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Thermo Electron Nicolet 380 User Manual Download Page 7

 

 Welcome! 

Congratulations on your purchase of a Nicolet™ 380 spectrometer 
from Thermo Electron! The Nicolet spectrometer system integrates 
advanced hardware features with the power and flexibility of 
Thermo Electron’s OMNIC™ or EZ OMNIC spectroscopy 
software.

*

 

 

 

 

 

If you have not used the spectrometer before, view the “Spectrometer 
Tour” and “Getting Started With OMNIC” tutorials available through 
Getting Started in the OMNIC Help menu. 

                                                 

*

 See the documentation that came with your spectrometer if your system is 

controlled with a dedicated application software package, such as Integra™ for 
liquid analysis or ECO™ for semiconductor wafer analysis. 

Nicolet 380 User’s Guide 

1

Summary of Contents for Nicolet 380

Page 1: ......

Page 2: ... 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 Technical Support Thermo Electron Corporation 5225 Verona Road M...

Page 3: ...he desiccant 16 Turning on components 17 Starting OMNIC 19 Stand by and rest modes 20 Installing a standard sample holder 21 Collecting a spectrum 22 How do I know if my spectrum is good 30 Saving the spectrum 31 Software Basics 32 The OMNIC window 32 Spectral window 33 Menu bar 33 Experiment drop down list box 33 Bench Status indicator 34 Toolbar 34 Selecting an experiment 35 Collecting a backgro...

Page 4: ... 47 Creating and printing a report 47 Spectrometer Basics 50 Major components 50 What s inside 51 What is on the rear panel 52 More About The Spectrometer 53 Sources detectors and beamsplitters 53 Improving the quality of spectral data 54 Improving the signal to noise ratio 55 Improving linearity and photometric accuracy 55 Using energy screens 57 About the moving mirror velocity 58 DC operation 5...

Page 5: ...About Using the Spectrometer 90 Maintenance and Service 94 Upgrading the computer recovering from viral attacks and reinstalling software 94 Running diagnostic tests 97 Basic diagnostics 97 Advanced diagnostics 98 Maintaining the spectrometer 99 Aligning the spectrometer 99 Aligning an accessory 101 Checking spectrometer performance 101 Checking purge 103 Servicing the spectrometer 104 Troubleshoo...

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Page 7: ...MNIC spectroscopy software If you have not used the spectrometer before view the Spectrometer Tour and Getting Started With OMNIC tutorials available through Getting Started in the OMNIC Help menu See the documentation that came with your spectrometer if your system is controlled with a dedicated application software package such as Integra for liquid analysis or ECO for semiconductor wafer analys...

Page 8: ...d process FT IR spectra after the spectrometer is installed Included is information on using the OMNIC software as well as chapters on how to operate maintain and service the spectrometer Depending on the model spectrometer you purchased the instrument may be operating under OMNIC EZ OMNIC or both spectroscopy software packages In this manual we refer to commands features and procedures that are u...

Page 9: ...information Important Follow instructions labeled Important to avoid damaging the system hardware or losing data 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 Warning Indicates a potentially hazardous situation which if not avoided could result in death or serious injury Danger I...

Page 10: ...in the next sections Wizards and tutorials The following wizards and tutorials are available on the system Unless otherwise noted all are accessible using the OMNIC Help menu Nicolet Installation Wizard This wizard starts automatically the first time you start OMNIC and walks you step by step through installing the spectrometer testing communications between the computer and the spectrometer align...

Page 11: ...sktop Getting Started With OMNIC Getting started with OMNIC introduces you to basic software operation It includes 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 The notebook and report features are not available in EZ OMNIC Nicolet 380 U...

Page 12: ...Spectrometer Tour When you finish this tutorial you will be familiar with the major components in the spectrometer Thermo Electron Corporation 6 ...

Page 13: ... 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 Learning OMNIC The learning OMNIC help menu item gives you access to tutorials that explain how to use OMNIC to collect spectra and perform a number of other software operations Nicolet 380...

Page 14: ...ional hardware changing replaceable parts maintaining the spectrometer and setting up the system for a variety of experiments If you ever have a problem with the spectrometer use this tutorial to access troubleshooting information and get part number and ordering information Thermo Electron Corporation 8 ...

Page 15: ...one and fax numbers as well as e mail and web site addresses Library Creation Wizard 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 or choose Create Library from the Analyze menu of EZ OMNIC Nicolet 380 User s Guide 9 ...

Page 16: ...n line Help system lets you quickly find answers to your questions about using the software If a dialog box or window contains a Help button click it to see information about the dialog box or window Thermo Electron Corporation 10 ...

Page 17: ...he F1 function key to see a discussion topic for the currently displayed or selected feature dialog box or window If you are using EZ OMNIC The EZ OMNIC version of OMNIC includes the features you need to perform common spectroscopy tasks If you are using EZ OMNIC some of the features described in this manual are not available Read and follow the instructions for the features that are in your softw...

Page 18: ... If you select Use Correlation Search the correlation search algorithm is used for the search and the search is performed over the full spectral range For more information about the search expert find search expert in the OMNIC Help system Index and go to the Specifying the search results topic Create Library command A special command called Create Library appears in the Analyze menu to allow you ...

Page 19: ...at all times 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 Note If you have a dedicated system such as a Liquid Analysis System that normally uses a software package other than OMNIC or EZ OMNIC skip this chapter In this first experiment you will Power on the spectrometer Select an experiment Colle...

Page 20: ...hecking purge If the spectrometer is purged make sure the pressure regulator is set between 10 and 20 psig and the flowmeter reads approximately 15 scfh The settings for systems equipped with Smart Purge are given in the next section read this section first Important Flow rates greater than 15 scfh cause vibrations that can affect data quality Thermo Electron recommends keeping the flow rate at ap...

Page 21: ...s to protect the beamsplitter and other optical components from being damaged by exposure to water vapor and other airborne contaminants Spectrometer Help Topics contains step by step information about installing purge equipment and setting the controls for the first time It also contains information about inspecting and replacing the purge filter The Spectrometer Tour available through Getting St...

Page 22: ...licking the Check Desiccant button on the Diagnostic tab of the Experiment Setup dialog box If the level exceeds the factory specified limit a message informs you Be sure to change the desiccant so that the optics will be protected If the spectrometer is in storage check the round blue indicator on the desiccant holder under the beamsplitter compartment cover monthly Change the desiccant if the in...

Page 23: ...t came with the accessories 2 Turn on the computer and printer Follow the instructions that came with these components Warning Always follow the safety precautions in this manual and in the Spectrometer Safety Guide that came with the system whenever you use the spectrometer 3 Turn on the spectrometer by pressing the power switch labeled I O to the on position Important Never block the cooling ven...

Page 24: ...ur for best results before collecting spectra 4 Observe the status indicators Power and Scan flash in various sequences as the system runs through its diagnostic routines When the routines are finished the Power indicator stays lit You can start the spectroscopy software OMNIC EZ OMNIC or other Thermo Electron software as soon as the diagnostic routines finish Scan indicator Power indicator Thermo...

Page 25: ...OMNIC shortcut on the Windows desktop Alternatively you can click the Start button on the Windows taskbar point to Programs All Programs in Windows XP point to the Thermo Nicolet folder and then click OMNIC or EZ OMNIC Depending on how the program has been configured dialog boxes may appear asking for a user name and password Type the requested information and then choose OK The OMNIC window appea...

Page 26: ...nterferometer stops scanning the spectrometer enters rest mode and the Scan indicator glows continuously Any data collection activity causes the interferometer to begin scanning If the Power indicator flashes or does not light or if the Scan indicator does not light the Bench Status indicator in OMNIC displays a red X and troubleshooting tips appear on the screen If you cannot resolve the problem ...

Page 27: ... Height adjustment screw Accessory support Sample holder If you are using separate Snap In sample compartment baseplates for different accessories and sample holders you can quickly switch baseplates to install the sample holder For information about using Snap In baseplates view Removing the Snap In baseplate in Spectrometer Help Topics Nicolet 380 User s Guide 21 ...

Page 28: ... the support before installing the sample or filter see the first illustration in this section Replace the support when you are finished using the slot Do not discard the support it is needed for installing slide mounted accessories Collecting a spectrum In the data collection procedure that follows you will select an experiment and then collect a background spectrum and a polystyrene sample spect...

Page 29: ... Transmission E S P experiment First click the arrow button at the right end of the Experiment drop down list box to display a list of available experiments The Default Transmission experiment appears in the list Select the experiment by clicking its name in the list The parameters in the Experiment Setup dialog box are now set correctly for collecting a polystyrene sample spectrum These parameter...

Page 30: ...an alternative you could click the Collect Sample button in the OMNIC toolbar or select Collect Sample from the Collect menu The Collect Sample window appears and then a dialog box showing the default title for the sample spectrum Thermo Electron Corporation 24 ...

Page 31: ...ound be collected before every sample a message appears asking you to prepare to collect a background spectrum For a transmission experiment this means that you need to remove any accessories other than a standard sample holder and samples from the sample compartment as explained in the next steps A sample might be installed in the transmission sample holder Nicolet 380 User s Guide 25 ...

Page 32: ...is installed in the sample holder or Smart Accessory clips slide the sample out of the holder and remove it from the sample compartment and close the cover If the spectrometer purged allow 1 minute for the purge to reach equilibrium before going to the next step If you find that carbon dioxide and water vapor interfere with spectra you collect in the future wait 3 to 5 minutes Thermo Electron Corp...

Page 33: ...lected When all the data have been collected a message appears asking you to prepare to collect the sample spectrum 9 Install the thin film polystyrene sample labeled Secondary Polystyrene Standard 1 5 mil Polystyrene through the sliding door If the spectrometer purged allow 1 minute for the purge to reach equilibrium before continuing to the next step Nicolet 380 User s Guide 27 ...

Page 34: ...or choose OK to start collecting the sample data As data are collected the sample spectrum in the Collect Sample window is updated The progress of the collection is indicated by the gauge below the spectrum The number of scans collected so far and the total number of scans for the collection are displayed to the right of the gauge Thermo Electron Corporation 28 ...

Page 35: ...ral window automatically 11 Choose Yes to add the sample spectrum to the spectral window Choosing No would end the procedure without saving the spectrum Choosing More Scans would return you to the Collect Sample window allowing you to collect more scans with the More button Choosing View Collect Status would display information about the collection including any problems that occurred Here is an e...

Page 36: ...n add the spectrum to a spectral window if it is not added automatically If you ever have a problem with data collection while one or more quality checks are turned on the Collect Status indicator may change If the indicator is a yellow circle the spectrum has failed a spectral quality check a measured value was not within the allowed range but it is not serious enough to stop the collection If th...

Page 37: ...ath Use Save As when you want to save a spectrum using a new filename or path 1 Select the polystyrene spectrum by clicking it 2 Choose Save As from the File menu The Save As dialog box appears 3 Type a descriptive name such as POLY SPA following the directory path in the File Name box C My Documents OMNIC Spectra POLY SPA The text can be either upper or lower case The default directory path for s...

Page 38: ...is and report records The sections that follow provide more information about the OMNIC spectroscopy software package If you are using a different package see the documentation that accompanied that package The OMNIC window The large window that appears on the screen when you start OMNIC is called the OMNIC window Thermo Electron Corporation 32 ...

Page 39: ...order that you ll find convenient as you use the software All of the menu commands are explained in detail in the on line tutorials or the OMNIC Help system Experiment drop down list box Below the menu bar is the Experiment drop down list box It lists all of the experiment files you have opened plus the default experiment file and an experiment file for any Smart Accessory m odule yo u m odule yo ...

Page 40: ...nd allowing you to access information on correcting it Toolbar At the left side of the window is the toolbar You can use Edit Toolbar in the Edit menu to position the toolbar at the top or right side of the OMNIC window as well In EZ OMNIC the default toolbar location is at the top Each button in the toolbar represents the action taken by a corresponding command or other feature To see the name of...

Page 41: ...s selected automatically or a list of appropriate experiments is made available for your selection If you want to check or change the parameters after selecting an experiment use Experiment Setup in the Collect menu To learn more view the Collecting a Spectrum tutorial available through Learning OMNIC in the Help menu If you need to change the source or detector see Spectrometer Help Topics for st...

Page 42: ...um for a transmission experiment make sure the sample compartment is empty except for the transmission sample holder if you are using it You can initiate background data collection at any time by using the Collect Background button or Collect Background in the Collect menu If you are using separate Snap In sample compartment baseplates for different accessories and sample holders you can quickly s...

Page 43: ...pectra you collect are in absorbance units or transmittance units Sometimes it is useful to convert a collected spectrum to other Y axis units In this example you will convert the units of the spectrum you collected in the preceding chapter 1 Select the spectrum by clicking it 2 If the spectrum is in absorbance click the Transmittance button on the toolbar If the spectrum is in transmittance click...

Page 44: ...several other units as well In OMNIC Help Topics find converting spectrum in the Index and go to the topic that deals with the units you are interested in Before going to the next section convert the spectrum to absorbance so that it is ready for you to learn how to label a peak Thermo Electron Corporation 38 ...

Page 45: ...h as the X and Y values of the pointer location or the limits of the selected spectral region Annotating spectra Follow these steps to use the annotation tool to label a peak in the polystyrene spectrum Once you have labeled a peak you will understand how to use the annotation tool to record information you wish to save with the spectra 1 Select the annotation tool by clicking it The annotation to...

Page 46: ... You could also perform other operations on the label using the annotation tool To modify a newly created label edit the selected text before pressing Enter To modify an existing label click it and then type a new label and press Enter To delete an existing label click it and then press the Delete key In OMNIC Help Topics find tool annotation in the Index and go to Annotation tool for more informa...

Page 47: ...crapbook libraries not available in EZ OMNIC Spectral searching Search libraries are most often used to identify an unknown spectrum If you are unsure of the composition of a sample you can perform a spectral search using a search library We recommend using the search expert if available in your version of OMNIC to determine how to perform a spectral search and the kinds of search results to displ...

Page 48: ...r your samples The software compares your sample spectrum with the reference spectra in each compound type and reports the best match from each type QC comparisons are also useful for detecting minute differences in spectra If you need to detect small changes in the parts per million range in your samples or identify samples that are spectroscopically very similar you could create a QC library wit...

Page 49: ...rary Setup from the Analyze menu The Library Setup dialog box appears with the Search Libraries tab displayed The Library Directories box lists the directories that are currently being used for spectral searches and QC comparisons All the libraries in the listed directories are available for the QC comparison Nicolet 380 User s Guide 43 ...

Page 50: ...rectory to the list choose Add Directory In the dialog box that appears locate and select the LIBS directory and then choose OK 4 Click the QC Libraries tab to display the available QC libraries The available QC libraries appear in the Available QC Libraries And Groups box The libraries listed in the QC Libraries And Groups box are the libraries with which the spectrum will be compared Thermo Elec...

Page 51: ...e Library Setup dialog box and begin a QC comparison at any time by choosing QC Compare from the Analyze menu When you begin a comparison the QC Compare window appears At the bottom of the window a gauge shows the progress of the comparison When the comparison is finished the sample spectrum and the library spectrum that best matches it are displayed in panes in the upper portion of the window Com...

Page 52: ...library for text topic for more information OMNIC s Library Manager available in the Analyze menu gives you the ability to view the spectra and related information contained in commercial and user libraries of spectra Note Library Manager is not available in EZ OMNIC Use View Library in the Analyze menu instead to view library information Creating a user library OMNIC s Library Creation Wizard mak...

Page 53: ...cannot add spectra to a commercial library nor can you move copies of commercially collected reference spectra into libraries you create In OMNIC Help Topics find adding spectrum to user library in the Index and go to the Adding a spectrum to a user library topic or the Adding user library spectra to another user library topic for more information Creating and printing a report OMNIC makes it easy...

Page 54: ...scription option This lets you identify items that are too small to be seen clearly 3 Choose Select to make the example template the current template for printing reports When you print the report OMNIC will automatically fill in the items in the template with the appropriate information and images For example if an item in the template is linked to the active spectral window the contents of that ...

Page 55: ...his Collection time You can click the Zoom button to see an enlarged image of the report The preview lets you check the content of the report before printing it 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 Nicolet 380 User s Guide 49 ...

Page 56: ... View the Spectrometer Tour tutorial available through Getting Started in the OMNIC Help menu for more information about the internal and external components Major components The following illustrations show spectrometer from the front with different options installed Status indicators Humidity indicator Desiccant access cover co Detector fill port optional Sample compartment sliding door Sample c...

Page 57: ...ayout of the spectrometer with covers removed to reveal components Electronics module Interferometer Detector mirror Validation wheel optional Sample mirror A e Optional source Sample compartment Beam path Detector Source Automated aperture Laser utomated xternal beam mirror optional Source mirror Nicolet 380 User s Guide 51 ...

Page 58: ...panel Cooling vents Power supply ies Auxiliary signals Purge fitting Accessor Computer 50 40 30 20 10 50 40 30 20 10 50 40 30 20 10 50 40 30 20 10 See the Spectrometer Tour tutorial for complete descriptions of the components on the rear panel Important Never block the cooling vents 50 40 30 20 10 50 40 30 20 10 50 40 30 20 10 50 40 30 20 10 The electronics module inside the spectrometer could ove...

Page 59: ...ion Even after the spectrometer is turned off the external housing of the source remains hot for up to 15 minutes To avoid being burned by a currently installed source allow enough time for it to cool before handling it For more information about using different sources find source in the Index of OMNIC Help Topics and go to the Specifying the source type topic If you need to install an energy scr...

Page 60: ...at the spectra you collect have high wavelength precision This means that the frequency axis X axis location of peaks in a spectrum is consistently reproducible and within IUPAC International Union of Pure and Applied Chemistry published specifications You must also be certain that the spectrometer responds linearly to the samples you are studying This means that absorption band intensity is direc...

Page 61: ...r the resulting spectrum might be distorted and accuracy and stability could be reduced This is more likely to occur with an MCT detector than with a DTGS detector which generally does not require the use of an energy screen See the next section for more about this View Energy screens in the Installing new hardware book in Spectrometer Help Topics for instructions on installing an energy screen Im...

Page 62: ...ubstantial difference in their sizes photometric accuracy could be a problem In some cases system performance improves if you use a bandwidth limiting filter or energy screen Filters improve the signal to noise ratio of the data and also prevent detector saturation by allowing only energy in your particular area of interest to pass to the detector element Energy screens help prevent detector satur...

Page 63: ...of the infrared energy that each screen passes It also lists the detectors typically used with each screen as a starting point for correcting linearity problems Screen Transmitted Detectors Typically Used With Screen None 100 DTGS A 30 MCT A B 10 C 3 D 1 These are nominal values that may vary due to diffraction and detector variations To correct for photometric accuracy you may need to add a heavi...

Page 64: ... the Bench tab For DTGS detectors set Velocity to 0 63 or lower if you are analyzing a low throughput sample Higher velocities decrease the detector s sensitivity and increase the noise in the spectrum This is not a concern for MCT A detectors you can generally obtain good results using any available velocity setting DC operation In the U S A a power pack accessory allows you to operate the spectr...

Page 65: ...sing Minimize or eliminate noise and vibration Minimize or eliminate exposure to magnetic fields Minimize or eliminate exposure to dust or other airborne particulate matter The documentation that came with the accessory provides information about connecting the power pack or powering the spectrometer from a vehicle It also contains information about the safe operating environment for a DC powered ...

Page 66: ...the accessory name Smart ARK This is a horizontal ATR attenuated total reflection accessory with high stability complete purge capabilities tool free alignment and high performance specifications It includes integral purge tubes that seal the accessory from the atmosphere and a cast aluminum body for exceptional stability Smart Collector Diffuse reflection enables analysis of highly light scatteri...

Page 67: ... corrosive caustic intractable or abrasive samples making it a good choice for almost any sample type Smart Golden Gate This is a horizontal single reflection ATR accessory that features an extremely durable diamond crystal It handles a wide range of sample types including hard or brittle solids corrosive liquids and hard powders Smart Mid IR FiberPort This high throughput accessory lets you analy...

Page 68: ...and solids using a wide variety of transmission cells and infrared cards Smart Orbit This single reflection ATR accessory features a durable diamond crystal and a swivel pressure tower that ensures consistent pressure from sample to sample You can use the accessory to perform analyses from the near IR to the far IR Smart Performer This single reflection ATR accessory features a horizontal sampling...

Page 69: ...s fit into the sample compartment and require that you remove the Snap In baseplate before installing the accessory For information on using Snap In baseplates view Changing the Snap In baseplate in the Using your spectrometer book in Spectrometer Help Topics Note Additional Snap In sample compartment baseplates are available for use with each accessory to make changing accessories easier Call The...

Page 70: ...or use in both ambient and elevated temperature conditions Gas cell heating transfer optics purge gas manifold and sample window options are available to accommodate a variety of sample gases and sampling conditions Infrared microscopes Thermo Electron offers microscopes that attach directly to the right side of the spectrometer Microscopes can be installed between the spectrometer and other acces...

Page 71: ... standard for validation with Thermo Electron s Val Q software Validation wheel The validation wheel is used with Val Q to validate the performance of the spectrometer The wheel automatically moves standard samples into the beam path at the appropriate times during the validation procedure The samples are traceable to standards from the National Institute of Standards and Technology NIST An option...

Page 72: ...ccessory is also useful if your laboratory air supply is contaminated with volatile solvents oil or other reactive materials Purge gas generator If you do not have in house facilities to supply compressed air or nitrogen for system purge Thermo Electron offers several purge gas generators Purge kit This kit includes all the hardware you need to regulate the pressure and flow of purge gas for the s...

Page 73: ... one step by selecting a stored experiment from the Experiment drop down list box below the OMNIC window menu bar To set the experiment parameters individually use Experiment Setup in the Collect menu If you install a Smart Accessory the system automatically sets the software parameters or a list of appropriate experiments is made available for your selection and you can begin collecting spectra F...

Page 74: ...ex and go to Collecting a sample spectrum or Collecting a background spectrum How do I specify the Y axis unit for collecting spectra You can change the format of a collected spectrum by using the Transmittance or Absorbance button on the toolbar Absorbance Transmittance or Other Conversions in the Process menu Final Format on the Collect tab in Experiment Setup For more information about setting ...

Page 75: ...hen should I save interferograms with my spectra Save interferograms if you think you may want to restore the original data after it has been processed or if you want to keep an archive of the original data In OMNIC Help Topics find saving interferograms in the Index and go to File handling What does the Collect Sample window show The window displays the live spectrum as it is being collected plus...

Page 76: ... Background checks Interferogram checks When OMNIC performs a check and detects a problem the Collect Status indicator is displayed as a yellow circle or a red X Click the indicator or click the View Collect Status button at the end of data collection to see a summary of data collection problems encountered during the collection and other information about the collection When a collected spectrum ...

Page 77: ...ubtract the spectrum from another spectrum find peaks in the spectrum or quantify components in the spectrum View Common Problems with IR Spectra in the Collecting a Spectrum tutorial available through Learning OMNICin the OMNIC Help menu In OMNIC Help Topics find baseline in the Index and go to Correcting a baseline manually Converting spectra to other units Which Y axis unit should I use for a s...

Page 78: ...pectra collected using a reflection technique There is often a linear relationship between the concentration of a component and its log 1 R value See the unit entitled Typical IR Transmission Spectrum in the Collecting a Spectrum available through Learning OMNIC for more information In OMNIC Help Topics Index z Find absorbance and go to Converting spectra to absorbance z Find transmittance and go ...

Page 79: ...nge of the spectrum is broader than that of the library spectra use the region tool to select the region of the spectrum that coincides with the library spectra before you start the search You can also use the view finder to display the region to search The Search command operates on the selected region or on the displayed region if a region is not selected In OMNIC Help Topics find library in the...

Page 80: ...e region before searching These methods avoid the loss of spectral information that results from blanking Kramers Kronig dispersion Correcting for dispersion effects in spectrum using specular or diffuse reflection and preparing the spectrum for searching against a library of absorbance spectra ATR correction Correcting spectra collected usingATR attenuated total reflection for variation in the de...

Page 81: ...n on the Library Names tab of Library Manager available through the Analyze menu to create a user library If you are using EZ OMNIC use Create Library in the Analyze menu Once a library is created you can add spectra to it with Add To Library in the Analyze menu or by dragging the spectrum to the library s book on the Library Names tab of Library Manager You can use a search library you create jus...

Page 82: ...brary 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 Type the text to search for in the Text In Selected Item box and then choose Search The search results appear in the table based on the options you have set To see information ...

Page 83: ...he parameters Collect Sample to collect the spectrum and Add To Library to add the spectrum to the library If you are using EZ OMNIC you can add collected spectra to a user library with Add To Library in the Analyze menu In OMNIC Help Topics find library in the Index and go to Collecting a spectrum and adding it to a user library or Adding spectra to a user library What does the search expert do T...

Page 84: ...se Name box A sequential number will be appended to the base name when the spectra are saved If you want the interferograms saved with the spectra turn on Save Interferograms Individual spectra are saved with the extension SPA 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 us...

Page 85: ...ch laboratory application or for each sample type See the Windows documentation for information on creating directories You can specify which folder to use when you use Save or Save As in the File menu to save spectra This will make it easier to find a spectrum in a particular category when you use Open in the File menu to open a spectrum In OMNIC Help Topics find spectrum in the Index and go to S...

Page 86: ...display the Delete Files dialog box Locate and select the directory containing the notebook data files with the extension NBK You will have to set the List Files Of Type box to All to see NBK files listed Select the file you want to delete and then choose OK Reports and printing How can I specify a printer for printing information Use Printer Setup in the File menu See the Windows documentation fo...

Page 87: ...menu not available in EZ OMNIC to view a report as it would appear on paper The report is displayed using the current report template that is the template you specified with Template or the one you are viewing and working with If the report is displayed as you want it to appear on paper you can print it by using the Print button In OMNIC Help Topics find template in the Index and go to Selecting e...

Page 88: ... in a particular spectral window Start by selecting the spectra for which you want to specify a color and then choose Display Setup from the View menu Click the desired color in the color array and then choose OK When the spectra are no longer selected such as after you select a different spectrum they will be displayed in the color you clicked In OMNIC Help Topics find spectra in the Index and go...

Page 89: ...splays all the spectra so that they are not cut off at the top or bottom and use the same Y scale This allows you to compare the band intensities of different spectra Match Changes the Y scale of the spectra to be the same as that of the selected spectrum The selected spectrum s scale is not changed This allows you to compare the band intensities of different spectra Offset Shifts the spectra vert...

Page 90: ...tion tool to drag the spectrum up or down You can also use the Roll Zoom window available in the View menu to move a spectrum up or down In OMNIC Help Topics find spectrum in the Index and go to Selection tool View finder or Rolling and zooming spectra How can I move a spectrum into another spectral window Use the selection tool to drag the spectrum from one spectral window to another A copy of th...

Page 91: ... Use the peak height tool to click the top of the peak Then drag the baseline handles to adjust the baseline used for the measurement The corrected measured above the baseline and uncorrected height values appear in the readout above the palette In OMNIC Help Topics find peak in the Index and go to Peak height tool How can I find the area of a peak Use the peak area tool to drag across the peak Th...

Page 92: ...n the Operation drop down list box View the Using Spectral Math tutorial available through Learning OMNIC in the OMNIC Help menu In OMNIC Help Topics find spectrum in the Index and go to Performing arithmetic operations on spectra What should I use subtraction for Subtract is commonly used to remove spectral features of solvent residues or pure components from the spectrum of a mixture of compound...

Page 93: ...ifference 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 In OMNIC Help Topics find spectrum in the Index and go to Subtracting spectra Customizing OMNIC...

Page 94: ...dual peaks In OMNIC Help Topics find peaks in the Index and go to Finding peaks above a specified height or find label and go to Annotation tool How can I close a task window such as the Find Peaks window Click the Close button if available in the upper right corner of the window You can also double click the button at the left end of the window s title bar if the window is not maximized or the bu...

Page 95: ... View menu turn on Sampling Information and then specify the types of information you want displayed by turning on options in the Sampling Information box In OMNIC Help Topics find displaying sampling information in the Index and go to Displaying sampling information How can I copy a spectrum and paste it into a text document Select the spectrum and choose Copy from the Edit menu This places the s...

Page 96: ... Topics find Energy screens in Installing new hardware help book Do I need to use a bandwidth limiting filter If you are using a highly sensitive detector such as an MCT A detector and your experiment deals with information in a narrow range of frequencies a bandwidth limiting filter can prevent the detector from becoming saturated or producing a distorted signal Bandwidth limiting filters improve...

Page 97: ...hat the cover is removed In Spectrometer Help Topics find Removing the main cover in Servicing your spectrometer help book When should I align the spectrometer Align the spectrometer in the following situations The ambient temperature has changed by at least 5 Celsius degrees about 9 Fahrenheit degrees You are about to perform a spectrometer validation with Val Q or other software This ensures tha...

Page 98: ...er with a hole in the top If during a work session you find that the detector signal intensity is decreasing the dewar may need to be refilled with liquid nitrogen In Spectrometer Help Topics find Cooling a detector in Using your spectrometer help book When should I change the desiccant When the humidity indicator on the spectrometer cover turns pink change the desiccant packs If the packs are pri...

Page 99: ...on a spectrometer component by choosing Advanced Diagnostics from the Collect menu This starts the Bench Diagnostics program which provides information on the status of the component as well as troubleshooting information replacement procedures and information on ordering replacement parts See the Troubleshooting your spectrometer and Ordering parts books in Spectrometer Help Topics for instructio...

Page 100: ...dering and installing replacement parts Upgrading the computer recovering from viral attacks and reinstalling software As computer technology advances and your experiments and analyses become more complex you may wish to upgrade the computer being used with the spectrometer At other times due to viral attacks or hardware failures you may need to reinstall the spectroscopy software and drivers Use ...

Page 101: ...d other add on cards the drivers and software must be installed before the hardware Read and follow the installation instructions that accompany the card s Incorrectly installed software hardware and drivers can render the computer inoperable In many cases the installation instructions are included on a compact disc that was shipped with the card Adobe Acrobat Reader software frequently is require...

Page 102: ...ope systems or printers 8 Shutdown and power off the computer and then install the add on serial ports 9 If the computer requires an add in card to meet the required number of USB 2 0 ports do not include hubs in your count power on the computer and install the USB 2 0 port driver software that accompanied the add on card If the computer does not require an add in USB2 card skip to step 11 10 Shut...

Page 103: ...ox appears 3 Click the Diagnostic tab The Diagnostic tab appears showing icons for the major components of the spectrometer with a live display of the signal from the detector 4 To run the diagnostic tests for a component click that component s indicator icon A dialog box appears showing the status of the component If the operating values for the component are within proper limits a check mark app...

Page 104: ...the spectrometer configuration Get troubleshooting tips Follow these steps to run the diagnostics 1 Make sure the main sample compartment is empty Remove any samples and sampling accessories except a transmission sample holder 2 Start the Bench Diagnostics software To do this choose Advanced Diagnostics from the Collect menu You can also close OMNIC or EZ OMNIC click the Start button in Windows po...

Page 105: ... of the spectrometer are included in the Maintaining your spectrometer book in Spectrometer Help Topics This tutorial includes common maintenance procedures such as changing the desiccant checking the purge filter and cleaning the outside of the spectrometer Aligning the spectrometer To ensure optimum system performance high signal intensity low noise and good sensitivity you should align the spec...

Page 106: ...o Main 4 Set Gain on the Bench tab to 1 Important Do not use Autogain 5 Click the Align button on the Diagnostic tab When you click the Align button the system begins to optimize the detector signal for maximum energy throughput Alignment should take 2 to 4 minutes The live display of the detector signal changes as each interferogram is collected The positive peak and negative peak intensities are...

Page 107: ...e with the accessory When you manually adjust an accessory watch the largest interferogram peak in the live display on the Bench tab The larger this peak the better is the signal intensity Note The largest interferogram peak can be positive or negative If you are unable to see the display turn on Tone on the Bench tab before adjusting the accessory The tone reaches its highest pitch when the signa...

Page 108: ...en choose Bench Diagnostics See Performing advanced diagnostic tests in the Troubleshooting Hardware Problems chapter for more information on running the Bench Diagnostics software 4 Click the Performance Tests button and then follow the instructions that appear on the screen Note If the noise readings are greater than normal or have changed significantly contact technical support If special perfo...

Page 109: ...r reactive or infrared absorbing materials Use dried air or nitrogen to purge the spectrometer Other gases even inert gases such as argon can damage the spectrometer and should never be used for this purpose We recommend that you leave the purge on at all times This keeps the spectrometer free of undesirable gases protects the optics and improves the system s thermal stability In Spectrometer Help...

Page 110: ...iling components For instructions on diagnosing spectrometer problems ordering parts and replacing parts choose Spectrometer Help Topics from the Help menu If the source laser module electronics module or power supply must be replaced refer to the replacement parts list made available when you choose Spectrometer Help Topics from the Help menu Call Thermo Electron or visit our website to order the...

Page 111: ...tion a message says the sample and background spectra have the wrong resolution The resolution of the current background spectrum does not match the resolution selected for the sample spectrum collection Change the Resolution to match the background and collect the spectrum again Use the Resolution parameter on the Collect tab of the Experiment Setup dialog box The Quantify command is dimmed No qu...

Page 112: ...g Experiment Setup and save it using a new filename if you do not want to overwrite it Then open the experiment in the FACTORY directory whose filename is same as the original experiment and save it in the OMNIC PARAM directory The desired experiment does not appear in the Experiment drop down list box The experiment was installed with the software but has not yet been opened If the experiment was...

Page 113: ...ecome warm A message appears explaining the problem and allowing you to access information on correcting it If the indicator is a red X the spectrometer has failed a diagnostic test and requires corrective action A message appears explaining the problem and allowing you to access information on correcting it This chapter lists some simple troubleshooting measures you can take to solve problems wit...

Page 114: ...tarting OMNIC The data cable is loose disconnected or damaged Shut down the computer and turn off the spectrometer Check the data cable If it is damaged replace it If the cable is loose or disconnected reconnect it Turn on the spectrometer and wait until the spectrometer start up diagnostics finish Then turn on the computer and restart OMNIC The computer port used for communicating with the spectr...

Page 115: ...ment laser if necessary See the Ordering parts and Servicing your spectrometer books in Spectrometer Help Topics to find part number and ordering and installation instructions The spectrometer is overheated You can check whether the temperature of the electronics board is within the acceptable range by clicking the electronics indicator on the Diagnostics tab of the Experiment Setup dialog box Mak...

Page 116: ... is appropriate for the AC power source In Spectrometer Help Topics see Miscellaneous parts in the Ordering parts book for power cord descriptions and part number information The ground prong on the power cord has been removed or is defective The power cable or power supply is defective Replace the power cord In Spectrometer Help Topics see Miscellaneous parts in the Ordering parts book for power ...

Page 117: ...Diagnostic tab of the Experiment Setup dialog box A sampling accessory is not installed properly Make sure the accessory is installed according to the instructions that came with it A detector that was just installed is not seated properly Make sure the hole and slot in the detector plate fit over the pins on the spectrometer baseplate See Replacing the detector in the Servicing your spectrometer ...

Page 118: ...ator is on check the interferogram on the Bench tab of the Experiment Setup dialog box if the interferogram is not present check the beam path and detector The beam path is obstructed Remove the obstruction The automated aperture is set incorrectly Check the Aperture parameter on the Bench tab of the Experiment Setup dialog box For an MCT A detector set Aperture to 10 For a DTGS detector set Apert...

Page 119: ...ter is too high Make sure the ambient temperature is between 16 and 27 C 60 and 80 F An error message appears when you try to scan The light source is not working Check the source indicator on the Diagnostic tab of the Experiment Setup dialog box If necessary replace the source An MCT detector is not cooled Check and cool the detector The spectrometer is out of alignment Align the spectrometer usi...

Page 120: ...is out of alignment Align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box 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 baseline is not stable The desiccant cannot absorb any more water vapor Check the humidity indicator ...

Page 121: ... off the power and unplugging the power cord The laser or electronics module is defective Check the laser indicator on the Diagnostic tab of the Experiment Setup dialog box If there is a red slash through the laser indicator click the indicator to view information about the laser operation If the laser frequency is outside the specified range call Thermo Electron to have the electronics module rep...

Page 122: ...A component has failed Call Thermo Electron for service The baseline is not stable The purge flow rate is too high Lower the flow rate until the baseline is stable The spectrometer is out of alignment Align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box The laser detector is misaligned Use the Bench Diagnostics software to check the laser levels fo...

Page 123: ...e spectrometer If the action does not solve the problem contact technical support In OMNIC Help Topics find troubleshooting in the Index and go to Troubleshooting for more information Problem Possible Cause Solution A spectrum contains fringes or channeling The sample has parallel highly reflective sides that cause the infrared beam to bounce within the sample when it is placed perpendicular to th...

Page 124: ... source and optional purge kit Contact Thermo Electron for details The spectrometer is purged but the air dryer does not remove carbon dioxide Replace the air dryer with one that removes carbon dioxide or use nitrogen to purge the spectrometer Contact Thermo Electron for more information A spectrum contains water peaks that interfere with your data The desiccant cannot absorb any more water vapor ...

Page 125: ...wing mode Put the microscope in infrared mode and collect the spectrum again A sample film in an ATR experiment is being held against the ATR crystal with uneven pressure or has poor contact with the crystal Make sure the sample is held evenly and has good contact with the crystal The resolution is set too low Set Resolution on the Collect tab of the Experiment Setup dialog box to a value that let...

Page 126: ...tup dialog box to align the spectrometer The spectrometer has not been on long enough to reach thermal equilibrium For best results allow the spectrometer at least one hour to stabilize after turning it on Remove the sample holder and collect the background again The spectrometer is not properly purged Check the system to make sure the correct purge gas is being used and that the flow rate is corr...

Page 127: ... use a higher numerical setting on the Collect tab of the Experiment Setup dialog box The moving mirror velocity is set too high for the detector Set Velocity on the Bench tab of the Experiment Setup dialog box to a lower value The sample in an ATR experiment is not in good contact with the ATR crystal Reapply the sample to obtain more consistent contact between the sample and the ATR crystal Nico...

Page 128: ...lable 8 air dryer 67 airborne contaminants 60 align 92 100 ambient temperature 60 annotation 39 aperture 52 argon 104 ATR 61 62 63 gain 102 ATR corrections 75 Autogain 101 b background 35 background spectra 71 baseline 72 115 baseline correct 75 baseplate 65 baseplates Smart 21 Snap In 21 beampath 52 114 beamport 52 beamsplitter 54 112 bench status 34 bench status indicators 20 blank 75 buttons T ...

Page 129: ... 94 98 103 105 diffuse reflection 61 120 gain 102 display parameters 83 DTGS 55 59 DTGS CsI 55 dust 60 e electronics module 116 e mail 2 emergencies 2 energy screens 56 57 58 environmental conditions 60 Ever Glo 55 experiment selecting 33 setting software parameters 33 experiment parameters 71 experiments selecting 35 extended tests 103 external beam 66 EZ OMNIC Add to Library 78 basic information...

Page 130: ...110 115 116 117 libraries adding spectra to 47 78 commercial 47 compound types 42 creating 9 46 76 creating with EZ OMNIC 12 displaying spectra 77 matches 45 preparing spectra for searching 74 saving spectra in 79 scrapbook 46 search expert 41 searching 74 specifying directories 43 storing data in 46 troubleshooting 107 types 41 using search expert 78 using to identify spectra 41 using with EZ OMN...

Page 131: ...oring 108 printing 47 quality checks 71 reports 47 saving spectra 31 OMNIC continued scan gauge 28 selecting default configuration 23 selecting default experiments 23 selecting experiments 35 setting experiment parameters 33 setting velocity 59 spectral quality indicators 30 spectrometer status indicators 34 standard experiment troubleshooting 107 starting 19 status indicators 108 tool palette 39 ...

Page 132: ...reviewing 49 Roll Zoom 85 RPT 47 s sample installing 22 27 sample compartment windows 112 sample holder installing 21 installing sample or filter in 22 sample wheel 64 saturation 56 screens 58 91 search 41 Search Expert 78 search methods 12 signal to noise 56 Smart Accessory 26 61 Smart baseplate 65 Snap In sample compartment baseplates 21 software 95 source 52 54 instructions for replacing 54 spe...

Page 133: ...h 87 water peaks 119 X Y axis values 86 zooming in 85 spectral range 55 spectrometer aligning 92 100 ambient temperature 114 automated aperture 113 baseplates 36 basic information 51 battery 59 beamsplitter 54 changing desiccant 93 checking performance 102 clearances 110 clearing sample compartment 26 component locations 51 conditioning power 66 connectors 53 cooling detector 93 data collection bu...

Page 134: ... text searches 46 TGA 66 thermogravimetric analysis 66 tool palette annotation tool 39 readout 39 toolbar 34 changing 12 transmission 63 66 troubleshooting aligning spectrometer and accessories 100 applications 118 baseline 115 diagnostics 94 98 105 scan error 114 software 106 spectra 118 turning off Installation Wizard 5 tutorials 4 creating libraries 9 data collection 69 FT IR theory 7 sampling ...

Page 135: ...x X axis 55 XT KBr 55 y Y axis 37 69 72 84 z zoom 85 Nicolet 380 User s Guide 129 ...

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