Thermo Scientific Nicolet Series User manual

Nicolet Series FT-IR Spectrometers
Nicolet iS20
User Guide
269-335700 Revision A November 2018

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WARNING Avoid an explosion or fire hazard. This instrument or accessory is not
designed for use in an explosive atmosphere.

Thermo Scientific Nicolet iS20 User Guide iii
C
Chapter 1 Welcome. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
About the Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Finding Other PDF Documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Ordering Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Chapter 2 Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Turning the Power On and Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Indicators and Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Installing a Smart Accessory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Collecting Data With the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Collecting Data With the Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Setting the Purge Gas Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Aligning Your Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Verifying the Laser Frequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Cooling a Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 3 Installing or Replacing Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Installing a Purge Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Installing a Sample Compartment Extension Kit. . . . . . . . . . . . . . . . . . . . . . . . 13
Installing Baseplate-mounted Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Installing Slide-mounted Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Installing Other Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Replacing the Power Supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Changing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Installing Sidewall Adapters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Chapter 4 Maintaining Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Cleaning Your Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Static Electricity Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Maintaining Detector Dewars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Checking the Humidity Indicator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Replacing the Humidity Indicator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Replacing the Desiccant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Regenerating the Desiccant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Contents

Contents
iv Nicolet iS20 User Guide Thermo Scientific
Checking and Changing the Purge Gas Filter . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Chapter 5 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Using the Troubleshooting Topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Instrument Problems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Error Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Thermo Scientific Nicolet iS20 User Guide 1
Welcome
The Thermo Scientific™ Nicolet™ iS™20 spectrometer has integrated validation features, a
powerful software suite, and many other features that make it easy for you to collect data. It
was designed to allow you to install optional hardware and perform several service and
maintenance procedures yourself, and this help system, or electronic documentation, contains
detailed information about performing such procedures.
If you are using the electronic help version of this document, you can access information by
double-clicking the book in the Contents tab that interests you, and then double-clicking the
topic you want to read. There is also an Index tab where you can search for topics by phrase or
keyword, and there is a Find tab that allows you to search for specific words.
Conventions Used
Safety precautions and other important information use the following format:
WARNING Indicates a hazardous situation which, if not avoided, could result in death or
serious injury.
CAUTION Indicates a hazardous situation which, if not avoided, could result in minor or
moderate injury.
NOTICE Follow instructions with this label to avoid damaging the system hardware or
losing data.
Note Contains helpful supplementary information.
Tip Provides information that can make a task easier.

Welcome
About the Help System
2Nicolet iS20 User Guide Thermo Scientific
About the Help System
To view the electronic Help version of this document, choose Spectrometer Help Topics from
the Help menu in OMNIC software.
Finding Other PDF Documents
PDF files of system documentation are in the electronic documentation package provided
with your instrument.
Ordering Parts
To o r d er p a r t s , contact us.
If you need to send the instrument or an accessory to us for repair, call or e-mail us first for
any shipping requirements or other instructions.
Contacting Us
For Technical Support, please contact: www.thermofisher.com
If you have problems with your system, refer to the Troubleshooting information for help, or
call Technical Support.
Note To expedite and assist in problem diagnosis, please be prepared to send us a copy of
your diagnostics log file. The diagnostic log includes a history of important system
parameters and events that occur during system operation. To copy the diagnostics log to
your Windows desktop, start OMNIC software and choose File > Copy Diagnostics File
to Desktop. Attach this file to an e-mail message to our Technical Support group.

Operation
Turning the Power On and Off
Thermo Scientific Nicolet iS20 User Guide 3
Operation
Turning the Power On and Off
To turn the system power on or off, press the power switch on the power supply.
Indicators and Buttons
The status indicators for the instrument are located on the touch panel, which is on the main
cover of the instrument. This panel also has buttons that allow you to operate the instrument.
•Background button. Acquires a background spectrum, which shows the response of the
instrument when no sample is present.
•Sample button. Measures the current sample installed in the instrument sample
compartment. The sample data is ratioed with the background data, which leaves only
the signals from the sample.
Humidity indicator
Scan bar
Background button Sample button
Workflow button
Stop button
OK/Enter button

Operation
Indicators and Buttons
4Nicolet iS20 User Guide Thermo Scientific
•Workfl ow button. Can be used to assign a software workflow (macro) to the touch panel
for automated operations with the instrument. For information about creating macros,
see the Macros Basic User Guide in your instrument documentation set. To assign a
Macros Basic macro (.mac) file to the operations panel, open OMNIC software and
choose Collect (menu) > Experiment Setup > Advanced (tab). Then choose Browse
next to Macro For Macro Button and select the macro file.
•Humidity indicator.The humidity indicator monitors the level of humidity inside the
spectrometer. The status is indicated by the color of the indicator:
•OK/Enter button. Can be used to confirm a message box displayed in OMNIC software.
•Stop button. Can be used to cancel a message box displayed in OMNIC software.
•Scan bar. Provides instrument status information. Scan states:
– Solid-pulsing green light—Instrument is ready for use.
– Moving green light—Data collection is in progress.
– Solid-pulsing yellow light—Scheduled maintenance required. For more information,
click the System Status icon (shield) in OMNIC software. See the OMNIC Help
system for details.
– Quick-pulsing red light—Instrument requires attention. For more information, see
System Status in OMNIC software.
BLUE
(good)
LIGHT BLUE
(Change desiccant)
PINK
(Call service)

Operation
Installing a Smart Accessory
Thermo Scientific Nicolet iS20 User Guide 5
Installing a Smart Accessory
To install a Smart Accessory™ in the sample compartment, lower the accessory into the sample
compartment and press gently downward until the accessory locks in place. Then rotate the
accessory lock (located on the top of the instrument at the back edge of the sample
compartment) so that it holds down the accessory.
Collecting Data With the Instrument
For information about collecting data with your instrument, please see the getting started
manual that came with the instrument.
Collecting Data With the Module
You must use Thermo Scientific™ OMNIC™ software to collect data. OMNIC can be started
by using the OMNIC shortcut on your system desktop. For additional information, please see
the OMNIC help (available through the Help menu in OMNIC) or the printed
documentation that came with the system microscope or spectrometer.
Note
• If you want to remove a Smart Accessory, simply reverse the steps in this procedure.
When you are not using an accessory, store it in a dust-free environment like a cabinet
or box.
• For information about installing other kinds of accessories, see Installing Other
Accessories.

Operation
Setting the Purge Gas Controls
6Nicolet iS20 User Guide Thermo Scientific
Setting the Purge Gas Controls
You must connect a source of purge gas (dry air or nitrogen) to purge your instrument of
moisture and other environmental contaminants. For best results the purge gas should be
dried to a dew point of -70 °C (-94 °F) or below. Use the following instructions to set the
purge gas controls.
1. Open the shutoff valve.
2. Adjust the pressure regulator until the gauge indicates that the pressure is between 0.7 and
1.4 bar (70 to 140 kPa, or 10 to 20 psig).
NOTICE We recommend that you maintain seal and desiccation and/or purge your
instrument at all times. Equipment damage due to failure to maintain seal and desiccation
and/or purge is not covered under the warranty. If you have questions about this
requirement, please contact us.
CAUTION Never use a flammable gas to purge your instrument. The purge gas must be
free of moisture, oil, carbon dioxide and other reactive or infrared-absorbing materials. To
prevent laser damage, use only dried air or nitrogen to purge your instrument.

Operation
Aligning Your Spectrometer
Thermo Scientific Nicolet iS20 User Guide 7
3. Set the flowmeter to 10 scfh.
Aligning Your Spectrometer
Your instrument can be aligned automatically using OMNIC software. Alignment optimizes
the energy throughput to the detector. Alignment can change slightly over time, particularly
in locations that have large temperature swings or excessive vibration.
To align the spectrometer, use the Align button on the Diagnostic tab of the Experiment
Setup dialog box (available through the Collect menu in OMNIC software). For more
information, see OMNIC Help Topics in the Help menu.
Verifying the Laser Frequency
Use the Laser Verification button on the Diagnostic tab in the Experiment Setup dialog box in
OMNIC software to verify the laser.
For optimum system performance, verify the laser frequency according to the following
schedule:
NOTICE Flow rates greater than 10 scfh can cause vibration that can affect data
quality. We recommend keeping the flow rate at approximately 10 scfh.
Note The instrument is aligned automatically each time you run a Performance
Verification (PV) test. We recommend running a PV test at least once a month.
Spectrometer environment Spectrometer state Recommended Schedule
Stable Always powered on every 3 months
Unstable (e.g., temperature or
humidity constantly changing)
Powered on and off
frequently
every day or once a week

Operation
Cooling a Detector
8Nicolet iS20 User Guide Thermo Scientific
To verify the laser frequency
1. From the OMNIC software main screen, choose Collect > Experiment Setup.
2. Click Laser Verification on the Diagnostic tab.
3. As prompted, remove all accessories and samples from the instrument and then click OK.
4. Click Start Verification.
When the verification is completed, one of the following occurs:
• A message indicates the laser frequency has been verified. Click OK to finish.
• The newly measured laser frequency appears below the previously measured
frequency and a message indicates the laser frequency has been optimized. Click OK
to finish.
Cooling a Detector
If you have an MCT detector, you must cool it with liquid nitrogen before you can collect
data.
Time needed:
40 minutes or less
Tools needed:
• Protective clothing and eye wear
• A small plastic laboratory funnel
• A one-liter, metal vacuum bottle
•Liquidnitrogen
Note The laser is verified automatically each time you run a Performance
Verification (PV) test. We recommend running a PV test at least once a month.
Note
• A detector dewar should maintain its insulating vacuum for several years. If the
vacuum leaks, the insulation will lose effectiveness.

Operation
Cooling a Detector
Thermo Scientific Nicolet iS20 User Guide 9
1. Open the detector dewar cover and remove the plastic stopper from the dewar.
2. Fill the metal vacuum bottle with liquid nitrogen.
3. Insert the funnel into the detector dewar and pour the liquid nitrogen slowly into the
funnel. (A small amount of liquid nitrogen typically spills out of the funnel. This will not
harm your instrument.)
WARNING Avoid freeze burns. Liquid nitrogen is extremely cold and therefore potentially
hazardous.
• When you use liquid nitrogen, always follow standard laboratory safety practices, and
make sure your dewar is made to use with liquid nitrogen. Wear protective clothing
and eye wear, and avoid letting liquid nitrogen come into contact with your skin.
• Make sure you pour the liquid nitrogen slowly when you fill the vacuum bottle or the
detector dewar. Pouring too quickly can cause liquid nitrogen spray out. Wear
protective clothing and eye wear, and follow standard laboratory safety practices to
prevent injury.
NOTICE Do not spill liquid nitrogen on or near the detector window. If the
window’s O-ring seal is cooled very rapidly, the dewar may lose its vacuum and expose
the detector element to damaging atmospheric pressure.
iS20

Operation
Cooling a Detector
10 Nicolet iS20 User Guide Thermo Scientific
Fill the funnel and then let it drain completely two or three times. Wait until the vapor
plume disappears and then repeat until the dewar is filled.
4. Remove the funnel.
5. Wait until the vapor plume disappears, and then replace the plastic stopper and close the
dewar cover.
6. Wait 20 minutes, and then repeat the preceding steps to make sure the dewar is
completely filled.

Installing or Replacing Hardware
Installing a Purge Kit
Thermo Scientific Nicolet iS20 User Guide 11
Installing or Replacing Hardware
Installing a Purge Kit
Purging your instrument protects the internal components from moisture and other
environmental contaminants by maintaining an internal atmosphere of dry air or nitrogen. If
your instrument is not already equipped to purge, you must install a purge kit. To install a
purge kit, use the following procedure.
Time needed:
30 minutes or less
Tools needed:
• A 3/4 inch open-ended wrench
• An 11/16 inch open-ended wrench
• A shutoff valve (with a 1/4 inch male or 3/8 inch female fitting)
•Pipetape
1. Install a shutoff valve and either a 1/4 inch male fitting or a 3/8 inch female fitting on the
purge gas source. (Choose a shutoff valve and fittings that are appropriate for the purge
gas source.)
NOTICE We recommend that you maintain seal and desiccation and/or purge your
instrument at all times. Equipment damage due to failure to maintain seal and desiccation
and/or purge is not covered under the warranty. If you have questions about this
requirement, please contact us.
Note
• To order parts, contact us.
• For best results the purge gas should be dried to a dew point of -70 °C (-94 °F) or
below.
WARNING Never use a flammable gas to purge your instrument. The purge gas must be
free of moisture, oil, carbon dioxide and other reactive or infrared-absorbing materials. To
prevent laser damage, use only dried air or nitrogen to purge your instrument.

Installing or Replacing Hardware
Installing a Purge Kit
12 Nicolet iS20 User Guide Thermo Scientific
2. If you used a 1/4 inch male fitting, proceed to the next step.
If you used a 3/8 inch female fitting on the purge gas source, install the 3/8 inch to
1/4 inch reducing nipple that was included with your purge kit. Wrap the reducing
nipple with Teflon pipe tape before you install it, and use an 11/16 inch open-ended
wrench to tighten the connection.
3. Wrap the reducing nipple or the 1/4 inch male fitting with Teflon pipe tape, and then
install the pressure coupling. Use a 3/4 inch open-ended wrench to tighten the
connection.
4. Install the purge filter, pressure regulator and flow meter, and then snap the assembly into
the pressure coupling.

Installing or Replacing Hardware
Installing a Sample Compartment Extension Kit
Thermo Scientific Nicolet iS20 User Guide 13
5. Connect the purge kit to your instrument, set the purge gas controls, and then snap the
flow coupler into the back of the instrument.
Installing a Sample Compartment Extension Kit
Time needed:
10 minutes or less
Tools needed:
• 4-in1 tool (included with your instrument)
• A 5/32 inch hex wrench
1. Remove any Smart Accessory, and then disconnect any cables that are connected at the
back of the sample compartment.
2. Place the sample compartment extension on the front of the sample compartment.
Make sure the pins in the same compartment base fit into the holes in the sample
compartment extension.
Note To o r d e r p a r t s , c o n t a c t u s .

Installing or Replacing Hardware
Installing Baseplate-mounted Accessories
14 Nicolet iS20 User Guide Thermo Scientific
3. Place the screws that came with the sample compartment extension kit into the holes in
the sample compartment extension, and then use the 4-in1 tool with a Phillips bit
installed to tighten the screws. (The screws should be just finger-tight.)
4. Install the sample compartment cover.
You are now ready to install baseplate-mounted accessories.
Installing Baseplate-mounted Accessories
To install the standard sample compartment baseplate (or an accessory mounted on that
baseplate), first make sure the sample compartment extension kit is installed. Then orient the
baseplate with the finger hole toward the front and lower the baseplate into the sample
compartment. The baseplate fits over several alignment pins, which hold it in place.

Installing or Replacing Hardware
Installing Slide-mounted Accessories
Thermo Scientific Nicolet iS20 User Guide 15
Installing Slide-mounted Accessories
The Smart OMNI-Transmission accessory can be used to measure slide-mounting samples
and to install most slide-mounting accessories. If you don’t have the Smart
OMNI-Transmission accessory, the standard sample holder can accommodate slide-mounting
accessories (such as a variable angle ATR) as well as thin film samples and optical filters. To
install a slide-mounting sample or accessory, slide the sample or accessory into one pair of
slots in the standard sample holder.
Use the adjustment screw to position the sample vertically so that it is roughly centered in the
infrared beam.
Installing Other Accessories
Note The following procedure explains how to install accessories that are not Smart
accessories. This procedure applies only if a sample compartment extension kit has been
installed.
NOTICE Your accessory must be mounted on one of our baseplates. If it is not, you can
remove an accessory from one of our baseplates and install your accessory on that
baseplate, or visit our web site at www.thermo.com/spectroscopy for assistance.

Installing or Replacing Hardware
Replacing the Power Supply
16 Nicolet iS20 User Guide Thermo Scientific
1. Remove any Smart Accessory, or if a Smart Accessory is not installed, remove the
baseplate. Disconnect any cables that are connected at the back of the sample
compartment.
2. If the accessory is purged through the windows in the side of the sample compartment,
install sidewall adapters.
3. Install the accessory.
Use the instructions that came with the accessory to make any adjustments or perform
any alignment procedures that are necessary.
Replacing the Power Supply
Time needed:
5 minutes or less
Tools needed:
None
1. Turn off the instrument.
2. Disconnect the old power supply.
NOTICE Use only Thermo Scientific certified replacement parts. To order parts, contact
us.
WARNING
• To avoid a shock hazard, do not attempt to remove the cover of the power supply.
• Before you replace the power supply, always make sure you have turned off your
instrument and disconnected the power supply from the wall outlet or power strip.