Page 2 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.
Page 3: Table Of Contents
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...
Page 4 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...
Page 5 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...
Page 7: Welcome
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...
Page 8: About This Manual
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.
Page 9: Questions Or Concerns
If you have questions or concerns about safety or need or concerns 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...
Page 10: System Requirements
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 Thermo Electron Corporation...
Page 11: Installing Omnic
One additional PCI slot if you plan to use a microscope with video capability If you purchased your computer from Thermo Electron, your Installing OMNIC 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...
Page 12: Where To Find The Information You Need
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. Thermo Electron Corporation...
Page 13: On-Line Help
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.
Page 14 (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: Thermo Electron Corporation...
Page 15: Finding Answers To Your Questions
Finding answers Use the following sections to help you locate the information you need in the on-line and printed documentation. The on-line to your questions documentation is available in the Help menu of OMNIC. The basics How do I turn on the system? Spectrometer Tour (available through Getting Started)...
Page 16 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” Thermo Electron Corporation...
Page 17 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” Which beamsplitter and detector should I use? Collecting spectra Spectrometer Help Topics...
Page 18 “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.) Thermo Electron Corporation...
Page 19 “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...
Page 20: Before You Collect Spectra
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.
Page 21: Checking The Purge
Checking the purge If your spectrometer is purged but you don’t have the Smart Purge option, make sure the pressure regulator is set between 20 and 40 pounds per square inch (psi) and the flowmeter reads Skip this section if you purchased approximately 30 standard cubic feet per hour (scfh).
Page 22: Smart Purge Settings
* 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.
Page 23: Checking The Desiccant
Checking If your spectrometer is sealed and desiccated, a bag of desiccant is located under the beamsplitter compartment cover. The desiccant the desiccant protects the beamsplitter and other optical components by reducing the amount of water vapor inside spectrometer. See “Checking and changing desiccant”...
Page 24: Turning On The System Components
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. Thermo Electron Corporation...
Page 25: Cooling The Detector
After you turn on the spectrometer, let it stabilize for at least 15 minutes (one hour for best results) before collecting spectra. See “Turning on the spectrometer power” in the “Spectrometer Basics” chapter if you need more information. 4. Turn on the printer and then the computer. Turn on the printer and computer as explained in the documentation that came with those components.
Page 26: Starting Omnic
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. Thermo Electron Corporation...
Page 27: Selecting An Experiment
Selecting The parameter settings for collecting spectra are stored in experiment files. You load the settings you wish to use when you an experiment select an experiment from the Experiment drop-down list box below the OMNIC menu bar (see the example below). A number of experiments are included with OMNIC for performing a wide variety of data collections.
Page 28 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. Thermo Electron Corporation...
Page 29: Your First Experiment
Your First Experiment This chapter will get you started collecting spectra with your spectrometer and working with the data using OMNIC. You will learn how to do the following things: • Open a configuration. • Select an experiment. • Collect a sample spectrum. •...
Page 30: The Omnic Window
When a spectrum is displayed in a spectral window, you can use OMNIC commands to perform operations on it. For example, you can change the spectrum’s format or search it against a spectral library to identify it. Thermo Electron Corporation...
Page 31: Menu Bar
Menu bar Below the title bar is the menu bar, which contains all of the OMNIC menu names. (Depending on which optional software you purchased, the menu names in your menu bar may be somewhat different from those shown.) The menus are arranged in an order that you’ll find convenient as you use the software.
Page 32: Bench Status Indicator
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. Thermo Electron Corporation...
Page 33: Collecting A Sample Spectrum
Collecting a A sample spectrum is usually ratioed against a background spectrum. The background spectrum measures the response of the sample spectrum spectrometer without a sample in place. Dividing the sample spectrum by the background—called “ratioing”—removes the effects caused by the instrument and atmospheric conditions so that the peaks in the final spectrum are due solely to the sample.
Page 34: Installing The Standard Sample Holder
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. Thermo Electron Corporation...
Page 35 If your sample holder is not installed on a baseplate, use a flat-blade screwdriver and the slotted screws to attach the holder to a baseplate as shown below. Then install the baseplate in the sample compartment. If there is a sample in the holder, remove the sample.
Page 36: Collecting The Sample Spectrum
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. Thermo Electron Corporation...
Page 37 Select the Default - Transmission experiment by clicking it. A number of other experiments are provided with OMNIC for performing a wide variety of data collections. You can select these experiments by using the Open button in the Experiment Setup dialog box. After you have selected one of them the first time, the experiment will appear in the Experiment drop-down list for future selection.
Page 38 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. Thermo Electron Corporation...
Page 39 6. Look through the sliding door to make sure there is no sample in the sample holder and then press the OK/Enter button to start data collection. If there is a sample in the sample holder, remove it before pressing the button: If your spectrometer is purged but does not have the Smart Purge option...
Page 40 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. Thermo Electron Corporation...
Page 41 For more information about installing samples, view “Installing samples” in the Spectrometer Tour (available through Getting Started). As data are collected, the sample spectrum in the Collect Sample window is updated. Here is an example: The progress of the collection is indicated by the gauge below the spectrum.
Page 42 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). Thermo Electron Corporation...
Page 43: How Do I Know If My Spectrum Is Good
How do I know if The Collect Status indicator near the bottom of the Collect Sample window shows the status of the collection. When the indicator is a my spectrum is good? green check mark, it shows that the spectrum has passed all of the selected spectral quality checks made so far.
Page 44: Converting The Spectrum's Units
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. Thermo Electron Corporation...
Page 45 The spectrum is converted to % transmittance units: The Process menu allows you to convert spectra to several other units as well. These units are discussed in detail in the OMNIC on- line Help system. In OMNIC Help Topics find “converting spectrum”...
Page 46: Labeling A Peak With The Annotation Tool
Region Peak height Annotation Spectral cursor Peak area Selection 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. Thermo Electron Corporation...
Page 47 When you use a tool, the readout above the palette may display information for the tool operation, such as the X and Y values of the pointer location or the limits of the selected spectral region. Here is an example of X and Y values displayed in the readout when the selection tool is selected and the pointer is within the spectral display: Follow these steps to label a peak in the polystyrene spectrum:...
Page 48 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. Thermo Electron Corporation...
Page 49: Verifying The Composition Of The Sample
Verifying the You can verify the composition of your polystyrene sample by automatically comparing the collected spectrum with the spectra in a composition QC (Quality Control) library. The software compares the sample spectrum with reference spectra in the appropriate category in the of the sample library and then tells you whether the sample matches a library spectrum.
Page 50 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. Thermo Electron Corporation...
Page 51 The libraries listed in the QC Libraries And Groups box are the libraries with which your spectrum will be compared. 5. Add the Polystyrene Quality Control Sample library to the comparison list. To do this, click the appropriate library name in the Available QC Libraries And Groups box, and then click the Add button.
Page 52 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. Thermo Electron Corporation...
Page 53: Creating A User Library
Creating a OMNIC’s Library Creation Wizard makes it easy to create your own spectral libraries. Creating your own library lets you customize the user library information in the library depending on your needs. You set the library parameters (including the resolution and spectral range) and specify which checks and corrections to perform.
Page 54: Creating And Printing A Report
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. Thermo Electron Corporation...
Page 55 You can create your own report templates by using the Create button, or you can modify one of the existing templates whenever you want to design a new template. Save the template with a new name after you make your changes. In OMNIC Help Topics find “report template, selecting”...
Page 56 5. If you have a printer connected to the computer, choose Print to print the report. The Print dialog box appears allowing you to set some parameters that affect printing. 6. Choose OK. The report is printed on your system printer. Thermo Electron Corporation...
Page 57: Spectrometer Basics
Spectrometer Basics This chapter describes the major components of your Nicolet 4700 or Nicolet 6700 spectrometer, including the light source, beamsplitter and detector. It then explains what you will need to know before collecting data in various spectral ranges. In the Spectrometer Tour (available through Getting Started) view “From the front,”...
Page 58: Using The Data Collection Buttons
“How to cable an accessory” section of the “Accessories” chapter. Using the The buttons on the top of the spectrometer let you quickly perform some basic operations with the spectrometer without using your data collection buttons keyboard or mouse. (OMNIC must be running.) Thermo Electron Corporation...
Page 59 Press the Sample button to collect a sample spectrum. This has the same effect as choosing Collect Sample from the Collect menu. In OMNIC Help Topics find “spectrum” in the Index and go to “Collecting a sample spectrum” for more information. Press the Background button to collect a background.
Page 60: What's Inside
Source select optics (optional) Near-IR source (optional) Polarizer SabIR port Fixed mirror or optional Sample holder (optional) SeaPort optics In the Spectrometer Tour (available through Getting Started) view “Inside the spectrometer” for complete descriptions of your spectrometer components. Thermo Electron Corporation...
Page 61: What Is On The Rear Panel
What is on The rear panel includes a power connector, right-and left-side accessory connectors, computer connector (USB 2.0, not a hub), the rear panel? auxilliary signals connector, and purge gas input. You may also find optional Auxilliary and/or dual channel connectors on the rear panel. Danger Avoid shock hazard.
Page 62: Turning On The Spectrometer Power
Leaving the spectrometer on increases stability and consistency of performance. 4. Turn on the printer and then the computer. Thermo Electron Corporation...
Page 63 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.
Page 64: Using A Light Source
Using a light source The Nicolet 4700 comes with a single infrared light source. The Nicolet 6700 is available with a single internal source or with optional dual sources. If your spectrometer does not have the dual- source option, you will need to change sources in order to use a different internal source.
Page 65 Rest mode – Rest mode lowers the temperature of the source so that its life is extended. The source automatically shifts into Rest mode when the spectrometer moves into sleep mode. You can configure the source to enter Rest mode at specific times. When you resume data collection activity, the source automatically re-enters Normal mode.
Page 66: Using Beamsplitters And Detectors
Using A number of beamsplitters and detectors are available for use in the Nicolet 4700 and Nicolet 6700 spectrometers. You can change the beamsplitters detector type in either model, but the beamsplitter type can be changed only in the Nicolet 6700. Not all beamsplitters and detectors and detectors can be used together.
Page 67 BEAMSPLITTER Near-IR Mid-IR* Far-IR DETECTOR XT-KBr Solid Substrate Quartz DTGS Best Best (KBr window)** DTGS Best (Csl window) DTGS Best (PE window) MCT-A Best Best MCT-B Best Best Best InSb PbSe Best Best Best InGaAs Best Best = Optimum beamsplitter-detector combination. OK = Compatible beamsplitter-detector combination.
Page 68 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... Thermo Electron Corporation...
Page 69 Light Range Beamsplitter Detector Spectral Range (cm Source mid-IR DTGS-KBr 7,400 - 350 MCT-A ‡ 7,400 - 600 MCT-B ‡ 7,400 - 400 DTGS TEC 7,100 - 350 DTGS-CsI 6,400 - 350 DTGS-CsI 6,400 - 225 ¶ MCT-A ‡ 6,400 - 600 MCT-B ‡...
Page 70: Improving The Quality Of Your Spectral Data
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. Thermo Electron Corporation...
Page 71 Note The maximum intensity of a mid-IR single-beam spectrum is typically found near 2,000 cm Note If the distance from the baseline to 0 is greater than 20% of the spectrum’s maximum intensity value, your detector electronics may be overloaded. Contact technical support for assistance. The distorted signal may cause problems with photometric accuracy.
Page 72 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 DTGS MCT-A * These are nominal values that may vary due to diffraction and detector variations. Thermo Electron Corporation...
Page 73 To correct for photometric accuracy, you may need to add a “heavier” screen (one that transmits less infrared energy). With corrections for photometric accuracy you will notice some reduction in the signal-to- noise ratio but will obtain more reliable quantitative data. Generally, the signal-to-noise ratio is reduced less than is the signal intensity.
Page 74 Detector Aperture Setting DTGS MCT-A, MCT-B, InSb, PbSe, Si, InGaAs In OMNIC Help Topics find “aperture” in the Index and go to “Setting the aperture size” for information about changing the aperture setting. Thermo Electron Corporation...
Page 75 How to improve the If you primarily analyze qualitative data, you may wish to optimize the system for a better signal-to-noise ratio. This can be particularly signal-to-noise ratio important when you are working with scattering samples and samples that absorb more infrared energy. These samples produce smaller signals that can be “lost”...
Page 76: How To Collect Data In The Visible Spectral Range
(Only the Nicolet 6700 has an aperture.) Spectral Range Filter or Screen Aperture Gain 16,000 - 9,000 cm red filter 16,000 - 9,000 cm energy screen A 23,000 - 16,000 cm broad-band blue filter 26,000 - 21,000 cm narrow-band blue filter Thermo Electron Corporation...
Page 77: About The Moving Mirror Velocity
“Spectrometer Options” chapter for more information. While a wide range of moving mirror velocities are available on About the moving Nicolet 4700 and Nicolet 6700 spectrometers, some velocity settings mirror velocity cannot be used for collecting data at certain combinations of spectral...
Page 78: Spectrometer Options
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. Thermo Electron Corporation...
Page 79 The accessory has two wheels: wheel A is closest to the source. Each wheel can be moved to one of four positions. Both wheel A and wheel B have an open position for collecting spectra without a filter in the beam path. Positions 1, 2 and 3 are available for filters that you provide.
Page 80 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). Thermo Electron Corporation...
Page 81: Using The Energy Screen Wheel
In OMNIC Help Topics find “filter wheel” in the Index and go to “Controlling the filter wheel” for more detailed instructions. The optional energy screen wheel lets you automatically insert an Using the energy screen into the beam path to block out a portion of the energy energy screen wheel at all frequencies of the infrared beam.
Page 82 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. Thermo Electron Corporation...
Page 83 A 1% screen also is shipped with the wheel. Contact technical support if you wish to use this or other screens that you provide in the wheel. If you use the 1% screen or one of your own, be sure to change the description of the screen position on the Configure tab.
Page 84: Using The Internal 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. Thermo Electron Corporation...
Page 85 To set the polarization angle, type any number from 0 to 180 in the Polarizer Angle text box on the Bench tab of the Experiment Setup dialog box (available through Experiment Setup in the Collect menu). Use the up and down arrows to step the polarizer one degree at a time to optimize your signal.
Page 86 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. Thermo Electron Corporation...
Page 87: Accessories
Accessories This chapter briefly describes the types of sampling and system accessories that are available for your spectrometer. Complete descriptions and operating instructions are included with the accessories. Smart Accessories In addition to traditional accessories, a variety of Smart Accessories are available for your spectrometer.
Page 88 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. Thermo Electron Corporation...
Page 89 Smart Mid-IR FiberPort – This high-throughput accessory lets you analyze liquids remotely. The needle probe can reach “hard to get” samples, such as liquids in micro containers, hazardous environments or remote locations. The FiberPort is a unique optical interface that transfers IR energy from the spectrometer to the fiber optic cables and probes.
Page 90 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. Thermo Electron Corporation...
Page 91: Other Sampling Accessories For Different Applications
Additional Snap-In sample compartment baseplates are available for use with each accessory to make changing accessories easier. Call Thermo Electron if you are interested in ordering any of the following sampling accessories. Absolute transmission accessory – This accessory allows for the measurement of absolute transmission of samples with reflective surfaces.
Page 92 See “Using the filter wheel” in the “Spectrometer Options” chapter for complete information. Thermo Electron Corporation...
Page 93 Foundation Series – The innovative modular design of this accessory family provides access to several sampling devices using a common base. This allows experimental flexibility and an economical price. Available techniques include ATR, diffuse reflection, specular reflection, transmission and fiber optics. Gas cells –...
Page 94 Nicolet Centaurµs and Nicolet Continuµm infrared microscopes – Thermo Electron offers microscopes that attach directly to the side of the spectrometer. Microscopes can be installed between the spectrometer and other accessory modules. The microscopes provide fast, nondestructive microanalysis with minimal sample preparation and alignment.
Page 95 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...
Page 96: System Accessories
National Institute of Standards and Technology (NIST). An optional calibrated sample from the National Physical Laboratory (NPL) is also available. Some system accessories are installed by Thermo Electron. Call us if System accessories you are interested in ordering any of the following accessories.
Page 97: How To Cable An Accessory
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.
Page 98 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. Thermo Electron Corporation...
Page 99 Connectors on the The illustration below shows the optional connectors on the front of the spectrometer that you can use to pass signals to and from the front of the spectrometer sample compartment. Note These connectors are available only on systems that do not include the SabIR accessory or the microplate accessory.
Page 100 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.
Page 101: Detector/Motors Connector
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.
Page 102 Used for sample compartment digital communication. Used by the sample shuttle motor (positive). Positive 12 volts. Analog ground. Used by the sample compartment detector for positive analog input. Negative 12 volts analog. Used by the sample compartment detector for digital communication. Thermo Electron Corporation...
Page 103: Quick Answers To Your Questions About Using Omnic
Quick Answers to Your Questions About Using OMNIC 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.
Page 104 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.” Thermo Electron Corporation...
Page 105 What does gain do? Gain amplifies the detector signal intensity, making it larger relative to the level of electronic noise. This is helpful when the signal is weak, such as when you use some sampling accessories. You can let OMNIC automatically adjust the gain to maximize the signal by setting the Gain parameter to Autogain.
Page 106 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.” Thermo Electron Corporation...
Page 107: Converting Spectra To Other Units
Converting Which Y-axis unit should I use for a spectrum? spectra to other units The most commonly used units are % transmittance and absorbance. Use % transmittance if you plan to compare the spectrum visually with published reference spectra. Use absorbance units for quantitative analysis measurements.
Page 108: Using Spectral Libraries
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.) Thermo Electron Corporation...
Page 109 In OMNIC Help Topics find “spectral region” in the Index and go to “Region tool” or “View finder.” • If you collected the spectrum using specular or diffuse reflection, use Kramers-Kronig (dispersion) correction (available through Other Corrections in the Process menu) to correct it for dispersion effects and then search it against a library of absorbance spectra.
Page 110 Add To Window button, or go to the Library Spectra tab of Library Manager, display the desired spectrum on the tab and then double- click the spectrum. In OMNIC Help Topics find “library” in the Index and go to “Working with libraries.” Thermo Electron Corporation...
Page 111 How can I find a compound in a commercial library? If you are using OMNIC, Library Manager in the Analyze menu lets you search for the compound name. After you select the library on the Library Names tab, use the features on the Search For Text tab to locate the spectrum.
Page 112: Opening, Saving And Deleting Spectra
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” Thermo Electron Corporation...
Page 113 In OMNIC Help Topics find “saving, spectra” in the Index and go to “File handling.” Where should I save my spectra? 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.
Page 114 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.” Thermo Electron Corporation...
Page 115: Printing
Can I delete an entry from a report notebook? No. OMNIC’s report notebooks are similar to traditional laboratory notebooks in that information you add to them becomes part of the permanent record of your work. You can delete an entire notebook, however, by deleting the entire notebook file.
Page 116: Displaying Spectra
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.” Thermo Electron Corporation...
Page 117 How can I specify colors for displaying spectra? Choose Options from the Edit menu, click the View tab and then choose Colors. In the Colors dialog box click the color next to the spectrum number for which you want to specify the color and then click the desired color in the color array.
Page 118 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.” Thermo Electron Corporation...
Page 119 For information about Common Scale, find “spectra” and go to “Displaying spectra using the same Y-axis.” For information about Match Scale, find “spectra” and go to “Matching the Y scale of a spectrum.” For information about Offset Scale, find “spectra” and go to “Displaying spectra vertically offset.”...
Page 120 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.” Thermo Electron Corporation...
Page 121 How can I find the X and Y values of a point in a spectrum? Use the spectral cursor tool to click the point. The values are displayed in the readout above the palette. In OMNIC Help Topics find “X and Y values” in the Index and go to “Spectral cursor tool.”...
Page 122: Correcting Spectra
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. Thermo Electron Corporation...
Page 123 Choose Subtract from the Process menu. The difference spectrum is displayed full scale in the bottom pane. This spectrum is the result of subtracting the reference spectrum from the sample spectrum using the subtraction factor shown to the left of the result. If you are not satisfied with the subtraction result, you can change the subtraction factor.
Page 124 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.” Thermo Electron Corporation...
Page 125: Customizing Omnic
Customizing OMNIC How can I customize my OMNIC software? You can use Options in the Edit menu to set options that determine how the software operates. You can also customize the menus and the toolbar using Edit Menu and Edit Toolbar in the Edit menu. Use Save Configuration As in the File menu to save your customized settings in a configuration file.
Page 126: Other Questions
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.” Thermo Electron Corporation...
Page 127 How can I display information about how a spectrum was collected and processed? Select the spectrum and then click the Information button to the left of the title box. You can also double-click the spectrum’s title in the title box. In OMNIC Help Topics find “collection and processing information”...
Page 128 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. Thermo Electron Corporation...
Page 129: Quick Answers To Your Questions About Using The Spectrometer
Quick Answers to Your Questions About Using the Spectrometer 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...
Page 130 • 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. Thermo Electron Corporation...
Page 131 • You have just installed a laser, source, beamsplitter or detector. • The detector signal intensity has dropped significantly from its usual level. • You have just moved the spectrometer. In OMNIC Help Topics find “aligning, spectrometer” in the Index and go to “Aligning the spectrometer.”...
Page 132 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.”...
Page 133 Should I turn off the spectrometer when I’m not using We recommend that you leave the spectrometer on. This improves the thermal stability of the system and gives you more consistent results when you collect spectra. How can I diagnose problems with the spectrometer? The performance of the spectrometer is monitored while you collect spectra.
Page 134: Maintenance And Service
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.
Page 135: Running Diagnostic Tests On Spectrometer Components
Running If your system is not performing properly, you can use the Diagnostic tab in the Experiment Setup dialog box to check the diagnostic tests performance of spectrometer components and determine the source of the problem. on spectrometer components 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.
Page 136: Maintaining Your Spectrometer
“When should I align my spectrometer” in the preceding chapter for more information. If you have just turned on or moved the spectrometer, wait Note 15 minutes (one hour for best results) before you align it so that it will have time to stabilize. Thermo Electron Corporation...
Page 137 To align the spectrometer: 1. Remove any sample or accessory from the sample compartment (except a transmission sample holder). The beam path must be clear during alignment. Open the sample compartment as briefly as possible to maintain a constant purge. 2.
Page 138: Aligning An Accessory
“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. Thermo Electron Corporation...
Page 139 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. If special performance tests are available for your spectrometer, a button labeled “Extended Tests”...
Page 140: Servicing Your Spectrometer
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.
Page 141: Troubleshooting Software Problems
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.
Page 142 Use the Add Directory button on the Search previous version of directories listed in the dialog Libraries tab to add the directory. OMNIC are not listed box (typically LIBS within the in the Library Setup OMNIC directory). dialog box. Thermo Electron Corporation...
Page 143: Troubleshooting Hardware Problems
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.
Page 144 The laser is not functioning. 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”...
Page 145 Problem Possible Cause Solution The baseline is not The purge flow rate is too high. Lower the flow rate until the stable. baseline is stable. The spectrometer is out of Align the spectrometer using the alignment. Align button on the Diagnostic tab of the Experiment Setup dialog box.
Page 146 The power cable or power Replace the power cord. If the supply is defective. problem persists, replace the power supply. In Spectrometer Help Topics see “Changing the power supply in the “Replacing parts” book. Thermo Electron Corporation...
Page 147 Laser is flickering. Click laser indicator on Diagnostic tab of Experiment Setup dialog box to check laser operation. Call Thermo Electron for assistance. The system scans The spectrometer is out of Align the spectrometer using the normally but gives very alignment.
Page 148 See the instructions that came with the accessory. Detector and beamsplitter are not compatible. Make sure that selected detector and beamsplitter are compatible. Change detector or beamsplitter if necessary. Thermo Electron Corporation...
Page 149 Diagnostic tab of the Experiment Setup dialog box. For a Nicolet 6700 , replace the beamsplitter, if necessary. For a Nicolet 4700 , contact technical The spectrometer is out of support. alignment. Align the spectrometer using the...
Page 150 Experiment Setup dialog box. GC interface or microscope. The detector cable is loose at Check and tighten the cables. the accessory connector (on the rear of the spectrometer or on the back wall of the sample compartment). Thermo Electron Corporation...
Page 151 The laser is flickering. Click the laser indicator on the Diagnostic tab of the Experiment Setup dialog box to check the laser operation. Call Thermo Electron for assistance. The laser is off. Turn off the spectrometer power, unplug the power cord, remove the spectrometer cover and make sure the laser cable is seated properly.
Page 152 A component has failed. Call Thermo Electron for service. The beamsplitter is not properly For a Nicolet 6700 , check the seated. beamsplitter and reposition it if necessary. For a Nicolet 4700, call Thermo Electron for service. Thermo Electron Corporation...
Page 153 Align the spectrometer. If the located at 1024 ± 16 data points interferogram is still not located on the Bench tab of the correctly, call Thermo Electron for Experiment Setup dialog box. service. The beam path is obstructed. Remove the obstruction.
Page 154: Performing Advanced Diagnostic Tests
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. Thermo Electron Corporation...
Page 155 3. Follow the directions that appear on the screen to run the diagnostic tests. When you are finished viewing information in a window, you can use the navigation buttons to return to earlier windows. Click this button to return to the previous window: 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.
Page 156: Troubleshooting Applications Problems
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”...
Page 157 Replace the air dryer with one that but the air dryer does not removes carbon dioxide, or use remove carbon dioxide. nitrogen to purge the spectrometer. Contact Thermo Electron for more information. A spectrum contains The desiccant cannot absorb Check the humidity indicator and water peaks that interfere any more water vapor.
Page 158 Corrections in the Process menu. a specular reflection (Select Kramers-Kronig.) component. The infrared beam was Try using a less reflective sample. reflected from (instead of penetrating) a flat, shiny sample measured using a specular reflection accessory. Thermo Electron Corporation...
Page 159 Problem Possible Cause Solution The baseline of the The KBr pellet was made with Be sure to press the pellet properly. spectrum is not flat. coarsely ground KBr powder, or the KBr pellet was improperly pressed. The background spectrum for Remove the sample holder and collect a cast film was collected with the background again.
Page 160 Experiment Setup dialog box to a lower value. The sample in an ATR Reapply the sample to obtain more experiment is not in good consistent contact between the sample contact with the ATR crystal. and the ATR crystal. Thermo Electron Corporation...
Page 161: Index
Index absolute transmission accessory........85 Background button............53 absorbance units ............38 background spectrum accessories..............81 collected with sample holder in beam....153 aligning ............... 132 collecting ............32, 53 automated sample handling........85 defined ..............27 available ..............12 too old ..............151 cabling..............91 when to collect............27 descriptions ............
Page 162 ............ 131 identifying with subtraction......... 117 silicon..............70 cooled detector spectral range ............62 aperture size for ............. 67 types ..............60 cooling detector ............ 19, 125 using filter to reduce energy reaching....64 Thermo Electron Corporation...
Page 163 detector, continued… velocity too high for..........154 fax number ..............3, 7 which to use ............11 fiber optic accessory ..........83, 88 detector interface kit............. 86 filename for saving spectrum........37 Detector/Motors connector........... 95 filter dewar bandwidth-limiting ..........65 leaking..............144 for collecting data in visible spectral range ...70 diagnostics............
Page 164 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 Thermo Electron Corporation...
Page 165 mirror velocity.............. 71 parts moving ordering..............7 spectrum in pane ..........114 replacing ..............7 spectrum to another window ....... 114 pass-through connectors .........91, 94 stacked spectrum ..........114 pinouts ..............94 moving mirror password ...............20 velocity limitations..........71 pasting spectrum ............121 peak area...............115 height ..............115 Nicolet Centaurµs............
Page 166 ........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 Thermo Electron Corporation...
Page 167 saving source................58 configuration ............119 burned out ............144 interferograms ............99 external ..............59 spectra ..............107 glowing unevenly ..........143 spectra as group........... 108 installing ..............11 spectra automatically........... 106 not working............147 spectrum ..............37 replacing ..............134 Scan indicator..........18, 56, 145 which to use ............126 flashing intermittantly .........
Page 168 137 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 Thermo Electron Corporation...
Page 169 tutorials................6 Getting Started ............1 water vapor ..............151 service and repair ............ 7 removing peaks due to .........103 spectrometer tour............. 6 wavelength precision ............64 wavenumber accuracy...........67 web site ...............3, 7 uninterruptable power supply........91 Window options............111 units ................98 Windows metafile ............121 used for spectrum ..........
Page 170 Thermo Electron Corporation...

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