Thermo Electron Nicolet 4700 User manual

The information in this publication is provided for reference only. All information contained in
this publication is believed to be correct and complete. Thermo Electron Corporation shall not be
liable for errors contained herein nor for incidental or consequential damages in connection with
the furnishing, performance or use of this material. All product specifications, as well as the
information contained in this publication, are subject to change without notice.
This publication may contain or reference information and products protected by copyrights or
patents and does not convey any license under our patent rights, nor the rights of others. We do
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: [phone] or 608-276-6373
Fax: [phone]
E-mail: [email protected]
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

Contents
Welcome .............................................................................................1
About this manual ..........................................................................2
Questions or concerns ....................................................................3
System requirements ......................................................................4
Installing OMNIC...........................................................................5
Where to find the information you need ........................................6
Wizards and tutorials .................................................................6
On-line Help ..............................................................................7
Finding answers to your questions.............................................9
Before You Collect Spectra ..............................................................14
Checking the purge.......................................................................15
Smart Purge settings ................................................................16
Checking the desiccant.................................................................17
Turning on the system components..............................................18
Cooling the detector .....................................................................19
Starting OMNIC ...........................................................................20
Selecting an experiment ...............................................................21
Your First Experiment ......................................................................23
The OMNIC window....................................................................24
Spectral window ......................................................................24
Menu bar ..................................................................................25
Experiment drop-down list box ...............................................25
Bench Status indicator .............................................................26
Toolbar.....................................................................................26
Collecting a sample spectrum ......................................................27
Installing the standard sample holder ......................................28
Collecting the sample spectrum...............................................30

How do I know if my spectrum is good? .....................................37
Saving the spectrum .....................................................................37
Converting the spectrum’s units...................................................38
Labeling a peak with the annotation tool .....................................40
Verifying the composition of the sample .....................................43
Creating a user library ..................................................................47
Adding a spectrum to a user library .............................................47
Creating and printing a report ......................................................48
Spectrometer Basics..........................................................................51
Spectrometer components ............................................................51
Using the data collection buttons.............................................52
What’s inside?..........................................................................54
What is on the rear panel?........................................................55
Turning on the spectrometer power .............................................56
Using a light source......................................................................58
Using beamsplitters and detectors................................................60
Selecting the right beamsplitter and detector...........................60
Improving the quality of your spectral data.............................64
How to collect data in the visible spectral range..........................70
About the moving mirror velocity................................................71
Spectrometer Options .......................................................................72
Using the filter wheel ...................................................................72
Using the energy screen wheel.....................................................75
Using the internal polarizer ..........................................................78
Accessories .......................................................................................81
Smart Accessories ........................................................................81
Other sampling accessories for different applications .................85
System accessories .......................................................................90
How to cable an accessory ...........................................................91
Pass-through connectors ..........................................................91
Detector/Motors connector ......................................................95

Quick Answers to Your Questions About Using OMNIC ...............97
Collecting spectra.........................................................................97
Converting spectra to other units ...............................................101
Using spectral libraries...............................................................102
Opening, saving and deleting spectra.........................................106
Printing .......................................................................................109
Displaying spectra ......................................................................110
Correcting spectra.......................................................................116
Subtracting, adding, multiplying and dividing spectra ..............116
Customizing OMNIC .................................................................119
Other questions...........................................................................120
Quick Answers to Your Questions About
Using the Spectrometer.............................................................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

.

Welcome
Congratulations on your purchase of a Nicolet 4700 or Nicolet 6700
spectrometer from Thermo Electron! The spectrometer lets you
collect spectra in the mid-IR, far-IR and near-IR spectral ranges. The
system integrates advanced hardware features with the power and
flexibility of Thermo Electron’s OMNIC
software*.
If you have not used the spectrometer before, view the
“Spectrometer Tour” and “Getting Started With OMNIC” tutorial
available through Getting Started in the Help menu of OMNIC.
* Some dedicated systems use other Thermo Electron software packages.
Nicolet FT-IR User’s Guide 1

About this manual This manual explains how to use the system to collect and process
FT-IR spectra after a Nicolet 4700 or a Nicolet 6700 spectrometer is
installed. Included is information about using your OMNIC software
as well as chapters on how to operate, maintain and service the
spectrometer.
This manual describes some hardware features that are not available
on all Nicolet models. Use the instructions for the features on your
system.
Although the appearance of your spectrometer may vary from some
of the illustrations in this manual, the instructions are correct for
your system.
The following conventions are used in this manual to draw your
attention to the on-line documentation and other important
information.
This symbol tells you that you can find more information in the on-
line tutorials. To access a tutorial, click the Help menu in OMNIC.
?
This symbol tells you that you can find more information in the on-
line OMNIC Help system. Choose OMNIC Help Topics from the
Help menu.
This symbol tells you that you can find more information in this
manual.
2 Thermo Electron Corporation

Note Notes contain helpful supplementary information. S
Important Follow instructions labeled “Important” to avoid damaging the
system hardware or losing data. S
Caution Indicates a potentially hazardous situation which, if not avoided,
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: [phone] (U.S.A.) or
[phone] (worldwide)
Fax: [phone] (worldwide)
E-mail: [email protected]
World Wide Web: http://www.thermo.com/spectroscopy
Nicolet FT-IR User’s Guide 3

System requirements If you are supplying your own computer, be sure that it meets the
following requirements for hardware and software.
●One of the following versions of Windows®software:
-Windows 2000 (latest Service Pack recommended)
-Windows XP Professional (latest Service Pack
recommended)
●Microprocessor:
Intel®Pentium®III, 1.0 GHz (recommend)
Intel Pentium II, 400 MHz (minimum)
●Random access memory (RAM):
256 megabytes (recommended)
128 megabytes (minimum)
If you plan to use a microscope,
1 gigabyte (recommended)
512 megabytes (minimum)
●Disk drives:
5.0 gigabytes (recommended) hard disk drive
2.0 gigabytes (minimum) hard disk drive
1.44-megabyte floppy disk drive for 3.5-inch floppy disks
Quad speed CD-ROM drive
●Video:
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

●IO devices and card slots:
Sound card and speakers for listening to the audio portions of
tutorials
Keyboard and serial, USB or PS/2®-style mouse
Printer port (USB, parallel and/or serial) if you plan to print on a
local printer
One USB 2.0 connector (not a hub) for data transfer
Ethernet port if you plan to connect the system to a network
Internet connection if you plan to use the internet features of the
software
One additional serial port if you plan to use PLUS™ 2 Liquid
Analysis System, Centaurµs microscope with motorized stage, or
standard Continuµm microscope
Two additional serial ports if you plan to use a Continuµm
microscope with a motorized stage
Two additional serial ports and one additional USB 2.0
connection (not a hub) if you plan to use a Continuµm XL
microscope
One additional PCI slot if you plan to use a microscope with
video capability
Installing OMNIC If you purchased your computer from Thermo Electron, your
software is already installed. If you provided your own computer,
you need to install OMNIC on your hard drive. See the instructions
that came with the software CD, or read “Installing OMNIC or EZ
OMNIC” in the document titled OMNIC Spectroscopy Software that
came with your software. You can use these same instructions if you
ever need to reinstall the software.
Nicolet FT-IR User’s Guide 5

Where to find the
information you need
The on-line and printed documentation included with your system is
designed to let you find the information you need quickly. We
recommend first using the on-line documentation provided with
OMNIC when you have a question. OMNIC includes several on-line
tutorials, a wizard and a complete Help system. See “Starting
OMNIC” in the “Before You Collect Spectra” chapter for
information about starting OMNIC.
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 FT-
IR spectrometer works and the theory behind FT-IR spectroscopy.
The tutorial is available through Getting Started in the Help menu.
Sampling Techniques – This item in the Help menu gives you
access to the “Choosing a Sample Technique” tutorial, which helps
you choose the best technique for your analysis. Also available are
tutorials describing how to install and use a number of sampling
accessories, including Smart Accessories.
6 Thermo Electron Corporation

Learning OMNIC – This item in the Help menu gives you access to
tutorials that explain how to use OMNIC to collect spectra and
perform a number of other software operations.
Spectrometer Help Topics – This tutorial, available in the Help
menu, contains step-by-step instructions for installing optional
hardware, changing replaceable parts, maintaining your
spectrometer, and setting up the system for a variety of experiments.
If you ever have a problem with your spectrometer, use this tutorial
to access troubleshooting information and get part number and
ordering information.
Technical Support – This tutorial, available in the Help menu,
outlines the many support, training, and custom application services
available from Thermo Electron. It includes Technical Support
telephone and fax numbers, as well as e-mail and web site addresses.
The Library Creation Wizard prompts you, step by step, through
creating a user library of spectra. The wizard appears when you click
the Create Library button in Library Manager, available in the
Analyze menu in OMNIC.
On-line Help Choose the Help Topics that interest you from the Help menu to
display that Help system. It lets you quickly find answers to your
questions about using the software.
There are several other ways to enter a Help system:
•You can see information about many features in OMNIC (such
as a parameter in a dialog box) by clicking the feature using the
right mouse button. (If the active dialog box or window includes
a question mark button near the upper-right corner, you may
need to first click that button and then click the feature of interest
using the left mouse button.) A brief description of the item
appears, and in most cases one or more buttons that you can click
to display more detailed information. Here is an example:
Nicolet FT-IR User’s Guide 7

Click the Discussion button to display a complete discussion of
the item (or the dialog box or window that contains the feature).
Click the How To button to display a step-by-step procedure for
using the item (or the dialog box or window that contains the
item).
•The left pane in each help window lists the topics available in
that help system.
Here is an example of a help window showing the contents of
some of the books in the system:
8 Thermo Electron Corporation

Finding answers
to your questions
Use the following sections to help you locate the information you
need in the on-line and printed documentation. The on-line
documentation is available in the Help menu of OMNIC.
The basics How do I turn on the system?
Spectrometer Tour (available through Getting Started)...
“Powering up”
“Before You Collect Spectra” chapter...
“Turning on the system components”
How do I start the software?
“Before You Collect Spectra” chapter...
“Starting OMNIC”
How do I prepare the software for data collection?
Collecting a Spectrum (available through Learning OMNIC)...
“Preparing the Software”
How can I learn how to use the software?
View the tutorials listed when you point to Getting Started or
Learning OMNIC.
?
OMNIC Help Topics includes complete instructions for all the
OMNIC features. Use the Index tab or Contents tab to find the
information you need.
Nicolet FT-IR User’s Guide 9

Using the spectrometer
and changing parts
What’s inside the spectrometer?
Spectrometer Tour (available through Getting Started)...
“Inside the spectrometer”
How does the spectrometer work?
Beginner’s Guide to FT-IR (available through Getting Started)
How do I purge the system?
Spectrometer Help Topics...
“Installing purge controls” in “Installing optional hardware”
How do I use Smart Purge
?
Spectrometer Help Topics...
“Setting the Smart Purge controls” in “Installing optional
hardware”
How do I change beamsplitters?
Spectrometer Help Topics...
“Changing beamsplitters” in “Setting up experiments”
“Selecting a beamsplitter, detector, and source” in
“Setting up experiments”
10 Thermo Electron Corporation

How do I change detectors?
Spectrometer Help Topics...
“Selecting a beamsplitter, detector, and source” and
“Changing detectors” in “Setting up experiments”
How do I install a source?
Spectrometer Help Topics...
“Selecting a beamsplitter, detector, and source” and
“Installing a new source” in “Setting up experiments”
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

How do I collect a spectrum?
Collecting a Spectrum (available through Learning OMNIC)
“Your First Experiment” chapter
Accessories What accessories are available?
Spectrometer Tour (available through Getting Started)...
“Accessories”
“Accessories” chapter
How do I install an accessory?
Spectrometer Help Topics...
“Installing optional hardware” (Step-by-step instructions and, in
many cases, on-line videos help you install accessories. If your
accessory is not covered on-line, use the printed instructions.)
12 Thermo Electron Corporation

Maintenance and service How should I maintain my spectrometer?
Spectrometer Tour (available through Getting Started)...
“Service and maintenance”
Spectrometer Help Topics...
“Maintaining your spectrometer”
“Maintenance and Service” chapter
What should I do if there is a problem with the system?
Contact Thermo Electron technical support. Outside the U.S.A.,
contact the local Thermo Electron sales or service representative.
Phone: [phone] (U.S.A.) or
[phone] (worldwide)
Fax: [phone] (worldwide)
E-mail: [email protected]
World Wide Web: http://www.thermo.com/spectroscopy
Nicolet FT-IR User’s Guide 13

Before You Collect Spectra
Warning The Spectrometer Safety Guide that came with your system contains
important safety information. This guide is available in several
languages. Contact your local Thermo Electron office for
information about the languages that are available. Before you use
the system, read the entire guide. To prevent personal injury and
damage to equipment, follow the safety precautions contained in the
guide whenever you use the system. 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