accessory lets you
analyze liquids remotely. The needle probe can reach “hard to get”
samples, such as liquids in micro containers, hazardous
environments or remote locations. The FiberPort is a unique optical
interface that transfers IR energy from the spectrometer to the fiber
optic cables and probes. A complete line of fiber optic probes is
available for sampling a wide range of sample types.
Smart MIRacle
accessory with exceptional throughput and sensitivity. It can use
several crystal types and has a micrometer screw for precise control
of applied pressure.
Smart Multi-Bounce HATR – This multi-reflection horizontal
ATR accessory has a shorter pathlength and higher throughput than
traditional HATR accessory designs. It is the best choice for routine
analysis of strong infrared-absorbing samples. This accessory is
ideal for rapid quantitative and qualitative analyses, since sample
preparation is usually not necessary.
Smart OMNI-Sampler
features a spherical crystal that lets you measure a wide variety of
sample types. The unique tower design automatically applies the
optimum pressure while protecting the crystal. The accessory is ideal
for analyzing very small samples or sample areas and provides high
reproducibility.
Smart OMNI-Transmission
accessory lets you sample liquids, gases and solids using a wide
variety of transmission cells and infrared cards.
Smart Orbit
durable diamond crystal and a swivel pressure tower that ensures
consistent pressure from sample to sample. You can use the
accessory to perform analyses from the near-IR to the far-IR.
– This is a single-reflection horizontal ATR
– This single-reflection ATR accessory
– This easy-to-install transmission
– This single-reflection ATR accessory features a
Nicolet FT-IR User’s Guide 83
Smart Performer
horizontal sampling surface for collecting high quality spectra with
minimal sample preparation. The accessory uses a wide variety of
low cost crystals that are easy to install and remove.
Smart Refractor
fast analysis of coatings on reflective substrates using the grazing
angle specular reflection technique.
Smart SAGA
analysis of thin films on reflective substrates. The 80 degree angle of
incidence for this reflection-absorption accessory allows sensitive
measurements of films as thin as 0.1 nm.
Smart SpeculATR
reflection accessory allows versatility in measurement where a range
of sample morphologies may need to be analyzed.
Smart SplitPea
designed for fast analysis of solids, liquids, and powders. It is ideal
for analyzing hard materials, small samples or samples where only
minute quantities are available.
?
In OMNIC Help Topics find “accessory” in the Index and go to
“Specifying the accessory” for instructions for setting up and saving
experiments for custom accessories.
– This single-reflection ATR accessory features a
– This is top-loading accessory is designed for
– This advanced accessory is designed for the
– This single-bounce horizontal ATR/specular
– This horizontal ATR microsampling accessory is
84 Thermo Electron Corporation
Other sampling
accessories for
different applications
Note Additional Snap-In sample compartment baseplates are available for
You can install many of the sampling accessories yourself. After you
install an accessory, you may have to align it. Instructions for
aligning the spectrometer are included in the “Maintenance and
Service” chapter of this manual. Instructions for aligning an
accessory are provided in the documentation that came with that
accessory.
Some accessories fit into the sample compartment and require that
you remove the Snap-In baseplate before installing the accessory.
For information about using Snap-In baseplates, view “Removing
the Snap-In baseplate” in the “Setting up experiments” book in
Spectrometer Help Topics.
use with each accessory to make changing accessories easier.
Call Thermo Electron if you are interested in ordering any of the
following sampling accessories.
Absolute transmission accessory – This accessory allows for the
measurement of absolute transmission of samples with reflective
surfaces. The design prevents energy reflected from the sample from
entering the interferometer for remodulation. Using this accessory
involves replacing pinned-in-place mirrors before and after the
sample compartment.
Automatic sample wheel – This accessory holds multiple samples
and rotates them into the beam path for data collection. The sample
wheel is commonly used to measure multiple polymer or pressedpowder samples automatically.
S
Nicolet FT-IR User’s Guide 85
Auxiliary experiment module (AEM) – The AEM provides you
with an additional sample compartment. You can position it on the
right or left side of the spectrometer. With an AEM installed, you
can run routine analyses with the spectrometer and quickly switch
beam paths to the AEM to collect data from other samples without
removing accessories from the main sample compartment. Any
accessory or detector that can be installed in the spectrometer can be
installed in the AEM. The AEM has two detector locations.
Custom accessory baseplate
mount an accessory you have built or purchased from another
manufacturer. When you install the accessory and baseplate in the
sample compartment, the system automatically selects the Custom
Accessory experiment (or allows you to select from the experiments
you have saved for the baseplate).
Detector interface kit – A variety of accessories (that were
specifically designed for Nicolet FT-IR spectrometers) contain
detectors that are automatically recognized by your spectrometer.
The detector interface kit allows your spectrometer and OMNIC
software to recognize other detectors, including non-Thermo
Electron detectors.
Energy screen wheel – This accessory lets you prevent detector
saturation and signal distortion by using a screen to block a portion
of the infrared energy. See “Using the energy screen wheel” in the
“Spectrometer Options” chapter for complete information.
Filter wheel – This accessory (available for the Nicolet 6700 only)
lets you control the spectral range of the infrared light that reaches
the detector by inserting low pass or high pass filter into the beam
path. See “Using the filter wheel” in the “Spectrometer Options”
chapter for complete information.
– You can use this Smart baseplate to
86 Thermo Electron Corporation
Foundation Series – The innovative modular design of this
accessory family provides access to several sampling devices using a
common base. This allows experimental flexibility and an
economical price. Available techniques include ATR, diffuse
reflection, specular reflection, transmission and fiber optics.
Gas cells – A variety of short- and long-pathlength gas cells are
available. Cells include built-in transfer optics that fit into your
spectrometer. The cells are suitable for use in both ambient and
elevated temperature conditions. Gas cell heating, transfer optics
purge, gas manifold, and sample window options are available to
accommodate a variety of sample gases and sampling conditions.
GC interface – This interface attaches to the right side of the
spectrometer and must be connected to a gas chromatograph (GC).
You can then analyze IR spectra from GC experiments using the
OMNIC Series software.
Liquid Analysis System – This system lets you collect and process
quantitative analysis data for liquid samples. It uses OMNIC Integra
software, which contains methods for quantifying components in
specific types of liquids.
Microplate accessory – This accessory allows you to collect
transmission or diffuse reflectance spectra of multiple solid or liquid
samples consecutively. All the samples are loaded into the sample
chamber at one time into a 96 or 384 well microtiter plate. The
ejection, insertion, and movement of the well plate inside the sample
compartment is controlled by software.
Near-IR Heated Cuvette Holder E.S.P. – This accessory is
designed for analyzing samples that require a constant or elevated
temperature to obtain reproducible near-IR results. You can use it to
analyze liquids, gels and solids that have a low melting point, such
as waxes.
Nicolet FT-IR User’s Guide 87
Nicolet Centaurµs and Nicolet Continuµm infrared microscopes
– Thermo Electron offers microscopes that attach directly to the side
of the spectrometer. Microscopes can be installed between the
spectrometer and other accessory modules. The microscopes provide
fast, nondestructive microanalysis with minimal sample preparation
and alignment.
PAC 300 Photoacoustic E.S.P. – Photoacoustic spectroscopy (PAS)
is a powerful technique for the nondestructive spectroscopic analysis
of solid samples of all types. PAS is particularly applicable to
powders (including dark, highly absorbent samples), polymer
pellets, beads, and sheets and films. The PAC 300 Photoacoustic
E.S.P. accessory is fully integrated with the spectrometer and
computer. It automatically selects an OMNIC experiment, draws
power right from the spectrometer and includes an on-line tutorial.
Polarizer – This accessory lets you control the orientation of the
electric field vector of the infrared beam as it enters the sample
compartment. This is particularly useful for characterization of
monolayers, thin films and other sample types. See “Using the
polarizer” in the “Spectrometer Options” chapter for more
information.
Remote Start accessory – This accessory adds external trigger
capability to your spectrometer. With a press of the Start switch, you
can control the start of data collection or coordinate the start of an
external experiment.
SabIR
raw material identification, quality measurements, and sample
component analysis. The system is optimized for diffuse-reflectance
sampling of solids and powders. Materials may be sampled directly
or indirectly through packaging materials.
– This accessory provides remote sampling capability for
88 Thermo Electron Corporation
Sample shuttle – A sample shuttle lets you collect background
spectra without removing the sample from the sample compartment.
The shuttle automatically moves the sample out of the beam path
before background collection begins. Since the sample compartment
cover is not opened, the system purge is maintained.
Specular reflection accessories – Specular reflection provides a
nondestructive method for measuring surface coatings without
sample preparation. Specular reflection accessories can be used to
analyze surface-treated metals, paints, semiconductors, and resin and
polymer coatings.
TGA interface/TGA module – This interface is equipped with a
built-in, temperature-controlled flow cell and must be connected to a
thermogravimetric analysis (TGA) furnace. You can analyze the
evolved gases from TGA experiments using the OMNIC Series
software. The TGA interface is usually mounted in the sample
compartment of an AEM; the TGA module is usually installed on
the side of the spectrometer, leaving the AEM or spectrometer
sample compartment free for other experiments and accessories.
Transmission E.S.P.
most efficient sampling technique in FT-IR spectroscopy and can be
used for sampling liquids, gases or solids. A variety of cells and
sample holders are available for transmission analysis. All can be
mounted in the spectrometer sample compartment. Thermo
Electron’s E.S.P. (Enhanced Synchronization Protocol) technology
provides continuous communication between the accessory and
OMNIC to ensure that the accessory is operating correctly. This
accessory, or the validation wheel (described below), is required for
using an NPL or serialized polystyrene standard for validation with
Thermo Electron’s Val-Q
accessory – Transmission is the oldest and
software.
Nicolet FT-IR User’s Guide 89
System accessories
Validation wheel – The validation wheel is used with Val-Q to
validate the performance of the spectrometer. The wheel
automatically moves standard samples into the beam path at the
appropriate times during the validation procedure. The samples are
traceable to standards from the National Institute of Standards and
Technology (NIST). An optional calibrated sample from the
National Physical Laboratory (NPL) is also available.
Some system accessories are installed by Thermo Electron. Call us if
you are interested in ordering any of the following accessories.
Power line conditioner
spectrometer and other accessories from damage or malfunction due
to voltage dropouts, transient spikes, frequency shifts or other
disturbances in your electrical service.
Pure air dryer – If you have difficulty controlling moisture in your
laboratory, the pure air dryer provides additional protection for the
hygroscopic elements of your spectrometer. This accessory is also
useful if your laboratory air supply is contaminated with volatile
solvents, oil or other reactive materials.
Purge gas generator – If you do not have in-house facilities to
supply compressed air or nitrogen for system purge, Thermo
Electron offers several purge gas generators.
RSVP (Remote Support and Verification Program) – This
diagnostics option uses a data modem and remote control software to
allow control of your computer (and spectrometer) through the
modem link. An analog telephone line is required.
– Power line conditioners protect your
90 Thermo Electron Corporation
How to cable
an accessory
Pass-through connectors
Caution
Smart Purge Kit – This kit adds enhanced purging capability to
your spectrometer. When you open the sample compartment cover
or its sliding door, Smart Purge automatically increases the purge
gas flow rate for a short time. This keeps water vapor, carbon
dioxide and other unwanted gases out of the spectrometer while you
install or remove a sample. You can then collect spectra without
waiting for proper purge to be restored.
Uninterruptable power supply – An uninterruptable power supply
reduces the chance of a system shutdown if power is lost.
When you install an accessory in the sample compartment, you may
need to connect one or more cables from the accessory to connectors
on the rear wall of the compartment. You may also need to attach
cables from other peripherals (such as computers, custom controllers
or power supplies) to the accessory or from the accessory to the
connectors on the front of the spectrometer. The instructions that came
with the accessory contain specific information about connecting that
accessory.
Your spectrometer may be equipped with pass-through connectors
for use with special accessories. These connectors allow you to make
accessory cable connections through the spectrometer. This
eliminates the need to run cables through the seal on the sample
compartment cover or out the top of the sample compartment.
Improper or unsafe cabling can cause damage to your accessory and
create a safety hazard. Only qualified persons should cable a custom
accessory using these connectors. Thermo Electron is not
responsible for damage or injury resulting from improper or unsafe
cabling.
To use the pass-through connectors, connect the accessory inside the
sample compartment and connect the external power or
communications peripheral to the corresponding pass-through
connector on the front of the spectrometer.
S
Nicolet FT-IR User’s Guide 91
Connectors inside
the sample compartment
The following illustration shows the locations of the electrical
connectors inside the sample compartment:
Accessory connector for detector
signal or accessory control and power
Detector/Motors
Auxiliary
Purge
Out
Optional pass-through connector
for communication or other signal
Detector/Motors
– If you have a photoacoustic or other accessory
that has a detector or motor located in the spectrometer sample
compartment, connect the cable from the detector or motor to this
standard connector. This is
not a pass-through connector. See
“Detector/Motors connector” for information about using this
connector to connect custom hardware.
Auxiliary – Six pins on this optional connector can be used for
passing DC power input or other signals from the Auxiliary 1 and
Auxiliary 2 connectors on the front panel to an accessory. For
example, the automatic sample wheel and the ProfilIR accessory get
DC power through this connector when the DC power output of an
AC-to-DC converter is attached to the Auxiliary 1 connector on the
front panel. See “Using connectors for custom accessories” for
information about which pins are available for use.
92 Thermo Electron Corporation
Connectors on the
front of the spectrometer
Note
The illustration below shows the optional connectors on the front of
the spectrometer that you can use to pass signals to and from the
sample compartment.
These connectors are available only on systems that do not include
the SabIR accessory or the microplate accessory.
Auxiliary 1 – This connector passes power or other signals for the
accessory to three pins on the Auxiliary connector inside the sample
compartment. This connector could be used, for example, to attach
the DC output of an AC-to-DC converter to provide DC power to an
accessory in the sample compartment.
Auxiliary 2 – This connector passes signals to three pins on the
Auxiliary connector inside the sample compartment. This connector
could be used, for example, to allow an accessory in the sample
compartment to be controlled through your computer’s serial
(RS-232C) port.
See the next section for information about which pins are available
for use.
S
Nicolet FT-IR User’s Guide 93
Using the pass-through
connectors for
custom accessories
Warning
By connecting custom cables that use the pins on the pass-through
connectors, you can provide power and communication or other
signals for your custom accessories. The power and signals pass
through the spectrometer from the front to the sample compartment
and vice versa. Make sure your use of the connectors complies with
the voltage and current limitations given in the following Warning.
Improper or unsafe cabling can cause damage to your accessory and
may create a safety hazard. Only qualified persons should cable a
custom accessory using these connectors. Do not pass signals that
exceed ±15 VDC through these connectors. You must also limit the
current to a maximum of 800 mA. Thermo Electron is not
responsible for damage or injury resulting from improper or unsafe
cabling.
S
The following diagram shows schematically which pins of the
Auxiliary connector inside the sample compartment are connected
internally to pins of the Auxiliary 1 and Auxiliary 2 connectors on
the front of the spectrometer. Since none of these connected pins are
assigned by the Nicolet 4700 or Nicolet 6700, they are available for
use with custom accessories.
Sample Compartment
Connector
Front Panel
Connectors
8 765432 1
94 Thermo Electron Corporation
15 14 13
12
11 10 9
1234 5
789
6
(male)
1
Auxiliary
(female)
2
12345
789
6
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