not assume any liability arising out of any infringements of patents or other rights of third 

parties.

We make no warranty of any kind with regard to this material, including but not limited to the 

implied warranties of merchantability and fitness for a particular purpose.

Copyright © 2004 by Thermo Electron Corporation, Madison WI 53711. Printed in the United 

States of America. All world rights reserved. No part of this publication may be stored in a 

retrieval system, transmitted, or reproduced in any way, including but not limited to photocopy, 

photograph, magnetic or other record, without the prior written permission of Thermo Electron 

Corporation. 

For technical assistance, please contact: 

Thermo Electron Corporation 

5225 Verona Road 

Madison WI 53711-4495 

Telephone: 800-642-6538 or 608-276-6373 

Fax: 608-273-6883 

E-mail: techsupport.analyze@thermo.com 

Nicolet, OMNIC, Avatar, Val-Q, Centaurμs, RSVP, Smart Accessory, Continuμm, Smart Purge, 

OMNI-Transmission, FiberPort, Ever-Glo, Passport, Import, SeaPort, Solid-Substrate, Talon, 

PLUS, Vectra-Plus, Snap-In, SabIR, Sync, UpDRIFT, Smart Refractor, SpeculATR, SAGA, 

OMNI-Sampler, Smart Collector, Smart ARK, Gemini, Endurance, InspectIR, Orbit and E.S.P. 

are trademarks of Thermo Electron Scientific Instruments Corporation, a subsidiary of Thermo 

Electron Corporation. 

MIRacle is a trademark of PIKE Technologies. 

SplitPea is a trademark of Harrick Scientific Corporation.

DuraScope and DuraSamplIR are trademarks of SensIR Technologies. 

Windows is a trademark of Microsoft Corporation. 

Intel and Pentium are trademarks of Intel Corporation.

PS/2 is a trademark of International Business Machines Corporation. 

269-155800 
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
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
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.............................................................123

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

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
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
may result in minor or moderate injury. It may also be used to alert 

against unsafe practices. S

 Warning Indicates a potentially hazardous situation which, if not avoided, 

could result in death or serious injury. S

 Danger Indicates an imminently hazardous situation which, if not avoided, 

will result in death or serious injury. S

Questions 

or concerns 

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 

Nicolet FT-IR User’s Guide 3
- 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: 

15-inch SVGA 

4 megabytes of video RAM 

16-bit video card capable of displaying at least 256 colors with 

1024 by 768 resolution 

4 Thermo Electron Corporation
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 PLUSTM 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 

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
OMNIC” in the “Before You Collect Spectra” chapter for 

information about starting OMNIC. 

Wizards and tutorials 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
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
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
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 install a source?

Spectrometer Help Topics... 

“Selecting a beamsplitter, detector, and source” and 

“Installing a new source” in “Setting up experiments” 

Collecting spectra 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
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
“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
g pfy yy

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. S

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. 

• 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
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

SCFH AIR 80 100

120

140

0 160

20

40

60

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
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 

yes Some purge gas and pure air 

generators provide a flow rate of 

less than 50 scfh. 

50-99 scfh optional Using the tank will improve 

performance. 

100 scfh or 

greater 

no A flow rate of 100 scfh gives the 

best results. 

* 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. 

? 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.” 

16 Thermo Electron Corporation
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. 

 Note The Check Desiccant button measures humidity more accurately 

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. S

See “Ordering parts” in Spectrometer Help Topics to find the part 

number for ordering desiccant bags. 

Nicolet FT-IR User’s Guide 17
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. 

 Warning Always follow the safety precautions described in this manual and in 

the Spectrometer Safety Guide that came with your system. S

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. 

18 Thermo Electron Corporation
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. 

Cooling the detector 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. S

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. 

Nicolet FT-IR User’s Guide 19
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 

taskbar, point to Programs (All Programs in Windows XP), point 

to the Thermo Nicolet folder, and then click the OMNIC 

program. 

Depending on how the program has been configured, dialog 

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
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 , the correct experiment is selected 

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. 

Nicolet FT-IR User’s Guide 21
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
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
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
OMNIC Help system. 

Experiment 

drop-down list box 

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
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. 

 Note If you want to view the on-line videos to help troubleshoot a 

problem, put the spectrometer’s Tutorial CD into the computer’s 

CD-ROM drive. S

Toolbar 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. 

26 Thermo Electron Corporation
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
Height

adjustment

screw

Sample

holder

support

If you are using separate Snap-InTM 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
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
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
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
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 

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. 

32 Thermo Electron Corporation
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
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. 

34 Thermo Electron Corporation
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
automatically. S

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). 

 

36 Thermo Electron Corporation
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. 

Saving the spectrum 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
 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 

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. 

 

You can also 

choose % Transmittance 

from the Process menu.

38 Thermo Electron Corporation
?

The Process menu allows you to convert spectra to several other 

units as well. These units are discussed in detail in the OMNIC online 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
In the next section, you will label a peak in the absorbance 

spectrum using the annotation tool. 

Labeling a peak with 

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. 

Peak height

Selection

Region

Spectral cursor Peak area

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
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
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
Note If you were unsure of the composition of the sample, you could 

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. S

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. 

Nicolet FT-IR User’s Guide 43
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
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
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. 

Adding a spectrum 

to a user library 

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. 

 Note You cannot add spectra to a commercial library, nor can you move 

copies of commercially collected reference spectra into libraries you 

create. S

? 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. 

Nicolet FT-IR User’s Guide 47
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
? 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: 

You can click the Zoom button to 

see an enlarged image of the report.

Collection time: 

The preview lets you check the content of the report before 

printing it. 

Nicolet FT-IR User’s Guide 49
6. Choose OK. 

The report is printed on your system printer. 

50 Thermo Electron Corporation
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.) 

Data collection

buttons

Status indicators

Detector fill ports

Detector

compartment

Sliding door

Sample

compartment External beam port

Emission port for

external source

Beamsplitter

and desiccant

compartment

Nicolet FT-IR User’s Guide 51
data collection buttons 

some basic operations with the spectrometer without using your 

keyboard or mouse. (OMNIC must be running.) 

52 Thermo Electron Corporation
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
Electronics

Front detector

Detector

mirror

Back

detector

External

beam port

Interferometer Laser Beamsplitter

Beamsplitter

storage

Fixed mirror

or optional

emission optics

External

emission port

Passport optics

(optional)

External

beam port

Filter wheel

(optional)

Energy screen

wheel (optional)

Aperture

Infrared source

Source select

optics (optional)

Sample

compartment

Sample holder SabIR port Fixed mirror or optional

SeaPort optics

Polarizer

(optional)

Near-IR source

(optional)

In the Spectrometer Tour (available through Getting Started) view 

“Inside the spectrometer” for complete descriptions of your 

spectrometer components. 

54 Thermo Electron Corporation
 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
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. 

 Warning Always follow the safety precautions in this manual and in the 

Spectrometer Safety Guide that came with your system whenever 

you use the spectrometer. S

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. 

Note After you turn on the spectrometer, let it stabilize for 15 minutes 

(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. S

4. Turn on the printer and then the computer. 

 

56 Thermo Electron Corporation
external power supply to O.) 

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. S

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

Nicolet FT-IR User’s Guide 57
In Spectrometer Help Topics view “Installing a new source” in 

“Setting up experiments” if you need to install or change a source. 

 Caution Even after the spectrometer is turned off, the external housings of 

working IR sources remain hot for up to 15 minutes. To avoid being 

burned, allow the source to cool before touching it. S

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. 

58 Thermo Electron Corporation
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
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. 

Selecting the right 

beamsplitter and 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
DTGS

(Csl window)

DTGS

(PE window)

MCT-A

MCT-B

InSb

PbSe

Si

PbS

InGaAs

OK

X

X

X X OK Best

OK OK Best X

OK

OK

OK

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X X X

Best

Best

Best

Best

OK OK

OK OK

Best

Best

OK

OK OK

X

X

OK

OK

Best

Best

OK

Best

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. 

Nicolet FT-IR User’s Guide 61
visible quartz PbSe 13,000 - 2,800* ETC, white light

 Si† 25,000 - 8,600 White light 

CaF2 PbSe 13,000 - 2,000* ETC, white light

 Si† 14,500 - 8,600 White light 

near-IR quartz MCT-A‡ 11,700 - 2,800* ETC, white light

 MCT-B‡ 11,700 - 2,800* ETC, white light

 InSb‡,§ 11,500 - 2,800* ETC, white light

 PbSe 13,000 - 2,800* ETC, white light 

 PbS TEC (with SabIR ) 10,000 - 4,200* ETC, white light

InGaAs 12,000 - 3,800 ETC, white light

CaF2 MCT-A‡ 11,700 - 1,200* ETC, white light

 MCT-B‡ 11,700 - 1,200* ETC, white light

 InSb‡,

§ 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 

InGaAs 12,000 - 3,800 ETC, white light

XT-KBr MCT-A‡ 11,000 - 600* ETC, white light

 MCT-B‡ 11,000 - 400* ETC, white light

 InSb‡,

§ 11,000 - 1,850* ETC, white light 

 PbSe 11,000 - 2,000* ETC, white light 

 DTGS-KBr 11,000 - 375* ETC, white light

 DTGS TEC 11,000 - 375* ETC, white light 

InGaAs 12,000 - 3,800 ETC, white light

Continued on next page... 

62 Thermo Electron Corporation
 DTGS TEC 7,100 - 350 ETC 

DTGS-CsI 6,400 - 350 ETC 

 CsI¶ DTGS-CsI 6,400 - 225 ETC 

 MCT-A‡ 6,400 - 600 ETC 

 MCT-B‡ 6,400 - 400 ETC 

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 beamsplitterdetector 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). 

Nicolet FT-IR User’s Guide 63
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. 

Improving linearity 

and photometric accuracy 

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-1. You should see a straight line very near 0 intensity units. 

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. 

64 Thermo Electron Corporation
be overloaded. Contact technical support for assistance. S

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: 

• 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
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. 

When to use energy screens 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 

None 100 DTGS

A 30 MCT-A

B 10

C 3

D 1

* These are nominal values that may vary due to diffraction and detector variations.

66 Thermo Electron Corporation
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
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
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. 

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. S

In Spectrometer Help Topics view “Setting up experiments” for 

instructions for installing filters and energy screens. 

Nicolet FT-IR User’s Guide 69
? In OMNIC Help Topics find “aperture” in the Index and go to 

“Setting the aperture size” for information about changing the 

aperture setting. 

How to collect 

data in the visible 

spectral range 

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-1. 

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.) 

Spectral Range Filter or Screen Aperture Gain 

16,000 - 9,000 cm-1 red filter 32 1 

16,000 - 9,000 cm-1 energy screen A 32 1 

23,000 - 16,000 cm-1 broad-band blue filter 100 8 

26,000 - 21,000 cm-1 narrow-band blue filter 100 8 

70 Thermo Electron Corporation
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 

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-1, 

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. 

Important When you switch to a different detector (on either model 

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

Nicolet FT-IR User’s Guide 71
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. 

Using the filter wheel 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
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
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
energy screen wheel 

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
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
go to “Specifying the energy screens in the energy screen wheel” for 

more detailed instructions. 

Nicolet FT-IR User’s Guide 77
thin films and other sample types. 

Note The polarizer cannot be installed on spectrometers with sample 

compartment windows. S

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. 

78 Thermo Electron Corporation
? 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
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 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 – This is a horizontal ATR (attenuated total reflection) 

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 – Diffuse reflection enables analysis of highly 

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. 

Nicolet FT-IR User’s Guide 81
Smart DuraSamplIR – This single-reflection horizontal ATR 

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 – The Smart DuraScope combines the benefits 

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 – This single-reflection diamond ATR accessory 

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. 

82 Thermo Electron Corporation
available for sampling a wide range of sample types. 

Smart MIRacle – This is a single-reflection horizontal ATR 

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 – This single-reflection ATR accessory 

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 – This easy-to-install transmission 

accessory lets you sample liquids, gases and solids using a wide 

variety of transmission cells and infrared cards. 

Smart Orbit – This single-reflection ATR accessory features a 

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. 

Nicolet FT-IR User’s Guide 83
fast analysis of coatings on reflective substrates using the grazing 

angle specular reflection technique. 

Smart SAGA – This advanced accessory is designed for the 

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 – This single-bounce horizontal ATR/specular 

reflection accessory allows versatility in measurement where a range 

of sample morphologies may need to be analyzed. 

Smart SplitPea – This horizontal ATR microsampling accessory is 

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. 

84 Thermo Electron Corporation
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. 

 Note Additional Snap-In sample compartment baseplates are available for 

use with each accessory to make changing accessories easier. S

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. 

Nicolet FT-IR User’s Guide 85
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 – You can use this Smart baseplate to 

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. 

86 Thermo Electron Corporation
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
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 – This accessory provides remote sampling capability for 

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. 

88 Thermo Electron Corporation
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. accessory – Transmission is the oldest and 

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 software. 

Nicolet FT-IR User’s Guide 89
National Physical Laboratory (NPL) is also available. 

System accessories Some system accessories are installed by Thermo Electron. Call us if 

you are interested in ordering any of the following accessories. 

Power line conditioner – Power line conditioners protect your 

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. 

90 Thermo Electron Corporation
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. 

How to cable 

an accessory 

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. 

Pass-through connectors 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. 

 Caution 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. S

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. 

Nicolet FT-IR User’s Guide 91
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
 Note These connectors are available only on systems that do not include 

the SabIR accessory or the microplate accessory. S

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. 

Nicolet FT-IR User’s Guide 93
the voltage and current limitations given in the following Warning. 

 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. 

8 7 6 5 432 1

15 14 13 12 11 10 9

1 234 5

6 7 8 9

5 4 3 2 1

9 8 7 6

Auxiliary

1 (male)

2 (female)

Sample Compartment

Connector

Front Panel

Connectors

94 Thermo Electron Corporation
15 14 13 12 11 10 9

Detector/Motors

Make sure your use of the connector complies with the voltage and 

current limitations given in the following Warning. 

 Caution Improper or unsafe cabling can cause damage to your accessory and 

may create a safety hazard. Only qualified persons should connect a 

cable to the Detector/Motors connector. Do not use this connector 

for signals that exceed ±15 VDC. 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 table shows “pinout” information for the 

Detector/Motors connector. Use this information when designing a 

cable to connect your custom hardware to the connector. Refer to the 

preceding illustration for the locations of the numbered pins. 

Nicolet FT-IR User’s Guide 95
3 Positive 5 volts. 

4 Analog ground.

5 Used by the sample compartment detector for 

negative analog input. 

6 Positive 12 volts analog. 

7 Used by the sample compartment detector for digital 

communication. 

8 Positive 5 volts. 

9 Used for sample compartment digital communication. 

10 Used by the sample shuttle motor (positive). 

11 Positive 12 volts. 

12 Analog ground.

13 Used by the sample compartment detector for positive 

analog input. 

14 Negative 12 volts analog. 

15 Used by the sample compartment detector for digital 

communication. 

96 Thermo Electron Corporation
This chapter answers some common questions about using OMNIC. 

Each answer is followed by a reference telling you where to go for 

more information. 

Where a menu command name is given, the corresponding toolbar 

button is also shown. Depending on the software configuration you 

are using, a particular button may not be present in your toolbar. 

Collecting spectra How do I set the software for collecting spectra?

You can set the software in one step by selecting a stored experiment 

from the Experiment drop-down list box below the OMNIC window 

menu bar. To set the experiment parameters individually, use 

Experiment Setup in the Collect menu. 

If you install a Smart Accessory, the system automatically sets the 

software parameters (or a list of appropriate experiments is made 

available for your selection), and you can begin collecting spectra. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Preparing the Software” 

? In OMNIC Help Topics find “experiment” in the Index and go to 

“Selecting an experiment” or “Using Experiment Setup.” 

Nicolet FT-IR User’s Guide 97
Collecting a Spectrum (available through Learning OMNIC)... 

“Collecting the Spectrum of a Sample” 

? In OMNIC Help Topics find “spectrum” in the Index and go to 

“Collecting a sample spectrum” or “Collecting a background 

spectrum.” 

How do I specify the Y-axis unit for collecting spectra?

 

Choose Experiment Setup from Collect menu and then set Final 

Format on the Collect tab. 

You can change the format of a collected spectrum by using 

Absorbance, % Transmittance or Other Conversions in the Process 

menu. See the question and answer in the next section for a 

description of the available units. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Typical IR Transmission Spectrum” 

? In OMNIC Help Topics find “units” in the Index and go to 

“Selecting the final format.” 

98 Thermo Electron Corporation
setting the Gain parameter to Autogain. We recommend using this 

setting to ensure the best spectral quality. 

? In OMNIC Help Topics find “gain” in the Index and go to “Setting 

the gain.” 

When should I save interferograms with my spectra? 

Save interferograms if you think you may want to restore the 

original data after it has been processed or if you want to keep an 

archive of your original data. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Preparing the Software” 

? In OMNIC Help Topics find “saving, interferograms” in the Index 

and go to “File handling.” 

What does the Collect Sample window show?

The window displays the “live” spectrum as it is being collected plus 

a gauge indicating the progress of the collection, an indicator 

showing whether any problems have occurred and other information 

about the collection. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Collecting the Spectrum of a Sample” 

Nicolet FT-IR User’s Guide 99
OMNIC continuously monitors the quality of the data you collect, 

based on the parameters you set. The Quality tab in the Experiment 

Setup dialog box contains parameters for specifying the spectral 

quality characteristics that you want checked when you collect 

spectra. 

OMNIC offers four categories of spectral quality checks: 

• Spectrum checks 

• Parameter checks 

• Background checks 

• Interferogram checks 

When OMNIC performs a check and detects a problem, the Collect 

Status indicator is displayed as a yellow circle or a red X. Click the 

indicator (or click the View Collect Status button at the end of data 

collection) to see a summary of data collection problems 

encountered during the collection and other information about the 

collection. 

When a collected spectrum passes all of the selected quality checks, 

the Collect Status indicator appears as a green check mark. 

? In OMNIC Help Topics find “quality checks” in the Index and go to 

“Quality checks.” 

100 Thermo Electron Corporation
Kubelka-Munk units are useful for searching diffuse reflectance 

spectra against libraries of absorbance spectra. 

Use photoacoustic units for spectra collected using a photoacoustic 

accessory. 

Percent reflectance units are mathematically equivalent to 

% transmittance units, but using them for spectra collected using a 

reflection technique serves to identify the technique. 

Using log (1/R) units for spectra collected using a reflection 

technique is useful for quantitative comparisons, since there is often 

a linear relationship between the concentration of a component and 

its log (1/R) value. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Typical IR Transmission Spectrum” 

? In the OMNIC Help Topics Index... 

Find “absorbance” and go to “Converting spectra to absorbance.”

Find “transmittance (%)” and go to “Converting spectra to 

% transmittance.” 

Find “Kubelka-Munk units” and go to “Kubelka-Munk units.” 

Find “photoacoustic units” and go to “Photoacoustic units” topic. 

Find “reflectance (%)” and go to “% Reflectance units.” 

Find “log (1/R) units” and go to “Log (1/R) units.” 

Nicolet FT-IR User’s Guide 101
from the Analyze menu. 

? In OMNIC Help Topics find “library” in the Index and go to 

“Setting up a library search” or “Searching a spectral library.” 

How should I prepare my spectrum before searching it 

against a spectral library?

There are several corrections you can perform on a spectrum to 

obtain the best search results: 

?

• If the baseline of the spectrum is sloped, curved or shifted 

vertically, correct it using Baseline Correct in the Process menu.

In OMNIC Help Topics find “baseline” in the Index and go to 

“Correcting a baseline manually.” 

?

• If the spectrum has totally absorbing bands, eliminate them by 

using Blank in the Process menu. Be careful not to blank regions 

that contain other important spectral information. 

In OMNIC Help Topics find “blanking spectral region” in the 

Index and go to “Blanking a spectral region.” 

You can also use the region tool to select a region of the 

spectrum that does not include any totally absorbing bands or use 

the view finder to display the region before searching. (These 

methods avoid the loss of spectral information that results from 

blanking.) 

102 Thermo Electron Corporation
dispersion effects and then search it against a library of 

absorbance spectra. 

? In OMNIC Help Topics find “Kramers-Kronig transformation” 

in the Index and go to “Kramers-Kronig (dispersion) 

transformation.” 

• If you collected the spectrum using ATR (attenuated total 

reflection), use ATR correction (available through Other 

Corrections in the Process menu) to correct it for variation in the 

depth of penetration and then search it against a library of 

transmission spectra. 

? In OMNIC Help Topics find “ATR correction” in the Index and 

go to “ATR correction.” 

?

• If the spectrum has water or carbon dioxide peaks, use Other 

Corrections to remove these peaks. 

In OMNIC Help Topics find “water” in the Index and go to 

“H2O and CO2 correction.” 

Only those portions of the spectrum which are within the selected 

region (or displayed region if no region is selected) and within any 

of the regions you specified for the library using the Region Setup 

tab of the Library Setup dialog box will be included in the search. If 

the spectral range of the spectrum is broader than that of the library 

spectra, use the region tool to select the region of the spectrum that 

coincides with the library spectra before you start the search. You 

can also use the view finder to display the region to search. The 

Search command operates on the selected region, or on the displayed 

region if a region is not selected. 

Nicolet FT-IR User’s Guide 103
If you are using OMNIC, use the Create Library button on the 

Library Names tab of Library Manager (available through the 

Analyze menu) to create a user library. 

Once a library is created, you can add spectra to it with Add To 

Library in the Analyze menu or by dragging the spectrum to the 

library’s book on the Library Names tab of Library Manager. You 

can use a search library you create just as you would a commercial 

library to identify unknown spectra. You can use a QC library to 

verify the composition of a sample. If you create a scrapbook library, 

you can find spectra in it by searching for text (but not by spectral 

searching). 

When you create a library, you determine the kinds of information 

that will be saved with it. 

? In OMNIC Help Topics find “library” in the Index and go to 

“Creating a user library” and “Adding spectra to a user library.” 

How can I display a library spectrum in a spectral 

window?

If you are using OMNIC, locate and select the spectrum in Library 

Manager (available through the Analyze menu) and then click the 

Add To Window button, or go to the Library Spectra tab of Library 

Manager, display the desired spectrum on the tab and then doubleclick the spectrum. 

? In OMNIC Help Topics find “library” in the Index and go to 

“Working with libraries.” 

104 Thermo Electron Corporation
the Library Names tab, use the features on the Search For Text tab to 

locate the spectrum. Type the text to search for in the Text In 

Selected Item box, and then choose Search. The search results 

appear in the table based on the options you have set. To see 

information about a found spectrum, double-click its row in the 

table. 

? In OMNIC Help Topics find “library” in the Index and go to 

“Searching a library for text.” 

You can use the extended search feature (available on the Extended 

Search tab of the Library Setup dialog box) to find library spectra by 

searching for text in any field included in the library. For example, 

some libraries have fields for molecular weight, boiling point or 

manufacturer. 

? In OMNIC Help Topics find “extended search” in the Index and go 

to “Using extended search.” 

What is the easiest way to collect sample spectra and 

add them to a spectral library?

If you are using OMNIC, use the Collect Spectrum button on the 

Library Names tab of Library Manager (available through the 

Analyze menu) to collect a spectrum and add it to a user library. The 

software automatically sets the experiment parameters (for example, 

Resolution) so that the spectrum will be compatible with the selected 

library. This allows you to collect and add a compatible spectrum in 

one step instead of three (using Experiment Setup to set the 

parameters, Collect Sample to collect the spectrum and Add To 

Nicolet FT-IR User’s Guide 105
region from 2600 to 450 wavenumbers and then displays the 

specified number of library spectra that best match the unknown 

spectrum, plus comments about the search results. For example, the 

search expert may tell you that the best match is excellent but the 

second best match is also similar to the unknown. You will be able 

to display the list of matches to see their match values and index 

numbers. 

Opening, saving 

and deleting spectra 

?

How do I open a stored spectrum?

Choose Open from the File menu, locate the spectrum or spectra you 

want to open, select the filenames of the spectra and then choose 

OK. You can hold down the Control key to select multiple files. 

In OMNIC Help Topics find “spectrum” in the Index and go to 

“Opening spectra.” 

How can I save my collected spectra automatically? 

Choose Experiment Setup from the Collect menu and turn on Save 

Automatically on the Collect tab (Save Automatically is on by 

default). Specify a base name for naming the saved spectral data 

files in the Base Name box. A sequential number will be appended 

to the base name when the spectra are saved. If you want the 

interferograms saved with the spectra, turn on Save Interferograms. 

Individual spectra are saved with the extension .SPA. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Preparing the Software” 

106 Thermo Electron Corporation
You have several options for saving spectra; you may choose to use 

more than one. 

For a permanent record of the spectrum and any other information 

you want to record, use a report notebook. 

? In OMNIC Help Topics find “report notebook” in the Index and go 

to “Adding a report to a notebook.” 

You can also place spectra in descriptively named user libraries that 

you create. Keeping spectra in libraries allows you to find them by 

searching for text contained in the information saved with the 

spectra. 

? In OMNIC Help Topics find “spectrum” in the Index and go to 

“Adding a spectrum to a user library.” 

Note When you add a spectrum to user library whose resolution is lower, 

the spectrum is deresolved. For this reason it may be better in some 

cases to save your sample spectra as files on the hard disk and 

consider the copies of them added to a user library to be for 

searching purposes only. S

 

We recommend that you create descriptively named folders 

(directories) on your hard disk for different categories of spectra. For 

example, you could have a folder for each project you are working 

on, for each of your clients, for each laboratory application, or for 

each sample type. See your Windows documentation for information 

about creating directories. You can specify which folder to use when 

you use Save or Save As in the File menu to save spectra. This will 

make it easier to find a spectrum in a particular category when you 

Nicolet FT-IR User’s Guide 107
How can I save several spectra in one file as a group? 

Select the spectra and then choose Save Group from the File menu. 

To select more than one spectra, hold down the Control key and 

click each spectrum you want to select with the selection tool, and 

then release the Control key. Spectral groups are saved with the 

extension .SPG. 

? In OMNIC Help Topics find “saving, spectra” in the Index and go to 

“Saving a group of spectra.” 

How can I delete stored spectra?

Choose Delete Files from the File menu to display the Delete Files 

dialog box. Locate and select the spectral data files (with the 

extension .SPA, or .SPG for spectral group files) you want to delete 

and then choose OK. 

? In OMNIC Help Topics find “spectra” in the Index and go to “How 

to delete files.” 

108 Thermo Electron Corporation
You can delete an entire notebook, however, by deleting the entire 

notebook file. Choose Delete Files from the File menu to display the 

Delete Files dialog box. Locate and select the directory containing 

the notebook data files (with the extension .NBK). You will have to 

set the List Files Of Type box to All (*.*) to see .NBK files listed. 

Select the file you want to delete and then choose OK. 

Printing 

?

How can I specify a printer for printing information?

Use Printer Setup in the File menu. See your Windows 

documentation for details on setting the printer parameters. 

In OMNIC Help Topics find “printer” in the Index and go to 

“Setting up the printer.” 

How can I create and print reports of my work?

 

Use the commands in the Report menu. First use Template to select, 

edit or create a template for the report. Then use Preview/Print 

Report to view the report as it will appear on paper. Click the Print 

button to print the report. 

View Creating Reports (available through Learning OMNIC) to 

learn about OMNIC’s report features. 

? In OMNIC Help Topics find “template” in the Index and go to 

“Selecting, editing or creating a report template,” or find “report, 

previewing or printing” and go to “Previewing or printing a report.” 

Nicolet FT-IR User’s Guide 109
a report to a notebook.” 

How can I preview spectra or other information before 

printing?

Use Preview/Print Report in the Report menu to view a report as it 

would appear on paper. The report is displayed using the current 

report template; that is, the template you specified with Template or 

the one you are viewing and working with. If the report is displayed 

as you want it to appear on paper, you can print it by using the Print 

button. 

? In OMNIC Help Topics find “template” in the Index and go to 

“Selecting, editing or creating a report template,” or find “report, 

previewing or printing” and go to “Previewing or printing a report.” 

Displaying spectra How can I select more than one spectrum at a time?

After selecting the first spectrum by clicking it, hold down the 

Control key while you click each additional spectrum. You can also 

choose Select All from the Edit menu to select all the spectra in the 

window that are not hidden. 

? In OMNIC Help Topics find “spectra” in the Index and go to 

“Selection tool” or “Selecting all the spectra in a spectral window.” 

110 Thermo Electron Corporation
selected spectra, click the color next to Selected Spectrum and then 

click a color. Typically red is the color reserved for displaying 

selected spectra. 

? In OMNIC Help Topics find “spectra” in the Index and go to 

“Specifying colors for spectra and other features.” 

You can also specify colors for displaying spectra in a particular 

spectral window. Start by selecting the spectra for which you want to 

specify a color, and then choose Display Setup from the View menu. 

Click the desired color in the color array and then choose OK. When 

the spectra are no longer selected, such as after you select a different 

spectrum, they will be displayed in the color you clicked. 

? In OMNIC Help Topics find “spectra” in the Index and go to 

“Selecting a color for the currently selected spectra.” 

What is the difference between the Display Setup 

parameters and the Window options?

 

The parameters in the Display Setup dialog box affect the currently 

active spectral window only. The options in the Window options (in 

the Options dialog box, available through the Edit menu) affect all 

the new spectral windows that you create. After you create a new 

spectral window, you can change the way spectra are displayed in it 

by using Display Setup in the View menu. 

? In OMNIC Help Topics find “display parameters” in the Index and 

go to “Setting the display parameters,” or find “Window options” 

and go to “Window options.” 

Nicolet FT-IR User’s Guide 111
 

Full Scale displays the spectra so that they perfectly fit their panes 

vertically. Automatic Full Scale does this automatically when you 

change the display with the view finder or selection tool. The Y-axis 

displayed corresponds to the selected spectrum. 

Common Scale displays all the spectra so that they are not cut off at 

the top or bottom and use the same Y scale. This allows you to 

compare the band intensities of different spectra. 

Match Scale changes the Y scale of the spectra to be the same as that 

of the selected spectrum. (The selected spectrum’s scale is not 

changed.) This allows you to compare the band intensities of 

different spectra. 

Offset Scale shifts the spectra vertically so that they overlap less, 

making them easier to see. 

When you use these commands, keep in mind that the current Y-axis 

is always accurate for the currently selected spectrum but may not 

apply to other spectra in the window. 

? In the OMNIC Help Topics Index... 

For information about Full Scale or Automatic Full Scale, find 

“spectra” and go to “Displaying spectra full scale” or 

“Displaying spectra full scale automatically.” 

112 Thermo Electron Corporation
For information about Offset Scale, find “spectra” and go to 

“Displaying spectra vertically offset.” 

How can I zoom in on an area of a spectrum?

Draw a box around the area using the selection tool and then click 

inside the box. 

You can also use the Expand/Contract buttons at the left end of the 

view finder or drag the regions markers in the view finder to display 

a smaller spectral region. You can press and hold down the mouse 

button during these operations to continuously expand or contract 

the display. 

To expand and contract the spectra horizontally about the center, use 

the view finder's Horizontal Expand/Contract buttons (left-most). 

To expand and contract the spectra vertically about the center, use 

the Vertical Expand/Contract buttons (right-most). 

? The Roll/Zoom Window in the View menu also expands or contracts

an area. In OMNIC Help Topics find “Roll/Zoom Window 

command” in the Index and go to “Rolling and zooming spectra” for 

more information about expanding and contracting a spectral region.

Nicolet FT-IR User’s Guide 113
?

In OMNIC Help Topics find “Roll/Zoom Window command” in the 

Index and go to “Rolling and zooming spectra” for more information 

about moving spectrum. 

How can I move a spectrum into another spectral 

window?

 

Use the selection tool to drag the spectrum from one spectral 

window to another. A copy of the spectrum appears in the second 

window, and the original spectrum remains in the first window. You 

can also copy or cut the spectrum using Copy or Cut in the Edit 

menu and then paste it into another spectral window using Paste. 

? In OMNIC Help Topics find “spectrum” in the Index and go to 

“Selection tool,” or find “pasting, spectrum” and go to “Pasting 

items.” 

How can I move a stacked spectrum into another pane?

Use the selection tool to drag the spectrum from one pane into 

another. 

? In OMNIC Help Topics find “spectrum” in the Index and go to 

“Selection tool.” 

114 Thermo Electron Corporation
? In OMNIC Help Topics find “X and Y values” in the Index and go 

to “Spectral cursor tool.” 

How can I find the height of a peak?

Use the peak height tool to click the top of the peak. Then drag the 

baseline handles to adjust the baseline used for the measurement. 

The corrected (measured above the baseline) and uncorrected height 

values appear in the readout above the palette. 

? In OMNIC Help Topics find “peak” in the Index and go to “Peak 

height tool.” 

How can I find the area of a peak?

Use the peak area tool to drag across the peak. Then drag the 

baseline handles to adjust the baseline used for the measurement. 

The corrected (measured above the baseline) and uncorrected area 

values appear in the readout above the palette. 

? In OMNIC Help Topics find “area” in the Index and go to “Peak 

area tool.” 

Nicolet FT-IR User’s Guide 115
spectrum. 

Correcting a baseline will give you better results when you search 

the spectrum against a library, subtract the spectrum from another 

spectrum, find peaks in the spectrum or quantify components in the 

spectrum. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Common Problems with IR Spectra” 

? In OMNIC Help Topics find “baseline” in the Index and go to 

“Correcting a baseline manually.” 

Subtracting, 

adding, multiplying 

and dividing spectra 

How can I subtract a spectrum from another 

spectrum?

Use Subtract in the Process menu whenever you want to subtract one 

spectrum from another. Subtract is commonly used to remove 

spectral features of solvent residues or pure components from the 

spectrum of a mixture of compounds. 

Select the spectrum from which you want to subtract spectral 

features; this is the sample spectrum. Then hold down the Control 

key and select the spectrum with the features you want to subtract 

from the sample spectrum; this is the reference spectrum. 

 Note Subtract is available only when two spectra are selected. S

116 Thermo Electron Corporation
? In OMNIC Help Topics find “spectrum” in the Index and go to 

“Subtracting spectra.” 

What should I use subtraction for?

Subtract is commonly used to remove spectral features of solvent 

residues or pure components from the spectrum of a mixture of 

compounds. When you use Subtract, the software calculates data 

point by data point the difference between the two. 

Spectral subtraction is useful in a variety of situations, for example... 

• Eliminating solvent peaks in a spectrum of a sample that is 

dissolved in a solvent. 

• Separating components from a sample that is a mixture of two or 

more components. 

• Identifying an unknown contaminant by subtracting out the 

known sample material. 

• Ensuring quality by subtracting an original batch sample 

spectrum from a spectrum from the next batch. 

Nicolet FT-IR User’s Guide 117
operations to perform by typing a sequence of mathematical symbols 

and numbers. The software performs the operations on the Y values 

of the data points in the spectrum or spectra and then displays the 

result spectrum. 

When you choose the command, the Spectral Math window appears 

allowing you to type the desired operations in the Operation text 

box. You can also select one of the example operations provided in 

the Operation drop-down list box. 

View Using Spectral Math (available through Learning OMNIC). 

? In OMNIC Help Topics find “spectrum” in the Index and go to 

“Performing arithmetic operations on spectra.” 

118 Thermo Electron Corporation
settings in a configuration file. You can then open the file later to 

reset OMNIC to your preferences in one step. 

Collecting a Spectrum (available through Learning OMNIC)... 

“Preparing the Software” 

? In the OMNIC Help Topics Index... 

Find “options” and go to “Customizing OMNIC by setting 

options.” 

Find “menu” and go to “Customizing a menu.” 

Find “toolbar” and go to “Customizing a toolbar.” 

Find “configuration” and go to “Saving a configuration.” 

Find “configuration” and go to “Opening a configuration.” 

Nicolet FT-IR User’s Guide 119
?

In OMNIC Help Topics find “peaks” in the Index and go to “Finding 

peaks above a specified height,” or find “label” and go to 

“Annotation tool.” 

How can I close a task window (such as the Find Peaks 

window)?

Click the Close button (if available) in the upper-right corner of the 

window. You can also double-click the button at the left end of the 

window’s title bar (if the window is not maximized) or the button at 

the left end of the menu bar (if the window is maximized). 

? In OMNIC Help Topics find “task window” in the Index and go to 

“Task windows.” 

How can I select a spectral region for an operation?

Use the region tool to drag across the region in the pane. 

? In OMNIC Help Topics find “spectral region” in the Index and go to 

“Region tool.” 

120 Thermo Electron Corporation
? In OMNIC Help Topics find “collection and processing 

information” in the Index and go to “Collection and processing 

information.” 

If you want this kind of information displayed in a spectrum’s pane, 

choose Display Setup from the View menu, turn on Sampling 

Information and then specify the types of information you want 

displayed by turning on options in the Sampling Information box. 

? In OMNIC Help Topics find “displaying, sampling information” in 

the Index and go to “Displaying sampling information.” 

How can I copy a spectrum and paste it into a text 

document?

Select the spectrum and choose Copy from the Edit menu. This 

places the spectrum on the Clipboard in the form of a Windows 

metafile (this is the file format with the most flexibility for pasting 

into other programs). You can then paste the spectrum into a 

document by using a word processing program. 

? In OMNIC Help Topics find “copying, spectrum” in the Index and 

go to “Copying items.” 

Nicolet FT-IR User’s Guide 121
• To see information about a particular feature in OMNIC, click 

the feature using the right mouse button. A brief description of 

the feature appears, and in most cases one or more buttons that 

you can click to display more detailed information. Click the 

Discussion button to display a complete discussion of the feature 

(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 

feature (or the dialog box or window that contains the feature). 

• You can press the F1 function key at any time to see a discussion 

topic for the currently displayed or selected feature, dialog box 

or window. 

• If a dialog box or window contains a Help button, click it to see 

information about the dialog box or window (or the command 

that displayed it). 

• To see the Contents of the OMNIC Help system, choose OMNIC 

Help Topics from the Help menu. 

122 Thermo Electron Corporation
This chapter answers some common questions about using your 

spectrometer. Each answer is followed by a reference telling you 

where to go for more information. 

Do I need to use an energy screen with my detector? 

If you are using a highly sensitive detector such as a PbSe, 

Si, MCT-A or InSb detector and your experiment deals with 

information from a broad range of frequencies, you may wish to use 

an energy screen to prevent the detector from becoming saturated or 

producing a distorted signal. 

Spectrometer Help Topics... 

“Installing an energy screen” in “Setting up experiments” 

When do I need to open the spectrometer cover? 

You need to open the spectrometer cover to change sources. Also, 

you need to open the cover if you are installing a spectrometer 

component such as a laser. 

Nicolet FT-IR User’s Guide 123
first. 

Important If you have a CsI beamsplitter, protect it from the effects of water 

vapor by minimizing the time that the cover is removed. S

Spectrometer Help Topics... 

“Opening the main cover” in “Installing optional hardware” 

When should I align the spectrometer? 

Align the spectrometer in the following situations: 

• The ambient temperature has changed by at least 5 Celsius 

degrees (about 9 Fahrenheit degrees). 

• You are about to perform a spectrometer validation with Val-Q 

(or other software). This ensures that the validation is run with 

the best possible interferometer and electronics settings. 

• The spectrometer power was turned off for more than a few

minutes and has now been on for one hour. 

 Note We recommend that you leave the power on continuously, but if you 

do need to turn it off, allow the spectrometer to warm up for one 

hour and then align it before collecting spectra. S

• The spectrometer has been on continuously for one week without 

being aligned. We recommended aligning your spectrometer 

once a week or, for optimum performance, once a day. 

124 Thermo Electron Corporation
• You have just moved the spectrometer. 

? In OMNIC Help Topics find “aligning, spectrometer” in the Index 

and go to “Aligning the spectrometer.” 

“Maintenance and Service” chapter... 

“Aligning the spectrometer” in “Maintaining your spectrometer”

Does my detector need to be cooled with liquid 

nitrogen?

Detectors that have a dewar need to be cooled. Dewar detectors are 

fairly large metal cylinders with a hole in the top. These include 

MCT and InSb detectors. To determine if your detector requires 

cooling, open the detector compartment cover and see if the detector 

has a dewar. 

If during a work session you find that the detector signal intensity is 

decreasing, the dewar may need to be refilled with liquid nitrogen. 

Spectrometer Help Topics... 

“Cooling a detector” in “Setting up experiments” 

Nicolet FT-IR User’s Guide 125
desiccant is no longer effective, replace it. 

Spectrometer Help Topics... 

“Checking and changing desiccant” in “Maintaining your 

spectrometer” 

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. 

See “Ordering parts” in Spectrometer Help Topics to find the part 

number for ordering desiccant bags. The desiccant holder under the 

beamsplitter compartment cover holds one bag. 

Which source should I use? 

Use the source that is appropriate for the spectral range of your 

experiment (determined by the ranges of the beamsplitter and 

detector). Thermo Electron offers a mid-IR to far-IR source (ETC) 

and a near-IR source (white light). 

? In OMNIC Help Topics find “source” in the Index and go to 

“Specifying the source type.” 

“Spectrometer Basics” chapter... 

“Selecting the right beamsplitter and detector” in “Using 

beamsplitters and detectors” 

126 Thermo Electron Corporation
How can I diagnose problems with the spectrometer?

The performance of the spectrometer is monitored while you collect 

spectra. If a problem occurs, a troubleshooting message appears. 

See the “Troubleshooting” book in Spectrometer Help Topics for 

instructions for diagnosing spectrometer problems and ordering and 

replacing parts. 

 Note If you want to view the on-line videos to help you in troubleshooting 

a problem, put the Spectrometers Tutorials CD in the computer. S

You can also make a more thorough check on a spectrometer 

component by choosing Advanced Diagnostics from the Collect 

menu. This starts the Bench Diagnostics program, which provides 

information about the status of the component as well as 

troubleshooting information, replacement procedures and 

information about ordering replacement parts. 

? In OMNIC Help Topics find “diagnostics” in the Index and go to 

“Checking bench components.” 

How do I replace parts in the spectrometer?

Spectrometer Help Topics... 

 “Replacing parts” 

Nicolet FT-IR User’s Guide 127
peoote spectoete. We dee ateace as a

occasional procedure you perform to keep the spectrometer running 

efficiently. We define service as a procedure to replace a failing part 

in the spectrometer. 

 Warning Perform only those procedures described in this chapter. If there are 

other problems, contact Thermo Electron at one of the numbers 

below. Outside the U.S.A. call your local sales or service 

representative. Telephone numbers for all Thermo Electron 

Customer Support offices are provided with your system. 

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

See Spectrometer Help Topics for instructions for diagnosing 

spectrometer problems and ordering and replacing parts. 

128 Thermo Electron Corporation
 Note OMNIC continuously monitors the operation of the spectrometer 

hardware and shows its status with the Bench Status indicator below 

the menu bar of the OMNIC window. See “The OMNIC window” in 

the “Your First Experiment” chapter for more information. S

Follow these steps to run the spectrometer diagnostic tests: 

1. Make sure the main sample compartment is empty. 

Remove any samples and sampling accessories (except a 

transmission sample holder). 

2. Choose Experiment Setup from the Collect menu or the 

toolbar. 

The Experiment Setup dialog box appears. 

3. Click the Diagnostic tab. 

The Diagnostic tab appears showing icons for the major 

components of the spectrometer with a live display of the signal 

from the detector. 

Nicolet FT-IR User’s Guide 129
the acceptable range, an X appears in the Status column. 

5. When you are finished viewing the information, choose OK. 

Maintaining 

your spectrometer 

This section describes how to use the OMNIC software to align the 

spectrometer and accessories and run performance tests. 

View “Maintaining your spectrometer” in Spectrometer Help Topics 

for instructions for other common maintenance procedures, such as 

changing desiccant, cleaning the purge filter and cleaning the outside 

of the spectrometer. 

Aligning the spectrometer To ensure optimum system performance (high signal intensity, low

noise and good sensitivity), you should align the spectrometer at 

least once a week using the OMNIC software. See the answer to the 

question “When should I align my spectrometer” in the preceding 

chapter for more information. 

Note If you have just turned on or moved the spectrometer, wait 

15 minutes (one hour for best results) before you align it so that it 

will have time to stabilize. S

130 Thermo Electron Corporation
compartment as briefly as possible to maintain a constant purge. 

2. Choose Experiment Setup from the Collect menu or the 

toolbar. 

The Experiment Setup dialog box appears. 

3. Make sure Sample Compartment on the Bench tab is set to 

Main. 

4. Set Gain on the Bench tab to 1. 

 Important Do not use Autogain. S

5. Click the Align button on the Diagnostic tab. 

When you click the Align button, the system begins to optimize 

the detector signal for maximum energy throughput. Alignment 

should take 2 to 4 minutes. 

The live display of the detector signal changes as each 

interferogram is collected. The positive peak and negative peak 

intensities are shown next to Max and Min above the live 

display. The interferogram location will be shown next to 

Location (unless Single Beam is selected on the Bench tab). 

6. When the alignment is finished, close the Experiment Setup 

dialog box. 

Nicolet FT-IR User’s Guide 131
dialog box according to the accessory location. Set Gain to a value 

that gives a signal intensity that is appropriate for the accessory. 

ATR (attenuated total reflection) and diffuse reflection accessories 

typically use a Gain setting of 2 or 4. 

If you are not satisfied with the signal intensity after alignment, you 

can manually align most accessories to maximize the signal. For 

complete instructions, see the manual that came with the accessory. 

When you manually adjust an accessory, watch the largest 

interferogram peak in the live display on the Bench tab. The larger 

this peak, the better is the signal intensity. 

 Note The largest interferogram peak can be positive or negative. S

If you are unable to see the display, turn on Tone on the Bench tab 

before adjusting the accessory. The tone reaches its highest pitch 

when the signal is maximized. 

Checking 

spectrometer 

performance 

You can use the performance test to track long-term spectrometer 

performance. Run the test after you have installed the system and 

then weekly. Keep a record of the actual values obtained. When you 

run the test, the software measures the response of the spectrometer 

optics and atmospheric absorptions inside the spectrometer and then 

collects a “sample” spectrum with no sample in place. The result is a 

“100% line,” a display of system noise that appears as a generally 

flat line at 100% transmittance. 

132 Thermo Electron Corporation
2. Exit OMNIC. 

This ensures that the Bench Diagnostics software will run 

correctly. 

3. Start the Bench Diagnostics software. 

To do this, click the Start button on the Windows taskbar, point 

to Programs (All Programs in Windows XP), point to the 

Thermo Nicolet folder and then choose Bench Diagnostics. 

See “Performing advanced diagnostic tests” in the 

“Troubleshooting Hardware Problems” chapter for more 

information about running the diagnostics software. 

4. Click the Performance Tests button and then follow the 

instructions that appear on the screen. 

 Note If the noise readings are greater than normal or have changed 

significantly, call the Thermo Electron Technical Support for 

assistance. Outside the U.S.A., call your local service representative. 

Telephone numbers for all Thermo Electron offices are provided 

with your system. S

If special performance tests are available for your spectrometer, 

a button labeled “Extended Tests” (or another appropriate name) 

will appear. Click this button and follow the instructions that 

appear on the screen to perform the tests. 

Nicolet FT-IR User’s Guide 133
and replacing parts, choose Spectrometer Help Topics from the Help 

menu. S

If the source, laser module, electronics module or power supply must 

be replaced, refer to the replacement parts list made available when 

you choose Spectrometer Help Topics from the Help menu. Call 

800-642-6538 or 608-276-6373 to order the replacement assembly. 

If you are outside the U.S.A., contact your local Thermo Electron 

office. Telephone numbers for all Thermo Electron Customer 

Support offices are provided with your system. 

134 Thermo Electron Corporation
status oyousyste. a pobes oud, a essage autoatcay 

appears giving you access to more information. This chapter lists 

some simple troubleshooting measures you can take to solve 

software problems with OMNIC. If the action does not solve the 

problem, call your Thermo Electron service office. 

? In OMNIC Help Topics find “troubleshooting” in the Index and go 

to “Troubleshooting” for more information. 

Problem Possible Cause Solution

You cannot add a 

spectrum to a user 

library. 

The resolution of the spectrum 

is lower (higher numerical 

value) than that of the library. 

The spectrum is from a 

commercial library. 

Collect the spectrum at the same resolution 

as the library (first set Resolution on the 

Bench tab of the Experiment Setup dialog 

box) and then add it to the library. 

Only spectra you collect can be added to a 

user library. Commercial libraries cannot be 

altered and the spectra contained in them 

cannot be copied to other libraries. 

The Quantify 

command is dimmed. 

No quantitative analysis 

method is selected. 

No spectrum is selected. 

The quantitative analysis 

method is not appropriate for 

the selected spectrum. 

Select a quantitative analysis method using 

Quant Setup in the Analyze menu. 

Select a single spectrum. 

Select an appropriate method for the 

selected spectrum. 

Nicolet FT-IR User’s Guide 135
have the wrong 

resolution. 

collection. 

An experiment 

provided with OMNIC 

does not produce good 

results. 

The parameter settings in the 

experiment file have been 

changed so that the experiment 

is no longer useful. 

Restore the experiment to its default 

settings: First open the experiment using 

Experiment Setup and save it using a new 

filename if you do not want to overwrite it. 

Then open the experiment in the 

FACTORY directory whose filename is 

same as the original experiment and save it 

in the OMNIC\PARAM directory. 

The desired 

experiment does not 

appear in the 

Experiment dropdown list box. 

The experiment was installed 

with the software but has not 

yet been opened. 

If the experiment was designed for a Smart 

Accessory, install the accessory; the 

experiment will be opened automatically 

and will appear in the Experiment dropdown list box. If the experiment was not 

designed for a Smart Accessory, open it 

using Experiment Setup; it will be added to 

the list. 

Libraries created with 

previous version of 

OMNIC are not listed 

in the Library Setup 

dialog box. 

The libraries are not in one of 

directories listed in the dialog 

box (typically LIBS within the 

OMNIC directory). 

Use the Add Directory button on the Search 

Libraries tab to add the directory. 

136 Thermo Electron Corporation
spectrometer and informs you if a problem is found. The Bench 

Status indicator below the menu bar shows the status of the 

spectrometer operation. When OMNIC performs a check and detects 

a problem, the Bench Status indicator is displayed as a yellow circle 

or a red X along with an message alerting you to the problem. 

If the indicator is a yellow circle, an MCT 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. 

This chapter lists some simple troubleshooting measures you can 

take to solve problems with the spectrometer. The Bench 

Diagnostics software is described at the end of the chapter. If your 

actions do not solve the problem, call Thermo Electron. 

For more troubleshooting information see the “Troubleshooting” 

book in Spectrometer Help Topics. 

 Warning Always follow the safety precautions included in this manual and in 

your Spectrometer Safety Guide when performing any of the 

following troubleshooting procedures. S

Nicolet FT-IR User’s Guide 137
The spectrometer is out of 

alignment. 

The laser is not functioning. 

The spectrometer is overheated. 

(You can check whether the 

temperature of the electronics 

board is within the acceptable 

range by clicking the 

electronics indicator on the 

Diagnostics tab of the 

Experiment Setup dialog box.) 

Align the spectrometer using the 

Align button on the Diagnostic tab 

of the Experiment Setup dialog box. 

Click the laser indicator on the 

Diagnostic tab of the Experiment 

Setup dialog box to check the laser 

operation. Call Thermo Electron to 

order a replacement laser if 

necessary. See the “Ordering parts” 

and “Servicing your spectrometer” 

books in Spectrometer Help Topics 

to find part number and ordering and 

installation instructions. 

Make sure the cooling vents on the 

back of the spectrometer are not 

blocked. Make sure the ambient 

temperature is between 16° and 

27°C (60° and 80°F). 

138 Thermo Electron Corporation
alignment. 

The laser detector is 

misaligned. 

The ambient conditions are 

outside the allowed ranges. 

The desiccant cannot absorb 

any more water vapor. 

The spectrometer cover was 

recently opened. 

Align button on the Diagnostic tab 

of the Experiment Setup dialog box. 

Use the Bench Diagnostics software 

to check the laser levels for proper 

balance. If the levels are out of 

tolerance, align the spectrometer 

using the Align button on the 

Diagnostic tab of the Experiment 

Setup dialog box. If the levels 

remain out of tolerance, call Thermo 

Electron for service. 

Make sure the conditions meet the 

requirements given in the 

“Environmental Considerations” 

chapter of Preparing Your Site. 

Check the humidity indicator and 

replace the desiccant and indicator if 

needed. 

Allow the spectrometer to purge for 

3 to 5 minutes after the cover is 

closed. 

Nicolet FT-IR User’s Guide 139
on. 

The spectrometer is not plugged 

in. 

The power cord is not properly 

rated for your electrical service. 

The ground prong on the power 

cord has been removed or is 

defective. 

The power cable or power 

supply is defective. 

fingertight. 

Make sure the power cord is 

securely connected to the power 

supply and a working outlet or 

power strip. 

Make sure the power cord is 

appropriate for your AC power 

source. In Spectrometer Help Topics 

see “Miscellaneous parts” in the 

“Ordering parts” book for power 

cord descriptions and part number 

information. 

Replace the power cord. In 

Spectrometer Help Topics see 

“Miscellaneous parts” in the 

“Ordering parts” book for power 

cord descriptions and part number 

information. 

Replace the power cord. If the 

problem persists, replace the power 

supply. In Spectrometer Help Topics 

see “Changing the power supply in 

the “Replacing parts” book. 

140 Thermo Electron Corporation
The system scans 

normally but gives very 

low signal intensity. 

The spectrometer is out of 

alignment. 

The moving mirror velocity is 

set too high. 

There is no interferogram. 

The beam path is obstructed. 

The aperture is set incorrectly 

on a Nicolet 6700. 

Continued on next page...

Align the spectrometer using the 

Align button on the Diagnostic tab 

of the Experiment Setup dialog box. 

Set Velocity on the Bench tab of the 

Experiment Setup dialog box to a 

lower velocity. 

If the Source status indicator is off, 

click the source indicator on the 

Diagnostic tab of the Experiment 

Setup dialog box to check the source 

current and voltage. If the Source 

indicator is on, check the 

interferogram on the Bench tab of 

the Experiment Setup dialog box; if 

the interferogram is not present, 

check the beam path and detector. 

Remove the obstruction. 

Check the Aperture parameter on the 

Bench tab of the Experiment Setup 

dialog box. For an MCT-A, MCT-B, 

InSb, PbSe, Si, or InGaAs detector, 

set Aperture to 32. For a DTGS

detector, set Aperture to 100. 

Nicolet FT-IR User’s Guide 141
temperature of the electronics 

board is within the acceptable 

range by clicking the 

electronics indicator on the 

Diagnostics tab of the 

Experiment Setup dialog box.) 

A sampling accessory is not 

installed properly or is not 

aligned. 

Detector and beamsplitter are 

not compatible. 

blocked. Make sure the ambient 

temperature is between 16° and 

27°C (60° and 80°F). 

Make sure the accessory is installed 

correctly and, if necessary, align it. 

See the instructions that came with 

the accessory. 

Make sure that selected detector and 

beamsplitter are compatible. Change 

detector or beamsplitter if necessary.

142 Thermo Electron Corporation
spectrometer alignment 

may fail.) 

The beam path is obstructed. 

The sample compartment 

windows are fogged. 

The beamsplitter is fogged. 

The spectrometer is out of 

alignment. 

A sampling accessory is not 

installed properly. 

A detector that was just 

installed is not seated properly. 

Remove the obstruction. 

Replace the windows. In 

Spectrometer Help Topics view 

“Replacing sample compartment 

windows” in “Replacing parts” to 

find part number, ordering and 

installation instructions. 

Check the laser signals by clicking 

the laser indicator on the Diagnostic 

tab of the Experiment Setup dialog 

box. For a Nicolet 6700, replace the 

beamsplitter, if necessary. For a 

Nicolet 4700, contact technical 

support. 

Align the spectrometer using the 

Align button on the Diagnostic tab 

of the Experiment Setup dialog box. 

Make sure the accessory is installed 

according to the instructions that 

came with it. 

Make sure the hole and slot in the 

detector plate fit over the pins on the 

spectrometer baseplate. See 

“Replacing the detector” in the 

“Servicing your spectrometer” book 

in Spectrometer Help Topics. 

Nicolet FT-IR User’s Guide 143
Electron to order a replacement 

source. In Spectrometer Help Topics 

view “Replacing your source” in 

“Replacing parts” to find part 

number, ordering and installation 

instructions. 

There is frost on the 

outside of the detector. 

The insulating vacuum chamber 

of the dewar has begun to leak. 

If you suspect your detector has a 

vacuum leak, view “Detector does 

not stay cooled” in the 

“Troubleshooting” book in 

Spectrometer Help Topics. 

You encounter problems 

when selecting external 

detectors on an AEM, 

GC interface or 

microscope. 

A custom detector is selected 

on the Bench tab of the 

Experiment Setup dialog box. 

The detector cable is loose at 

the accessory connector (on the 

rear of the spectrometer or on 

the back wall of the sample 

compartment). 

Set Detector to None on the Bench 

tab of the Experiment Setup dialog 

box. 

Check and tighten the cables. 

144 Thermo Electron Corporation
Note: After 1 hour 

without data collection 

activity, the 

interferometer stops 

scanning and the Scan 

light stays on. This is 

normal. Any data 

collection activity will 

cause the interferometer 

to begin scanning. 

The spectrometer is out of 

alignment. 

The electronics module needs to 

be reset. 

The laser is flickering. 

The laser is off. 

Continued on next page...

Align the spectrometer using the 

Align button on the Diagnostic tab 

of the Experiment Setup dialog box. 

Turn off the power to the computer 

and the spectrometer. Leave the 

power off for 15 seconds. Turn on 

the spectrometer and wait until the 

start-up diagnostics finish. Then turn 

on the computer and restart OMNIC. 

Click the laser indicator on the 

Diagnostic tab of the Experiment 

Setup dialog box to check the laser 

operation. Call Thermo Electron for 

assistance. 

Turn off the spectrometer power, 

unplug the power cord, remove the 

spectrometer cover and make sure 

the laser cable is seated properly. 

See “Replacing the laser” in the 

“Servicing your spectrometer” book 

in Spectrometer Help Topics for 

instructions. Warning: Never open 

the spectrometer cover without first 

turning off the power and 

unplugging the power cord. 

Nicolet FT-IR User’s Guide 145
The spectrometer is overheated. 

(You can check whether the 

temperature of the electronics 

board is within the acceptable 

range by clicking the 

electronics indicator on the 

Diagnostics tab of the 

Experiment Setup dialog box.) 

A component has failed. 

The beamsplitter is not properly 

seated. 

indicator to view information about 

the laser operation. 

If the laser frequency is outside the 

specified range, call Thermo 

Electron to have the electronics 

module replaced. 

If the laser voltage or current is 

outside the specified range, replace 

the laser. View “Replacing the 

laser” in the “Servicing your 

spectrometer” book in Spectrometer 

Help Topics for instructions. 

Make sure the cooling vents on the 

back of the spectrometer are not 

blocked. Make sure the ambient 

temperature is between 16° and 

27°C (60° and 80°F). 

Call Thermo Electron for service. 

For a Nicolet 6700, check the 

beamsplitter and reposition it if 

necessary. 

For a Nicolet 4700, call Thermo 

Electron for service. 

146 Thermo Electron Corporation
Diagnostic tab of the Experiment 

Setup dialog box to verify that the 

laser is burned out. Call Thermo 

Electron to order a replacement 

laser. View “Replacing the laser” in 

the “Replacing parts” book in 

Spectrometer Help Topics to find 

part number and ordering and 

installation instructions. 

An error message 

appears when you try to 

scan. 

The light source is not working. 

An MCT detector is not cooled. 

The interferogram peak is not 

located at 1024 ± 16 data points 

on the Bench tab of the 

Experiment Setup dialog box. 

The beam path is obstructed. 

The data cable between the 

spectrometer and the computer 

is not properly connected. 

The detector and beamsplitter 

are not compatible. 

Check the source indicator on the 

Diagnostic tab of the Experiment 

Setup dialog box. If necessary, 

replace the source. 

Check and cool the detector. 

Align the spectrometer. If the 

interferogram is still not located 

correctly, call Thermo Electron for 

service. 

Remove the obstruction. 

Turn off the spectrometer power and 

check the data cable connections. 

Change the detector or beamsplitter. 

Nicolet FT-IR User’s Guide 147
Use the diagnostics software to: 

• Run the spectrometer performance test 

• Test specific components of your spectrometer 

• Get information about replacement parts 

• Check the spectrometer configuration 

• Get troubleshooting tips 

Follow these steps to run the diagnostics: 

1. Make sure the main sample compartment is empty. 

Remove any samples and sampling accessories (except a 

transmission sample holder). 

2. Start the Bench Diagnostics software. 

To do this, choose Advanced Diagnostics from the Collect menu. 

You can also close OMNIC, click the Start button in Windows, 

point to Programs (All Programs in Windows XP), point to the 

Thermo Nicolet folder and then choose Bench Diagnostics. This 

gives you access to advanced features of the software, including 

the performance test, that are not available if you run the 

diagnostics from OMNIC. 

148 Thermo Electron Corporation
 

Click this button to return to the main Diagnostics window: 

 

To exit the Bench Diagnostics software, click the Close button at 

the far right end of the title bar. 

Nicolet FT-IR User’s Guide 149
sotwae autoatcay cecs te status ocoected teeogas, 

and background and sample spectra. When OMNIC performs a 

check and detects a problem with data collection or spectra, the 

Collect Status indicator is displayed as a yellow circle or a red X. 

You can click the indicator (or click the View Collect Status button 

at the end of data collection) to see a summary of data collection 

problems encountered during the collection and other information 

about the collection. 

This chapter lists some simple troubleshooting measures you can 

take to solve data collection problems with the spectrometer. If the 

action does not solve the problem, call your Thermo Electron service 

office. 

? In OMNIC Help Topics find “troubleshooting” in the Index and go 

to “Troubleshooting” for more information. 

Problem Possible Cause Solution

A spectrum contains 

fringes or channeling. 

The sample has parallel, 

highly reflective sides that 

cause the infrared beam to 

bounce within the sample 

when it is placed 

perpendicular to the beam. 

Create a new film using a matte press. 

Try roughening the film surface 

slightly with silicon carbide paper or 

other suitable abrasive. 

Rotate the sample so that the infrared 

beam passes through sample at 

Brewster’s angle. (Do not use this 

method if you are performing a 

quantitative analysis of sample.) 

150 Thermo Electron Corporation
p

interfere with your data. 

The spectrometer is not 

adequately purged. 

The spectrometer is not 

purged. 

The spectrometer is purged 

but the air dryer does not 

remove carbon dioxide. 

g ypp

Make sure you are using the correct 

purge gas and that purge flow rate is 

adequate. Allow the system 3 to 5 

minutes to reestablish purge before 

collecting the spectrum. 

Install an appropriate purge gas source 

and optional purge kit. Contact 

Thermo Electron for details. 

Replace the air dryer with one that 

removes carbon dioxide, or use 

nitrogen to purge the spectrometer. 

Contact Thermo Electron for more 

information. 

A spectrum contains 

water peaks that interfere 

with your data. 

The desiccant cannot absorb 

any more water vapor. 

The spectrometer is not 

adequately purged. 

The spectrometer is not 

purged. 

Check the humidity indicator and 

replace the desiccant and indicator if 

needed. 

Make sure you are using the correct 

purge gas and that purge flow rate is 

adequate. Allow the system 3 to 5 

minutes to reestablish purge before 

collecting the spectrum. 

Install an appropriate purge gas source 

and optional purge kit. Contact 

Thermo Electron for details. 

Nicolet FT-IR User’s Guide 151
The sampling cup in a diffuse 

reflection experiment is not in 

place or is tilted. 

An infrared microscope is in 

its viewing mode. 

A sample film in an ATR 

experiment is being held 

against the ATR crystal with 

uneven pressure or has poor 

contact with the crystal. 

The resolution is set too low.

Make sure the cup is properly 

positioned in the diffuse reflection 

accessory. For more information, view 

the appropriate tutorial available 

through Sampling Techniques in the 

Help menu. 

Put the microscope in infrared mode 

and collect the spectrum again. 

Make sure the sample is held evenly 

and has good contact with the crystal. 

Set Resolution on the Collect tab of 

the Experiment Setup dialog box to a 

value that lets you see small peaks. 

(Use a lower numerical setting to 

achieve higher resolution.) 

A spectrum contains 

derivative-shaped peaks. 

A sample in a diffuse 

reflection experiment also has 

a specular reflection 

component. 

The infrared beam was 

reflected from (instead of 

penetrating) a flat, shiny 

sample measured using a 

specular reflection accessory. 

Correct the spectrum by using Other 

Corrections in the Process menu. 

(Select Kramers-Kronig.) 

Try using a less reflective sample. 

152 Thermo Electron Corporation
The background spectrum for 

a cast film was collected with 

an empty sample holder in the 

infrared beam. 

The spectrometer is not 

properly aligned, causing a 

sloped baseline. 

The spectrometer has not been 

on long enough to reach 

thermal equilibrium. 

The spectrometer is not 

properly purged. 

Remove the sample holder and collect 

the background again. 

Use the Align button on the 

Diagnostic tab of the Experiment 

Setup dialog box to align the 

spectrometer. 

For best results allow the spectrometer 

at least one hour to stabilize after 

turning it on. 

Check the system to make sure the 

correct purge gas is being used and 

that the flow rate is correct. 

Nicolet FT-IR User’s Guide 153
The resolution was too high. 

The purge gas flow rate or 

pressure is too high. 

The detector is saturated. 

The moving mirror velocity is 

set too high for the detector. 

The sample in an ATR 

experiment is not in good 

contact with the ATR crystal. 

Reduce the resolution (use a higher 

numerical setting) on the Collect tab 

of the Experiment Setup dialog box. 

Check the pressure regulator; it should 

be set between 0.7 and 1.4 bar (70 and 

140 kPa, or 10 and 20 psig). Check the 

flowmeter; it should read 15 scfh 

(about 0.4 m3/hr). Adjust the flow rate 

if necessary. 

Add a bandwidth-limiting filter or an 

energy screen to reduce the signal 

strength. 

Set Velocity on the Bench tab of the 

Experiment Setup dialog box to a 

lower value. 

Reapply the sample to obtain more 

consistent contact between the sample 

and the ATR crystal. 

154 Thermo Electron Corporation
absolute transmission accessory................................... 85 

absorbance units........................................................... 38 

accessories.................................................................... 81 

aligning ............................................................... 132 

automated sample handling................................... 85 

available ................................................................ 12 

cabling................................................................... 91 

descriptions........................................................... 85 

detector.................................................................. 92 

installing...................................................... 6, 12, 85 

not aligned........................................................... 142 

not installed correctly.................................. 142, 143 

power..................................................................... 92 

system ................................................................... 90 

when to turn on ............................................... 18, 56 

Advanced Diagnostics........................................ 127, 148 

AEM............................................................................. 86 

air dryer................................................................ 90, 151 

aligning 

accessory ............................................................. 132 

spectrometer................................................ 124, 130 

annotation tool............................................................ 120 

aperture....................................................................... 141 

effect on resolution................................................ 67 

effect on wavenumber accuracy............................ 67 

for collecting data in visible spectral range........... 70 

incorrect .............................................................. 141 

resolution affected by............................................ 70 

size for cooled detector ......................................... 67 

size for detector..................................................... 67 

ATR accessory ........................................... 81, 82, 83, 84 

ATR correction........................................................... 103 

ATR sample contact................................................... 154 

Auxiliary 1 connector................................................... 93 

Auxiliary 2 connector................................................... 93 

Auxiliary connector...................................................... 92 

auxiliary experiment module........................................ 86 

Background button........................................................53 

background spectrum 

collected with sample holder in beam..................153 

collecting .........................................................32, 53 

defined ...................................................................27 

too old..................................................................151 

when to collect.......................................................27 

bandwidth-limiting filter...............................................65 

baseline 

correcting .....................................................102, 116 

not flat..................................................................153 

not stable..............................................................139 

sloped...................................................................153 

baseplate 

custom....................................................................86 

removing................................................................85 

baseplates 

Smart......................................................................28 

Snap-In...................................................................28 

beam path 

blocked.................................................141, 143, 147 

beamsplitter 

changing.................................................................10 

compatibility with detector....................................60 

fogged ..................................................................143 

not compatible with detector........................142, 147 

not properly seated...............................................146 

spectral range.........................................................62 

types.......................................................................60 

which to use ...........................................................11 

beamsplitter compartment cover.................................147 

Bench Diagnostics ......................................127, 129, 148 

Bench Status indicator ..................................................26 

blanking totally absorbing bands................................102 

Nicolet FT-IR User’s Guide 155
g pg

closing window...........................................................120 

Collect Sample window................................................99 

Collect Status indicator.........................................37, 150 

collecting 

background............................................................53 

background spectrum ............................................32 

sample spectrum........................................27, 30, 53 

spectrum ..................................12, 14, 23, 27, 30, 98 

color of spectrum........................................................111 

commercial library

finding compound in ...........................................105 

common scale .............................................................112 

components 

separating with subtraction..................................117 

computer 

saving spectra on hard disk .................................107 

when to turn on................................................19, 56 

configuration 

default....................................................................30 

opening..................................................................30 

saving ..................................................................119 

connector 

Auxiliary 1.............................................................93 

Auxiliary 2.............................................................93 

detector..................................................................92 

Detector/Motors.....................................................95 

pass-through ..........................................................91 

connectors 

Auxiliary pinouts...................................................94 

for custom accessories...........................................94 

pass-through ..........................................................94 

sample compartment..............................................92 

contaminants 

identifying with subtraction.................................117 

cooled detector 

aperture size for.....................................................67 

cooling detector ....................................................19, 125 

d 

data collection .......................................................... 9, 14 

default configuration .................................................... 30 

default experiment........................................................ 30 

deleting 

report notebook ................................................... 109 

spectrum.............................................................. 108 

depth of penetration ................................................... 103 

desiccant............................................................. 139, 151 

changing.............................................................. 130 

checking ................................................................ 17 

when to change ................................................... 126 

desiccant indicator................................................ 17, 126 

detector 

accessory............................................................... 92 

aperture size for..................................................... 67 

cable .................................................................... 144 

changing................................................................ 11 

compatibility with beamsplitter............................. 60 

connector............................................................... 92 

cooling .......................................................... 19, 125 

custom................................................................. 144 

energy screen ............................ 66, 69, 70, 123, 154 

external................................................................ 144 

frosted ................................................................. 144 

linearity ................................................................. 64 

not compatible with beamsplitter................ 142, 147 

not cooled............................................................ 147 

not installed properly .......................................... 143 

photometric accuracy ............................................ 65 

saturated ...................................... 64, 65, 66, 67, 154 

saturation............................................................. 123 

signal intensity .................................................... 131 

silicon.................................................................... 70 

spectral range ........................................................ 62 

types...................................................................... 60 

using filter to reduce energy reaching................... 64 

156 Thermo Electron Corporation
g pg

diagnostics.......................................................... 129, 148 installing in sample holder.....................................29 diffuse reflection accessory.................................... 81, 82 reducing energy reaching detector using ...............64 directory filter wheel ..............................................................72, 86 library.................................................................. 136 finding peaks...............................................................120 dispersion effects........................................................ 103 flammable gases............................................................15 Display Setup ............................................................. 111 flowmeter......................................................................15 distortion in spectrum................................................... 69 Foundation Series .........................................................87 documentation................................................................ 6 fringes in spectrum......................................................150 dual sources option....................................................... 58 frost on detector ..........................................................144 

FT-IR ..............................................................................6 

e full scale......................................................................112 

electronics module ..................................................... 145 

g defective.............................................................. 146 

replacing.............................................................. 134 gain ...............................................................................99 e-mail.......................................................................... 3, 7 for collecting data in visible spectral range ...........70 

energy screen.................................................. 66, 69, 154 gas cells.........................................................................87 detectors typically used with................................. 66 GC interface..................................................................87 energy passed with................................................ 66 Getting Started tutorial....................................................1 for collecting data in visible spectral range........... 70 grazing angle accessory ................................................84 optional wheel....................................................... 86 

resolution affected by............................................ 70 

when to use ......................................................... 123 h 

energy screen wheel ..................................................... 75 hardware requirements....................................................4 

error message during data collection.......................... 147 Help.....................................................................6, 7, 122 

Expand/Contract button ............................................. 113 

i experiment

default ................................................................... 30 Information button ......................................................121 not listed.............................................................. 136 infrared source ..............................................................58 restoring .............................................................. 136 InSb detector...............................................................125 selecting .................................................... 21, 25, 30 

Experiment drop-down list box.................. 21, 25, 30, 97 

Experiment Setup ................................................... 21, 25 

extended search feature .............................................. 105 

external detector......................................................... 144 

external source ............................................................. 59 

Nicolet FT-IR User’s Guide 157
optical filter ...........................................................29 saving spectra in.................................................. 107 

sample........................................................11, 29, 34 scrapbook ............................................................ 104 

sample holder ........................................................28 searching ............................................................. 102 

source ....................................................................11 spectrum cannot be added to............................... 135 

interferogram library search 

location................................................................147 extended search feature....................................... 105 

not present ...........................................................141 search expert ....................................................... 106 

saving ....................................................................99 specifying spectral regions for............................ 103 

interferometer library spectrum 

stand-by mode .....................................................145 displaying............................................................ 104 

IUPAC..........................................................................64 linearity ........................................................................ 64 

Liquid Analysis System ............................................... 87 

k liquid nitrogen for cooling detectors.......................... 125 

log (1/R) units ............................................................ 101 KBr pellet improperly pressed....................................153 

Kramers-Kronig correction ................................103, 152 

Kubelka-Munk units...................................................101 m 

macro............................................................................ 53 

l Macro button ................................................................ 53 

maintenance ................................................. 13, 128, 130 labeling peak...............................................................120 matched scale ............................................................. 112 laser math burned out............................................................147 subtracting........................................................... 116 defective ..............................................................146 when to use subtraction....................................... 117 detector misaligned..............................................139 math operations.......................................................... 118 flickering .....................................................141, 145 MCT detector ............................................................. 125 indicator.................................................................18 menu bar....................................................................... 25 

not on...................................................................145 

menu names.................................................................. 25 not working .........................................................138 microplate accessory .................................................... 87 replacing..............................................................134 microscope Laser indicator..............................................................56 descriptions........................................................... 88 

in viewing mode.................................................. 152 

158 Thermo Electron Corporation
peak 

n area.......................................................................115 

height ...................................................................115 Nicolet Centaurμs......................................................... 88 labeling ................................................................120 Nicolet Continuμm....................................................... 88 peaks noise ....................................................................... 65, 69 carbon dioxide .....................................................151 number of scans derivative-shaped in spectrum .............................152 signal-to-noise ratio affected by............................ 69 eliminating with subtraction ................................117 too low ................................................................ 154 finding..................................................................120 

noise.....................................................................154 

o none in spectrum..................................................152 

offset scale.................................................................. 112 totally absorbing in spectrum...............................151 

OK/Enter button........................................................... 53 water ....................................................................151 

OMNIC performance test..................................................132, 148 

customizing ......................................................... 119 photoacoustic accessory................................................88 

Help................................................................. 7, 122 photoacoustic units .....................................................101 

installing.................................................................. 5 photometric accuracy..............................................65, 66 

learning ............................................................... 6, 7 pinouts 

preparing for data collection ................................. 97 Auxiliary connectors..............................................94 

starting............................................................... 9, 20 Detector/Motors connector....................................96 

wizards and tutorials ............................................... 6 polarizer..................................................................78, 88 

OMNIC window........................................................... 24 power 

Open Configuration...................................................... 30 accessory................................................................92 

opening power cable defective .................................................140 

configuration ......................................................... 30 power cord ..................................................................140 

spectrometer cover.............................................. 123 Power indicator.......................................................18, 56 

spectrum.............................................................. 106 power line conditioner ..................................................90 

optical layout................................................................ 54 power supply.................................................................56 

ordering parts ................................................................. 7 defective...............................................................140 

not connected properly ........................................140 

p replacing ..............................................................134 

power switch.................................................................18 % reflectance units..................................................... 101 pressure regulator..........................................................15 % transmittance units................................................... 38 previewing report........................................................109 palette ........................................................................... 40 previewing spectrum before printing..........................110 

parameters printer setting.................................................................... 21 specifying.............................................................109 part numbers................................................................... 7 Printer Setup ...............................................................109 

Nicolet FT-IR User’s Guide 159
purge filter Roll/Zoom window ............................................ 113, 114 

cleaning ...............................................................130 RSVP............................................................................ 90 

purge gas generator ......................................................90 

s 

q SabIR............................................................................ 88 

QC comparison safety ............................................................................ 14 

setting up ...............................................................43 sample 

QC library.....................................................................43 installing.................................................... 11, 29, 34 

quality of spectrum.......................................................37 not present........................................................... 152 

quality standards.........................................................100 too thick .............................................................. 151 

Quantify......................................................................135 Sample button .............................................................. 53 

quantitative analysis .................................64, 65, 66, 135 sample compartment 

connectors............................................................. 92 

r windows fogged.................................................. 143 

sample film rear panel ......................................................................55 in ATR experiment ............................................. 152 region sample holder selecting...............................................................120 installing................................................................ 28 regions installing sample or filter in .................................. 29 specifying for library search................................103 sample shuttle............................................................... 89 remote diagnostics........................................................90 sample spectrum Remote Start accessory.................................................88 adding to spectral library..................................... 105 replacing parts in spectrometer...................................127 adding to spectral window .................................... 36 

report collecting................................................... 27, 30, 53 creating..........................................................48, 109 sample wheel................................................................ 85 previewing.....................................................49, 109 sampling accessories.................................................... 85 printing ..................................................................50 sampling cup missing or tilted ................................... 152 

report notebook sampling techniques....................................................... 6 deleting................................................................109 saturation.................................................................... 154 saving spectra in ..................................................107 detector................................................ 64, 65, 66, 67 report template 

creating..................................................................49 

selecting.........................................................48, 109 

requirements of system...................................................4 

160 Thermo Electron Corporation
Scan indicator................................................. 18, 56, 145 which to use .........................................................126 

flashing intermittantly ......................................... 143 Source indicator..............................................18, 56, 144 

scans spectra 

number of.............................................................. 35 saving as group ....................................................108 

scattering ...................................................................... 69 saving automatically ............................................106 

scrapbook library........................................................ 104 saving on hard disk ..............................................107 

sealed and desiccated ............................................. 33, 34 subtracting ...........................................................116 

sealed and desiccated system ............................... 17, 126 where to save .......................................................107 

search spectral library 

specifying spectral regions for............................ 103 adding spectrum to.........................................47, 105 

search expert............................................................... 106 creating ............................................................7, 104 

searching searching..............................................................102 

preparing spectrum for........................................ 102 spectral quality checks................................................100 

spectral library..................................................... 102 spectral regions 

selecting and velocity............................................................71 

experiment....................................................... 21, 30 detector-beamsplitter .............................................62 

report template .................................................... 109 for library search..................................................103 

spectral regions ................................................... 120 selecting ...............................................................120 

spectrum.............................................................. 110 visible.....................................................................70 

service .......................................................... 13, 128, 134 spectral window ............................................................24 

signal intensity ........................................................... 131 spectrometer 

low....................................................... 141, 142, 143 aligning ................................................................130 

signal-to-noise ratio................................................ 66, 69 components......................................................10, 51 

increased by bandwidth-limiting filter.................. 65 cover ....................................................................139 

silicon detector ............................................................. 70 data collect buttons................................................52 

Smart Accessories.................................................... 6, 81 diagnostics...........................................................127 

Smart Accessory........................................................... 97 how it works ..........................................................10 

Smart baseplate ...................................................... 28, 86 letting stabilize.......................................................19 

Smart Purge................................................ 10, 16, 33, 34 maintaining ............................................13, 128, 130 

Smart Purge Kit............................................................ 91 not aligned ...................138, 139, 141, 143, 145, 153 

Snap-In sample compartment baseplates ..................... 28 not plugged in ......................................................140 

software not purged....................................................151, 153 

learning ................................................................... 9 optical layout .........................................................54 

not started............................................................ 145 overheated............................................138, 142, 146 

preparing for data collection ................................... 9 performance test...................................................132 

requirements............................................................ 4 purging.............................................................15, 16 

starting..................................................................... 9 rear panel ...............................................................55 

troubleshooting ................................................... 135 replacing parts in..................................................127 

Nicolet FT-IR User’s Guide 161
troubleshooting....................................................137 specular reflection ...................................................... 152 

turned off.............................................................145 specular reflection accessory.................................. 84, 89 

turning on ........................................................18, 56 starting OMNIC ....................................................... 9, 20 

when to align .......................................................124 status indicators not lit ............................................... 140 

when to open cover of.........................................123 subtracting spectra...................................................... 116 

when to turn off...................................................127 system accessories........................................................ 90 

spectrum 

t adding to user library.............................................47 

background............................................................27 technical support ............................................................ 7 baseline not flat ...................................................153 telephone numbers ..................................................... 3, 7 cannot be added to library ...................................135 

temperature......................................... 138, 142, 146, 153 carbon dioxide peaks in.......................................151 outside allowed range ......................................... 139 collecting .................................12, 23, 27, 30, 53, 98 TGA interface .............................................................. 89 color.....................................................................111 TGA module ................................................................ 89 comparing with QC library spectra .......................43 

tool copying and pasting.............................................121 annotation............................................................ 120 correcting.............................................................102 peak area ............................................................. 115 correcting baseline of ..........................................116 peak height.......................................................... 115 creating report containing......................................48 region .................................................................. 120 deleting................................................................108 selection .............................................................. 114 derivative-shaped peaks in ..................................152 spectral cursor..................................................... 115 distorted.................................................................69 toolbar .......................................................................... 26 fringes or channeling in.......................................150 tools.............................................................................. 40 math operations...................................................118 

totally absorbing bands moving in pane ....................................................114 blanking .............................................................. 102 moving stacked....................................................114 training ........................................................................... 7 moving to another window..................................114 transmission accessory........................................... 83, 89 no peaks in...........................................................152 troubleshooting............................................................... 7 noise in ................................................................154 applications......................................................... 150 opening................................................................106 software............................................................... 135 preparing for search.............................................102 

spectrometer........................................................ 137 preparing to collect................................................14 turning off system .................................................. 19, 57 previewing before printing ..................................110 turning on computer............................................... 19, 56 quality....................................................................37 turning on spectrometer.......................................... 18, 56 saving ....................................................................37 turning on system........................................................... 9 

162 Thermo Electron Corporation
ppppy

p

units.............................................................................. 98 Windows metafile .......................................................121 

used for spectrum.......................................... 38, 101 wizards............................................................................6 

user library library creation.........................................................7 

adding spectrum to................................................ 47 

x creating.................................................................. 47 

saving spectra in.................................................. 107 X value........................................................................115 

user name ..................................................................... 20 

y v 

Y value........................................................................115 validation wheel ........................................................... 90 Y-axis..........................................................................112 Val-Q............................................................................ 90 

velocity

and spectral range.................................................. 71 z 

moving mirror....................................................... 71 zoom 

too high ............................................................... 141 Expand/Contract button.......................................113 

too high for detector............................................ 154 in on spectrum .....................................................113 

visible spectral range.................................................... 70 Zoom button ..........................................................49 

Nicolet FT-IR User’s Guide 163
164 Thermo Electron Corporation