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Nicolet FT-IR User`s Guide - The Molecular Materials Research Center

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1. sees 143 photometric accuracy seeseeeeeeeee 65 saturated csse 64 65 66 67 154 saturati Oe sino ete pee et t eco 123 signal intensity seen 131 SUNCOM sie iot pte Oe ree i 70 Spectral range need nl eee 62 TYPOS a sete ciet e ei e ee i edens 60 using filter to reduce energy reaching 64 detector continued velocity too high for sees 154 Which tose T A eee een 11 detector interface Kit eere 86 Detector Motors connector sese 95 dewar l akingzsc ente eR OE 144 C PTOStICS ost eh 129 148 diffuse reflection accessory eeee 81 82 directory libraty eet ter te ete 136 dispersion effects esses 103 Display Setup cie ea Pte 111 distortion in spectrum 69 documentation nete tte beet ree tete ias 6 dual sources option sesesseeeeeeeenrenneeene 58 e electronics module sse 145 defective mierna nena 146 Teplacig ete R 134 emallz cepe DID OR Dente 3 7 Energy Sereen rosee srera tete eter eins 66 69 154 detectors typically used with 66 energy passed with sese 66 for collecting data in visible spectral range 70 optional wheko nissedreng ep e eies 86 resolution affected by sss 70 when to USC cite etu vetet 123 energy screen wheel
2. eese 92 auxiliary experiment module sess 86 b Background button eee 53 background spectrum collected with sample holder in beam 153 ollec tig asi ione ee 32 53 defined 3 apa oerte ded er 27 tOO Old osien te reet eie 151 when to collect eese 27 bandwidth limiting filter eee 65 baseline CONTECH 5 Xetra reti eo ue 102 116 NOt Hat Rd enne et ERR eene 153 notstable e etie PO 139 Sloped araa e pee 153 baseplate CUSTOM i e ER S RE eevee eee Ae 86 TemoVIng 5 3e eb e e e NER RES 85 baseplates SIDSEU 3 cie ete tne Ye RRERS 28 Snap In sews ene ae Te des 28 beam path blocked gebaut 141 143 147 beamsplitter chari oesisodee nu entes 10 compatibility with detector eeeesss 60 fogged x seine POE 143 not compatible with detector 142 147 not properly seated seseeeeeee 146 spectral range e pt ee b ede 62 DES ene G dt e 60 Which touse nes esinin e e 11 beamsplitter compartment cover eene 147 Bench Diagnostics sesssssss 127 129 148 Bench Status indicator eee 26 blanking totally absorbing bands 102 Nicolet FT IR User s Guide 155 C cable not connected properly 138 140 144 147 c blimg accessoty onc tt Reiten 91 carbo
3. deett 151 derivative shaped in spectrum 152 eliminating with subtraction essssss 117 finding aS 120 nrc ER 154 none in spectrum ssseeseeeeeeeeeneen eene 152 totally absorbing in spectrum 151 og 151 performance test ette tette 132 148 Photoacoustic accessory 88 Photoacoustic units eeeeeeseeseeeeeeeeneenennenen 101 Photometric accuracy eseeseeeeeeeeenene 65 66 pinouts Auxiliary connectors 94 Detector Motors connector esses 96 polarizet 4 ute RERO ets 78 88 power ACCESSO cin tee nere ren e eoe ere RR ene 92 power cable defective sees 140 power cord iu e e Ui ds 140 Power indicator eeeeeeeeeeeeeeennneeene 18 56 power line conditioner essere 90 power supply tae ee gehen 56 defective tete deep 140 not connected properly sss 140 Iepl cmg onere nine 134 power Switch eene erre ttt eps 18 pressure regulator emis re ee treten ie 15 previewing Teport 2 2 tecti te p edad 109 previewing spectrum before printing 110 printer SDeCIEYHIg inu ete eee dabei 109 Printer Setup ics eines 109 Nicolet FT IR User s Guide 159 printing report iesire teer io tete ett 50 DUIg c uterine ete ttu 10 flow rate enne nennen 15 16 flow rate
4. eese 38 ACCESSOTIES x12 non e A cle eee ee aes 81 aligninig 4 4 el eee et ee ies 132 automated sample handling 85 AV AU ADCs cists oet t Uere 12 cabling xen geesue deutet 91 CESCLIPHONS eee cheat ettet Pee ere 85 detector i neat EO Dee 92 iist lling iere ees 6 12 85 not aligned ns ee uta 142 not installed correctly es 142 143 DOWGEN d necsttitoe o riori eto e c e aes 92 Arcu ys 90 when to turn on 0 00 eeeeceesesececceeeesstseeeeeeeeeeseaes 18 56 Advanced Diagnostics sss 127 148 AEM hue ena pipe e HER eden 86 a dEyer cete aote a a 90 151 aligning ACCESSOLY ie rene itp eee ette 132 Spectrometer c ni ende pereo 124 130 annotation tool oen nee t petere 120 aperture cete mre Er RO MER RI EAE IRIS 141 effect on resolution eene 67 effect on wavenumber accuracy ees 67 for collecting data in visible spectral range 70 IDCOIIGCt i a te eene TR eR gd e reed 141 resolution affected by esse 70 size for cooled detector sess 67 size for detectOL e eeepc ette 67 ATR accessory eeseeeeeeeeeeerenne 81 82 83 84 ACDR COITECUOD etre eer ee 103 ATR sample contact seeeeeeeeeeeene 154 Auxiliary 1 connector eseeeeeeeeeee 93 Auxiliary 2 connector eese 93 Auxiliary connector
5. essere 75 error message during data collection 147 Expand Contract button eese 113 experiment defaults 52s eae aii qae debt epit 30 NOt hsted 4 uei ee tees 136 T STO 23 iie eg ae ed 136 selecting neat REER 21 25 30 Experiment drop down list box 21 25 30 97 Experiment Setup eee 21 25 extended search feature sees 105 external detectors ee e rotes eie Rs 144 external Source in eee Rte e dee 59 f fax number sssssssssseeeeeeeeeee eene nennen nennen nnns 3 7 fiber optic accessory cece esceseeseeseeteeeecteceseeseeaeees 83 88 filename for saving spectrum 37 filter bandwidth limiting eere 65 for collecting data in visible spectral range 70 installing in sample holder 29 reducing energy reaching detector using 64 filter wheel eue Den ertet ee Hades 72 86 finding peaks a a e e etes 120 flammable gases esee 15 flowmeter ucc te eb ttm estet Herd 15 Foundation Series sisegun nana oiin aise 87 fringes in spectrum sees 150 froston detector aee eaten 144 FEIR E 6 full scale s Senate ei LU 112 Prin 99 for collecting data in visible spectral range 70 pas cells oem es 87 GC 1nterface eie e n 87 Getting Started tutorial esee 1
6. Lower the flow rate until the baseline is stable Align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box Use the Bench Diagnostics software to check the laser levels for proper balance If the levels are out of tolerance align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box If the levels remain out of tolerance call Thermo Electron for service Make sure the conditions meet the requirements given in the Environmental Considerations chapter of Preparing Your Site Check the humidity indicator and replace the desiccant and indicator if needed Allow the spectrometer to purge for 3 to 5 minutes after the cover is closed Nicolet FT IR User s Guide 139 The status indicators on The power supply connection Turn off the spectrometer and check the spectrometer cover on the back of the spectrometer the connections between the do not light when the is loose spectrometer and the power supply spectrometer is turned Make sure the lock ring is tightened on finger tight The spectrometer is not plugged Make sure the power cord is in securely connected to the power supply and a working outlet or power strip The power cord is not properly Make sure the power cord is rated for your electrical service appropriate for your AC power source In Spectrometer Help Topics see Miscellaneous parts in the O
7. Subtracting spectra What should I use subtraction for Subtract is commonly used to remove spectral features of solvent residues or pure components from the spectrum of a mixture of compounds When you use Subtract the software calculates data point by data point the difference between the two Spectral subtraction is useful in a variety of situations for example e Eliminating solvent peaks in a spectrum of a sample that is dissolved in a solvent e Separating components from a sample that is a mixture of two or more components Identifying an unknown contaminant by subtracting out the known sample material Ensuring quality by subtracting an original batch sample spectrum from a spectrum from the next batch Nicolet FT IR User s Guide 117 118 What other mathematical operations can I perform on my spectra You can manipulate spectra using any of the common math operations Use Spectral Math in the Process menu to perform these operations on one or two selected spectra You specify the operations to perform by typing a sequence of mathematical symbols and numbers The software performs the operations on the Y values of the data points in the spectrum or spectra and then displays the result spectrum When you choose the command the Spectral Math window appears allowing you to type the desired operations in the Operation text box You can also select one of the example operations provided in the Operation
8. Spectrometer Tour available through Getting Started Service and maintenance Spectrometer Help Topics Maintaining your spectrometer Maintenance and Service chapter What should I do if there is a problem with the system Contact Thermo Electron technical support Outside the U S A contact the local Thermo Electron sales or service representative Phone 1 800 642 6538 U S A or 608 273 5015 worldwide Fax 608 273 6883 worldwide E mail Techsupport analyze 9 thermo com World Wide Web http www thermo com spectroscopy Nicolet FT IR User s Guide 13 14 A Warning 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 a It s easy to collect spectra with your spectrometer By leaving the system turned on at all times with the needed components already installed you can keep it ready to use with a minimum of preparation Keeping the system on also improves its stability and gives you more consistent results All the things you need to check before collecting spectra are listed below each of these
9. in the Index and go to Displaying and using a toolbar for information about using and customizing the toolbar buttons 26 Thermo Electron Corporation Collecting a sample spectrum A sample spectrum is usually ratioed against a background spectrum The background spectrum measures the response of the spectrometer without a sample in place Dividing the sample spectrum by the background called ratioing Tremoves the effects caused by the instrument and atmospheric conditions so that the peaks in the final spectrum are due solely to the sample Here is a typical mid IR background spectrum E e o a E D c n NENNEN ene eee mE E 3500 3000 2500 2000 Wavenumbers cm 1 For most applications you don t need to collect a new background spectrum for each sample spectrum if you haven t changed the software parameters To obtain good results however collect a new background regularly perhaps once every four hours You can obtain the best results by collecting a new background for each sample but this is usually necessary only if you are running quantitative experiments Nicolet FT IR User s Guide 27 Installing the Ifthe standard sample holder is not already installed install it now standard sam pl e holder The following illustration shows the sample holder in place Accessory gt lt support holder adjustment screw If you are using separate Snap In sample compartment baseplates for d
10. This spectral range reflects the combination of the ranges of the ETC and white light sources as well as the limits of the beamsplitter detector combination The range achieved using one of these sources will not be as broad as the total range shown Si detectors can be used only with a white light tungsten halogen source i These detectors must be cooled with liquid nitrogen before use InSb detectors will not produce a signal under intense light During installation and alignment start with the smallest aperture setting T CsI beamsplitters are extremely hygroscopic sensitive to moisture Nicolet FT IR User s Guide 63 64 Improving the quality of your spectral data Improving linearity and photometric accuracy If you are using the spectrometer for quantitative analysis or other demanding applications you are concerned with the precision and accuracy of your spectra For these types of applications it is important that 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 your spectrometer responds linearly to the samples you are studying This means that absorption band intensity is directly proportional to the number of molecules subjected to the light beam thus as the number of molecules in the
11. When you print your report OMNIC will automatically fill in the items in the template with the appropriate information and images For example if an item in the template is linked to the active spectral window the contents of that window are included when you print the report 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 5 In OMNIC Help Topics find report template selecting in the Nu Index and go to Selecting editing or creating a report template for more information about using reports 4 Choose Preview Print Report from the Report menu A preview of the report appears showing the report items filled in with information about your spectrum Your report should look similar to this You can click the Zoom button to see an enlarged image of the report QC Compare Report Fn Feb 20 14 46 18 2004 GMT 06 00 6 Fn Feb 20 14 46 16 2004 GMT 06 00 gt Apsorbance A j AN x ad aA LA 5 do NV silica VES AJ 3500 3000 2500 s Wavenumbers cm 1 Collection time Fr Feb 20 14 46 18 2004 GMT 06 00 The spectrum matches Polystyrene The best match value is 99 99 and the critical match value is 50 00 The preview lets you check the content of the report before printing it Ni
12. macro in the Index and go to Specifying a macro for the Macro button for more information Nicolet FT IR User s Guide 53 What s inside The illustration below shows a top view of the optical layout of a typical Nicolet 6700 spectrometer with covers removed to reveal components Some components may not be present in your spectrometer Interferometer Laser Beamsplitter Beamsplitter storage Electronics ERR Fixed mirror Passport optics or optional optional I emission optics External niue emission port compartmen 5 Filter wheel External E l B optional peamport F D I External Back beam port detector Aperture Detector Energy screen mirror wheel optional Front detector 4 Infrared source Source select optics optional Near IR source optional Sample holder Polarizer SablR port Fixed mirror or optional optional SeaPort optics In the Spectrometer Tour available through Getting Started view f Inside the spectrometer for complete descriptions of your spectrometer components 54 Thermo Electron Corporation What is on the rear panel The rear panel includes a power connector right and left side accessory connectors computer connector USB 2 0 not a hub auxilliary signals connector and purge gas input You may also find optional Auxilliary and or dual channel connectors on the rear panel Accessor Accessory Computer Es Avoid shoc
13. 56 144 spectra saving AS group eseesseeneeeeneeen eee 108 saving automatically esee 106 saving on hard disk sess 107 SUDtracting eret tnn e He aas saei 116 where to SAVE iaieseenite reete 107 spectral library adding spectrum to eese 47 105 C EAE ioo ec e eso Er HE NERO eet S 7 104 searching a aude eve eter 102 spectral quality checks eee 100 spectral regions and velocity hated T 71 detector beamsplitter eene 62 for library Search seta 103 Selecting iuc eg ds 120 WISIDIG ia ne aede RRR Reden 70 spectral window eet eec erret 24 spectrometer ANPING ciet ro E ran 130 cofnponents a eene perro torio ino 10 51 COVED iii dti m EO I etas 139 data collect buttons eeeeeee 52 diagnostics eco etti e redes 127 howit works sie e Reed 10 letting stabilize cies esum 19 maintaining 0 eeeeeeeeeeeeeeeeeeseeeseeeeeeees 13 128 130 not aligned 138 139 141 143 145 153 not pluggedm ize aget 140 not purged eerte 151 153 Optical layout tue ERR 54 overheated eee 138 142 146 performance fest o iro edits 132 PUPS Bs uet dene ede otis 15 16 rear panel REIR PERDU 55 replacing parts in sse 127 Nicolet FT IR User s Guide 161 spectrometer continued SeTVICIDE 14er en or D d een eerie 13 128 134
14. Only qualified persons should connect a cable to the Detector Motors connector Do not use this connector for signals that exceed 15 VDC Limit the current to a maximum of 800 mA Thermo Electron is not responsible for damage or injury resulting from improper or unsafe cabling a The following table shows pinout information for the Detector Motors connector Use this information when designing a cable to connect your custom hardware to the connector Refer to the preceding illustration for the locations of the numbered pins Nicolet FT IR User s Guide 95 Pin Number Description 1 Do not use this pin 2 Used by the sample shuttle motor negative 3 Positive 5 volts 4 Analog ground 5 Used by the sample compartment detector for negative analog input 6 Positive 12 volts analog T7 Used by the sample compartment detector for digital communication 8 Positive 5 volts 9 Used for sample compartment digital communication 10 Used by the sample shuttle motor positive 11 Positive 12 volts 12 Analog ground 13 Used by the sample compartment detector for positive analog input 14 Negative 12 volts analog 15 Used by the sample compartment detector for digital communication 96 Thermo Electron Corporation Collecting spectra 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 in
15. aperture Size for a u hee teet 67 cooling detector essssssseeeeeeene 19 125 156 Thermo Electron Corporation copying spectrum 200 eee eeeesceeseeeeeeeeeeseeeaeeeeesseeseeesees 121 correcting baseline sseeeenee 102 116 SDeCtrum oe ette ee PR aere hg 102 Custom ACCESSOTIES aceite e e Re rend 94 CUVette insere ite terret ie rn Seabees e Rive pee e p 87 d data collection toises cece ccessccceessseccessseecessseeceenseeees 9 14 default configuration eere 30 default experiment eese 30 deleting report notebook iseseisana 109 Spectr M atento tities NAAA OE RE 108 depth of penetration seeeeeeeere 103 desiceant s oin ciet e tte erp er ens 139 151 changing eee RUD ERU 130 checking eae ee ee aas 17 when to change sss issues sete tete 126 desiccant indicator seeeeeeereeeenn 17 126 detector ACCESSOLY tended ete a Re RE ete 92 aperture SIZe TOL ciet ette des 67 Cale cance ay Ree 144 changing eo ate oce Re 11 compatibility with beamsplitter 60 COMME CON Su ierit ber te te oe aet 92 eoolingcti aede o eu 19 125 uitio 144 energy screen eseeeeeeeeeeee 66 69 70 123 154 external ees tenet ee editt 144 frosted ans esnure RII Bp 144 lineatityz io tere ette pe ha 64 not compatible with beamsplitter 142 147 not cooled cette e erre 147 not installed properly
16. chamber at one time into a 96 or 384 well microtiter plate The ejection insertion and movement of the well plate inside the sample compartment is controlled by software Near IR Heated Cuvette Holder E S P This accessory is designed for analyzing samples that require a constant or elevated temperature to obtain reproducible near IR results You can use it to analyze liquids gels and solids that have a low melting point such as waxes Nicolet FT IR User s Guide 87 86 Nicolet Centaurus and Nicolet Continuum 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 PAC 300 Photoacoustic E S P Photoacoustic spectroscopy PAS is a powerful technique for the nondestructive spectroscopic analysis of solid samples of all types PAS is particularly applicable to powders including dark highly absorbent samples polymer pellets beads and sheets and films The PAC 300 Photoacoustic E S P accessory is fully integrated with the spectrometer and computer It automatically selects an OMNIC experiment draws power right from the spectrometer and includes an on line tutorial Polarizer This accessory lets you control the orientation of the electric field vector of the infrared beam as it
17. if you want more information about comparing sample spectra with QC libraries 46 Thermo Electron Corporation Creating a user library J Adding a spectrum to a user library Note OMNIC s Library Creation Wizard makes it easy to create your own spectral libraries Creating your own library lets you customize the 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 The wizard leads you step by step through the process If you are using OMNIC start the Library Creation Wizard by choosing Library Manager from the Analyze menu and then clicking the Create Library button on the Library Names tab In OMNIC Help Topics find library creating in the Index and go to the Creating a user library topic for more information Once you have created a user library you can use the library to store spectra you have collected To do this select the spectrum and then choose Add To Library from the Analyze menu To move a copy of a spectrum you have collected from one user library into another use Library Manager in the Analyze menu You cannot add spectra to a commercial library nor can you move copies of commercially collected reference spectra into libraries you create A In OMNIC Help Topics find adding spectrum to user library in the Index and go to the Adding a spectrum to a user library
18. in the Index and go to Saving a group of spectra How can I delete stored spectra Choose Delete Files from the File menu to display the Delete Files dialog box Locate and select the spectral data files with the extension SPA or SPG for spectral group files you want to delete and then choose OK In OMNIC Help Topics find spectra in the Index and go to How to delete files Thermo Electron Corporation xX Printing J 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 Choose Delete Files from the File menu to display the Delete Files dialog box Locate and select the directory containing the notebook data files with the extension NBK You will have to set the List Files Of Type box to AII to see NBK files listed Select the file you want to delete and then choose OK How can I specify a printer for printing information Use Printer Setup in the File menu See your Windows documentation for details on setting the printer parameters In OMNIC Help Topics find printer in the Index and go to Setting up the printer How can I create and print reports of my work Use the commands in the Report menu First use Template to select edit or create a template f
19. topic or the Adding user library spectra to another user library topic for more information Nicolet FT IR User s Guide 47 48 Creating and OMNIC makes it easy to create and print a report containing the results of your work Follow the steps below printing a report 5 You can also view the Creating Reports tutorial available through J Learning OMNIC in the Help menu to learn how to create and print reports and add them to report notebooks 1 Thermo Electron Corporation Choose Template from the Report menu A dialog box appears allowing you to select a report template for the report Select the report template file named QCCOMP RPT This file contains a report template specially set up for this procedure The template has items for the spectral window spectrum time title and comments and QC comparison results When you select the template file a preview image of the template appears at the right This feature allows you to see what different templates look like so that you can pick one with the items you need for your report You can view the image as a graphical layout by selecting the Layout option This shows you how the printed report will look on paper You can also view the image with template items labeled by selecting the Description option This lets you identify items that are too small to be seen clearly Choose Select to make the example template the current template for printing reports
20. 5 ee eene te a 150 SOWAT thee ci epe Tee 135 Spectrometer5o eene eee eere epe eg 137 turning off SySteni iseinean keora 19 57 turning on computer s sseseeesseeeeerereerereresrereerererees 19 56 turning on spectrometer sese 18 56 turning on Systemics niei ataare ienai 9 TUEOFIOIS 6 255 033 Sectors tote Ue hit oe Macs ah te thor iiL n 6 Getting Started seeded 1 service and repair sse 7 spectrometer touf neierens 6 u uninterruptable power supply ener 91 UM tS si nanc ben id scons ERE RE ERN IUE 98 used for spectrum eese 38 101 user library adding spectrum to sese 47 CICaling eine aget niente dis 47 Savins spectra I x uoo repetens 107 user Dalle n aseo Ote I ES IR ERE cece OE ELE EP dence 20 V validation wheel eee 90 ValQ cente e ice e eb enun 90 velocity and spectral range aene nete ent 71 MOVING NUOT isi rne Ania iD e ER Res 71 too high eode D eee a 141 too high for detector esses 154 visible spectral range eere 70 W Water VapOt e eroi ate n RM ERES 151 removing peaks due to eee 103 wavelength precision eene 64 wavenumber accuracy 67 WeD SIte ze e eR RE ERES 3 7 Window options eerte 111 Windows metafile eese 121 Wizards EE 6 library cre tion ee ec Renten 7 X X Valle in RO d
21. 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 Spectrometer Help Topics Selecting a beamsplitter detector and source in Setting up experiments See the tables showing the compatibility of sources beamsplitters and detectors Spectrometer Basics chapter Selecting the right beamsplitter and detector in Using beamsplitters and detectors How do I install a sample Spectrometer Tour available through Getting Started Installing samples Nicolet FT IR User s Guide 11 How do I collect a spectrum Collecting a Spectrum available through Learning OMNIC i Your First Experiment chapter Accessories What accessories are available Spectrometer Tour available through Getting Started S Accessories if Accessories chapter How do I install an accessory Spectrometer Help Topics S Installing optional hardware Step by step instructions and in many cases on line videos help you install accessories If your accessory is not covered on line use the printed instructions 12 Thermo Electron Corporation Maintenance and service How should I maintain my spectrometer
22. If the laser frequency is outside the specified range call Thermo Electron to have the electronics module replaced If the laser voltage or current is outside the specified range replace the laser View Replacing the laser in the Servicing your spectrometer book in Spectrometer Help Topics for instructions Make sure the cooling vents on the back of the spectrometer are not blocked Make sure the ambient temperature is between 16 and 27 C 60 and 80 F Call Thermo Electron for service For a Nicolet 6700 check the beamsplitter and reposition it if necessary For a Nicolet 4700 call Thermo Electron for service Laser status indicator is off An error message appears when you try to scan The beamsplitter compartment cover is not fully closed The laser is burned out The light source is not working An MCT detector 1s not cooled The interferogram peak is not located at 1024 16 data points on the Bench tab of the Experiment Setup dialog box The beam path is obstructed The data cable between the spectrometer and the computer is not properly connected The detector and beamsplitter are not compatible Close the beamsplitter compartment cover Click the laser indicator on the Diagnostic tab of the Experiment Setup dialog box to verify that the laser is burned out Call Thermo Electron to order a replacement laser View Replacing the laser in the Replacing par
23. Problems esses 137 Performing advanced diagnostic tests esses 148 Troubleshooting Applications Problems sesssss 150 A Welcome Congratulations on your purchase of a Nicolet 4700 or Nicolet 6700 spectrometer from Thermo Electron The spectrometer lets you collect spectra in the mid IR far IR and near IR spectral ranges The system integrates advanced hardware features with the power and flexibility of Thermo Electron s OMNIC software If you have not used the spectrometer before view the f Spectrometer Tour and Getting Started With OMNIC tutorial available through Getting Started in the Help menu of OMNIC Some dedicated systems use other Thermo Electron software packages Nicolet FT IR User s Guide 1 2 About this manual This manual explains how to use the system to collect and process FT IR spectra after a Nicolet 4700 or a Nicolet 6700 spectrometer is installed Included is information about using your OMNIC software as well as chapters on how to operate maintain and service the spectrometer This manual describes some hardware features that are not available on all Nicolet models Use the instructions for the features on your system Although the appearance of your spectrometer may vary from some of the illustrations in this manual the instructions are correct for your system The following conventions are used in this
24. Purge automatically increases the purge gas flow rate for a short time This keeps water vapor carbon dioxide and other unwanted gases out of the spectrometer while you install or remove a sample You can then collect spectra without waiting for proper purge to be restored Uninterruptable power supply An uninterruptable power supply reduces the chance of a system shutdown if power is lost When you install an accessory in the sample compartment you may need to connect one or more cables from the accessory to connectors on the rear wall of the compartment You may also need to attach cables from other peripherals such as computers custom controllers or power supplies to the accessory or from the accessory to the connectors on the front of the spectrometer The instructions that came with the accessory contain specific information about connecting that accessory Your spectrometer may be equipped with pass through connectors for use with special accessories These connectors allow you to make accessory cable connections through the spectrometer This eliminates the need to run cables through the seal on the sample compartment cover or out the top of the sample compartment 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
25. User s Guide 137 Data is not displayed during collection 138 The data cable between the spectrometer and computer is not properly connected The spectrometer is out of alignment The laser is not functioning The spectrometer is overheated You can check whether the temperature of the electronics board is within the acceptable range by clicking the electronics indicator on the Diagnostics tab of the Experiment Setup dialog box Thermo Electron Corporation Turn the spectrometer power off and check the data cable connections Align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box Click the laser indicator on the Diagnostic tab of the Experiment Setup dialog box to check the laser operation Call Thermo Electron to order a replacement laser if necessary See the Ordering parts and Servicing your spectrometer books in Spectrometer Help Topics to find part number and ordering and installation instructions Make sure the cooling vents on the back of the spectrometer are not blocked Make sure the ambient temperature is between 16 and 27 C 60 and 80 F The baseline is not stable The purge flow rate is too high The spectrometer is out of alignment The laser detector is misaligned The ambient conditions are outside the allowed ranges The desiccant cannot absorb any more water vapor The spectrometer cover was recently opened
26. a To use the pass through connectors connect the accessory inside the sample compartment and connect the external power or communications peripheral to the corresponding pass through connector on the front of the spectrometer Nicolet FT IR User s Guide 9 Connectors inside The following illustration shows the locations of the electrical the sample compartment connectors inside the sample compartment Accessory connector for detector signal or accessory control and power ole Detector Motors Soy Exe Auxiliary Purge Out Optional pass through connector for communication or other signal Detector Motors If you have a photoacoustic or other accessory that has a detector or motor located in the spectrometer sample compartment connect the cable from the detector or motor to this standard connector This is not a pass through connector See Detector Motors connector for information about using this connector to connect custom hardware Auxiliary Six pins on this optional connector can be used for passing DC power input or other signals from the Auxiliary 1 and Auxiliary 2 connectors on the front panel to an accessory For example the automatic sample wheel and the ProfilIR accessory get DC power through this connector when the DC power output of an AC to DC converter is attached to the Auxiliary 1 connector on the front panel See Using connectors for custom accessories for information about which pi
27. 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 you are interested in ordering any of the following accessories Power line conditioner Power line conditioners protect your spectrometer and other accessories from damage or malfunction due to voltage dropouts transient spikes frequency shifts or other disturbances in your electrical service Pure air dryer If you have difficulty controlling moisture in your laboratory the pure air dryer provides additional protection for the hygroscopic elements of your spectrometer This accessory is also useful if your laboratory air supply is contaminated with volatile solvents oil or other reactive materials Purge gas generator If you do not have in house facilities to supply compressed air or nitrogen for system purge Thermo Electron offers several purge gas generators RSVP Remote Support and Verification Program This diagnostics option uses a data modem and remote control software to allow control of your computer and spectrometer through the modem link An analog telephone line is required Thermo Electron Corporation How to cable an accessory Pass through connectors A Caution Smart Purge Kit This kit adds enhanced purging capability to your spectrometer When you open the sample compartment cover or its sliding door Smart
28. available in the toolbar and in the Collect menu You can also use Experiment Setup to set up and save your own experiments or to check or change the parameter settings after you select an experiment If you install a Smart Accessory the correct experiment is selected automatically or a list of appropriate experiments is made available for your selection In the tutorial in the next chapter the Default Transmission or Transmission E S P experiment is used You will probably find that this experiment is suitable for most of your applications If you want to check or change the parameters after selecting an experiment use Experiment Setup in the Collect menu Nicolet FT IR User s Guide 21 22 Note You are now ready to collect spectra If you have not used the system before you can learn how to perform an experiment by viewing the Collecting a Spectrum tutorial available through Learning OMNIC in the Help menu or by using the tutorial in the next chapter of this manual If you need to change a source or detector view Replacing the source or Replacing the detector in the Servicing your spectrometer book in Spectrometer Help Topics 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 A Thermo Electron Corporation No
29. be added to the list Use the Add Directory button on the Search Libraries tab to add the directory FA A Warning Troubleshooting Hardware Problems OMNIC continuously monitors the operation and status of your spectrometer and informs you if a problem is found The Bench Status indicator below the menu bar shows the status of the spectrometer operation When OMNIC performs a check and detects a problem the Bench Status indicator is displayed as a yellow circle or a red X along with an message alerting you to the problem If the indicator is a yellow circle an MCT detector in the spectrometer has become warm A message appears explaining the problem and allowing you to access information about correcting it If the indicator is a red X the spectrometer has failed a diagnostic test and requires corrective action A message appears explaining the problem and allowing you to access information about correcting it This chapter lists some simple troubleshooting measures you can take to solve problems with the spectrometer The Bench Diagnostics software is described at the end of the chapter If your actions do not solve the problem call Thermo Electron For more troubleshooting information see the Troubleshooting book in Spectrometer Help Topics Always follow the safety precautions included in this manual and in your Spectrometer Safety Guide when performing any of the following troubleshooting procedures 4 Nicolet FT IR
30. beam increases the detected absorbance signal also increases at a consistent rate If you are studying samples that produce tiny spectral peaks or have weak spectral features or if you are looking for small changes in your samples make sure the signal to noise ratio is high enough to let you distinguish spectral features from the noise inherent in all experimental data This prevents the signals containing spectral information from being lost among the signals generated by the random movement of electrons building vibrations light source fluctuations and other such sources The next sections explain several ways you can optimize Thermo Electron detectors to improve the quality of your spectral data Some detectors including PbSe Si MCT A and InSb detectors are highly sensitive and can become saturated or produce a distorted non linear and photometrically inaccurate signal if the light energy is not reduced before it reaches the detector element or if the detector gain is set too high Look at a single beam spectrum in the low end region around 600 to 375 cm You should see a straight line very near 0 intensity units As a rule of thumb the distance from 0 to the baseline should be less than 1 of the spectrum s maximum intensity value If the detector is saturated you will see false energy in the low end region The baseline might be far above zero Thermo Electron Corporation Note Note The maximum intensity of a mid I
31. 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 Sample Background OK Stop Macro Enter 52 Thermo Electron Corporation E o D 3 o Background a To g 8 S o e o o UL Macro 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 This has the same effect as choosing Collect Background from the Collect menu In OMNIC Help Topics find background spectrum in the Index and go to Collecting a background spectrum for more information Press the OK Enter button to respond affirmatively for example to a software prompt during data collection This has the same effect as choosing OK or other affirmative response such as Yes within the software Press the Stop button to respond Cancel or No to a software prompt during data collection This has the same effect as choosing Cancel or No within the prompt Press the Macro button to start a macro you have specified with the Macro for Macro button field on the Advanced tab in Experiment Setup In OMNIC Help Topics find
32. correctly Detailed tutorials for installing operating and maintaining each Smart Accessory are provided on line To start a Smart Accessory tutorial click Sampling Techniques in the Help menu and then click the accessory name Smart ARK This is a horizontal ATR attenuated total reflection accessory with high stability complete purge capabilities tool free alignment and high performance specifications It includes integral purge tubes that seal the accessory from the atmosphere and a cast aluminum body for exceptional stability Smart Collector Diffuse reflection enables analysis of highly light scattering solids that are difficult to analyze using transmission techniques This method is also useful when the sample usually a powder must be analyzed without modification Nicolet FT IR User s Guide 81 82 Smart Diffuse Reflectance The diffuse reflection technique lets you analyze highly light scattering solids that are difficult to analyze using transmission techniques The technique is also useful when the sample usually a powder must be analyzed without modification This accessory lets you analyze a wide variety of sample types and features integral sample cups for convenient fast sampling Smart DuraSamplIR This single reflection horizontal ATR accessory has a viewing feature that makes it easy to position the sample and monitor the applied pressure The accessory is ideal for small samples and can be used to me
33. 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 Customizing OMNIC ge de J ia 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 You can then open the file later to reset OMNIC to your preferences in one step Collecting a Spectrum available through Learning OMNIC Preparing the Software In the OMNIC Help Topics Index Find options and go to Customizing OMNIC by setting options Find menu and go to Customizing a menu Find toolbar and go to Customizing a toolbar Find configuration and go to Saving a configuration Find configuration and go to Opening a configuration Nicolet FT IR User s Guide 119 Other questions T D How can I find and label peaks in spectra Use Find Peaks in the Analyze menu to find and label peaks above a specified threshold You can also use the annotation tool to label individual peaks In OMNIC Help Topics find peaks in the Index and go to Finding peaks
34. enters the sample compartment This is particularly useful for characterization of monolayers thin films and other sample types See Using the polarizer in the Spectrometer Options chapter for more information Remote Start accessory This accessory adds external trigger capability to your spectrometer With a press of the Start switch you can control the start of data collection or coordinate the start of an external experiment SabIR This accessory provides remote sampling capability for raw material identification quality measurements and sample component analysis The system is optimized for diffuse reflectance sampling of solids and powders Materials may be sampled directly or indirectly through packaging materials Thermo Electron Corporation Sample shuttle A sample shuttle lets you collect background spectra without removing the sample from the sample compartment The shuttle automatically moves the sample out of the beam path before background collection begins Since the sample compartment cover is not opened the system purge is maintained Specular reflection accessories Specular reflection provides a nondestructive method for measuring surface coatings without sample preparation Specular reflection accessories can be used to analyze surface treated metals paints semiconductors and resin and polymer coatings TGA interface TGA module This interface is equipped with a built in temperatur
35. filter 32 1 16 000 9 000 cm 1 energy screen A 32 1 23 000 16 000 cm broad band blue filter 100 8 26 000 21 000 cm narrow band blue filter 100 8 70 Thermo Electron Corporation About the moving mirror velocity Important You can use these filters and settings as a starting point and vary them as required by your experimental conditions To set the aperture and gain set the Aperture and Gain parameters on the Bench tab in the Experiment Setup dialog box In Spectrometer Help Topics view Setting up experiments for instructions for installing filters and energy screens The optional filter wheel available for the Nicolet 6700 only and energy screen wheel let you automatically move a filter and energy screen into the beam path before collecting data See Using the filter wheel and Using the energy screen wheel in the Spectrometer Options chapter for more information While a wide range of moving mirror velocities are available on Nicolet 4700 and Nicolet 6700 spectrometers some velocity settings cannot be used for collecting data at certain combinations of spectral range and resolution If you are collecting data over a spectral range above 7899 cm velocity settings faster than 2 53 cm s are not available To specify the velocity and spectral range set Velocity and Spectral Range on the Bench tab of the Experiment Setup dialog box To specify the resolution set Resolution on the Collect tab When
36. in Spectrometer Help Topics for instructions for other common maintenance procedures such as changing desiccant cleaning the purge filter and cleaning the outside of the spectrometer To ensure optimum system performance high signal intensity low noise and good sensitivity you should align the spectrometer at least once a week using the OMNIC software See the answer to the question When should I align my spectrometer in the preceding chapter for more information If you have just turned on or moved the spectrometer wait 15 minutes one hour for best results before you align it so that it will have time to stabilize A Thermo Electron Corporation 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 Choose Experiment Setup from the Collect menu or the toolbar The Experiment Setup dialog box appears 3 Make sure Sample Compartment on the Bench tab is set to Main 4 Set Gain on the Bench tab to 1 Important Do not use Autogain a 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 T
37. information Here is an example Nicolet FT IR User s Guide 7 8 Thermo Electron Corporation Displays the X and Y values of the pointer location Click the Discussion button to display a complete discussion of the item or the dialog box or window that contains the feature Click the How To button to display a step by step procedure for using the item or the dialog box or window that contains the item The left pane in each help window lists the topics available in that help system Here is an example of a help window showing the contents of some of the books in the system Servicing a Nicolet 6700 Spectrometer Servicing a Nicolet 6700 E spectrometer e Nicolet 6700 spectrometer warranty The Nicolet 5700 spectrometer was designed H Instaling optional hardware so that you can install optional hardware and Setting up experiments replace many of the components yourself IE S Maintaining your spectrometer E Replacing parts H Q amp Ordering parts When you see this icon s Troubleshooting the video link and watch fa part before trying it yourse Finding answers to your questions The basics J 4 Use the following sections to help you locate the information you need in the on line and printed documentation The on line documentation is available in the Help menu of OMNIC How do I turn on the system Spectrometer Tour available through Getting Started Poweri
38. network Internet connection if you plan to use the internet features of the software One additional serial port if you plan to use PLUSTM 2 Liquid Analysis System Centaurus microscope with motorized stage or standard Continuum microscope Two additional serial ports if you plan to use a Continuum microscope with a motorized stage Two additional serial ports and one additional USB 2 0 connection not a hub if you plan to use a Continuum XL microscope One additional PCI slot if you plan to use a microscope with video capability If you purchased your computer from Thermo Electron your software is already installed If you provided your own computer you need to install OMNIC on your hard drive See the instructions that came with the software CD or read Installing OMNIC or EZ OMNIC in the document titled OMNIC Spectroscopy Software that came with your software You can use these same instructions if you ever need to reinstall the software Nicolet FT IR User s Guide 5 Where to find the information you need 6 Wizards and tutorials The on line and printed documentation included with your system is designed to let you find the information you need quickly We recommend first using the on line documentation provided with OMNIC when you have a question OMNIC includes several on line tutorials a wizard and a complete Help system See Starting OMNIC in the Before You Collect Spectra chapter for information about start
39. or 608 276 6373 Fax 608 273 6883 E mail techsupport analyze 9 thermo com Nicolet OMNIC Avatar Val Q Centaurus RSVP Smart Accessory Continuum Smart Purge OMNI Transmission FiberPort Ever Glo Passport Import SeaPort Solid Substrate Talon PLUS Vectra Plus Snap In SabIR Sync UpDRIFT Smart Refractor SpeculATR SAGA OMNI Sampler Smart Collector Smart ARK Gemini Endurance InspectIR Orbit and E S P are trademarks of Thermo Electron Scientific Instruments Corporation a subsidiary of Thermo Electron Corporation MIRacle is a trademark of PIKE Technologies SplitPea is a trademark of Harrick Scientific Corporation DuraScope and DuraSamplIR are trademarks of SensIR Technologies Windows is a trademark of Microsoft Corporation Intel and Pentium are trademarks of Intel Corporation PS 2 is a trademark of International Business Machines Corporation 269 155800 5 Contents Welcome t HH HM 1 About this manual uec ei sheets Coates ee toe soie iui iis 2 Questions OF CONCETNS oco esed bx pi Ini god Indes uns Frid n pud DE magnons 3 System requirements 1 5 coit erence tI IE ueMGxuDvIU Bad IU aee V Mua qoM RN 4 Installing OMNI C iecit qpecun abite n tesi otii ln phesu uxo eR d 3 Where to find the information you need sese 6 Wizards and tutorials edo aber EE tn Ei dice ipie in ibus 6 On line rli rn 7 Finding answers to your questions eeeeeeeeene 9 Bef
40. sleep and stand by modes 57 SfAtUS cie impr RR UN REIR RERUMS 26 temperatute er err ea Ripe 153 theory cos ae etae dte am e aleve c dest 6 COU ineo eo ne pai eee ie 6 troubleshooting eeeeeeeeeeene 137 turned Oft eri ete tes 145 t ftiing ON sedente estratto res R teet ee ss 18 56 when to align essere 124 when to open cover Of esses 123 when to turn off 127 spectrum adding to user library ceeceeseeseeceeeteeeeeeseeesees 47 background eR tte ARR 27 baseline not flat etes 153 cannot be added to library s 135 carbon dioxide peaks in esses 151 collecting eere 12 23 27 30 53 98 color otiose sencoo pae dee eit ves 111 comparing with QC library spectra 43 copying and pasting esssseeeeee 121 COITGCUD oe Rete ete 102 correcting baseline Of sese 116 creating report containing eeeeeeeeeree 48 dele ng etie edet edi 108 derivative shaped peaks in ss 152 distorted 5 ttr Rs 69 fringes or channeling in sss 150 math operations eese 118 moving in pane 114 moving stacked ero 114 moving to another window sess 114 o peaks 1n iade eee titio 152 ner Sum RE 154 OPEM Dr aiowceten a AR Ea 106 preparing for
41. spectrometer and quickly switch beam paths to the AEM to collect data from other samples without removing accessories from the main sample compartment Any accessory or detector that can be installed in the spectrometer can be installed in the AEM The AEM has two detector locations Custom accessory baseplate You can use this Smart baseplate to mount an accessory you have built or purchased from another manufacturer When you install the accessory and baseplate in the sample compartment the system automatically selects the Custom Accessory experiment or allows you to select from the experiments you have saved for the baseplate Detector interface kit A variety of accessories that were specifically designed for Nicolet FT IR spectrometers contain detectors that are automatically recognized by your spectrometer The detector interface kit allows your spectrometer and OMNIC software to recognize other detectors including non Thermo Electron detectors Energy screen wheel This accessory lets you prevent detector saturation and signal distortion by using a screen to block a portion of the infrared energy See Using the energy screen wheel in the Spectrometer Options chapter for complete information Filter wheel This accessory available for the Nicolet 6700 only lets you control the spectral range of the infrared light that reaches the detector by inserting low pass or high pass filter into the beam path See U
42. the purge gas source You can use OMNIC to set the duration of increased purge flow In OMNIC Help Topics find purge in the Index and go to Setting Smart Purge Thermo Electron Corporation Checking the desiccant Desiccant Note If your spectrometer is sealed and desiccated a bag of desiccant is located under the beamsplitter compartment cover The desiccant protects the beamsplitter and other optical components by reducing the amount of water vapor inside spectrometer See Checking and changing desiccant in the Maintaining your spectrometer book in Spectrometer Help Topics if you need to change the desiccant If your spectrometer is in use check the humidity level inside it monthly more often in very humid climates by clicking the Check Desiccant button on the Diagnostic tab of the Experiment Setup dialog box If the level exceeds the factory specified limit a message informs you Be sure to change the desiccant so that the optics will be protected If your spectrometer is in storage check the round blue indicator on the desiccant holder under the beamsplitter compartment cover monthly Change the desiccant if the indicator has turned pink Keep all covers closed tightly while the spectrometer is in storage The Check Desiccant button measures humidity more accurately than the indicator For this reason you should rely on the button to monitor the performance of the desiccant when the spectrometer is in u
43. thinner sample Collect a new background spectrum to use for ratioing your sample spectra Make sure you are using the correct purge gas and that purge flow rate is adequate Allow the system 3 to 5 minutes to reestablish purge before collecting the spectrum Install an appropriate purge gas source and optional purge kit Contact Thermo Electron for details Replace the air dryer with one that removes carbon dioxide or use nitrogen to purge the spectrometer Contact Thermo Electron for more information Check the humidity indicator and replace the desiccant and indicator if needed Make sure you are using the correct purge gas and that purge flow rate is adequate Allow the system 3 to 5 minutes to reestablish purge before collecting the spectrum Install an appropriate purge gas source and optional purge kit Contact Thermo Electron for details Nicolet FT IR User s Guide 151 A spectrum contains no peaks A spectrum contains derivative shaped peaks 152 No sample is in the infrared beam path The sampling cup in a diffuse reflection experiment is not in place or is tilted An infrared microscope is in its viewing mode A sample film in an ATR experiment is being held against the ATR crystal with uneven pressure or has poor contact with the crystal The resolution is set too low A sample in a diffuse reflection experiment also has a specular reflection component The infrared beam wa
44. use the Vertical Expand Contract buttons right most The Roll Zoom Window in the View menu also expands or contracts an area In OMNIC Help Topics find Roll Zoom Window command in the Index and go to Rolling and zooming spectra for more information about expanding and contracting a spectral region Nicolet FT IR User s Guide 113 114 How can I move a spectrum up or down in its pane to see it better Use the selection tool to drag the spectrum up or down The Roll Zoom window available in the View menu to move a spectrum up or down In OMNIC Help Topics find Roll Zoom Window command in the Index and go to Rolling and zooming spectra for more information about moving spectrum How can I move a spectrum into another spectral window Use the selection tool to drag the spectrum from one spectral window to another A copy of the spectrum appears in the second window and the original spectrum remains in the first window You can also copy or cut the spectrum using Copy or Cut in the Edit menu and then paste it into another spectral window using Paste In OMNIC Help Topics find spectrum in the Index and go to Selection tool or find pasting spectrum and go to Pasting items How can I move a stacked spectrum into another pane Use the selection tool to drag the spectrum from one pane into another In OMNIC Help Topics find spectrum in the Index and go to Selection tool Thermo Ele
45. 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 EXIICNITCIE o Ez Be Edit collect view Process Analyze Report Window Help 15 x iss Default Transmission X JBench Status o o c S S o 2 lt Pss T 2000 Wavenumbers cm 1 536 4 090 Qa us bal E E ul ac a ie m e D 36 Thermo Electron Corporation How do I know if my spectrum is good v4 Collect Status Saving the spectrum The Collect Status indicator near the bottom of the Collect Sample window shows the status of the collection When the indicator is a green check mark it shows that the spectrum has passed all of the selected spectral quality checks made so far After the collection is finished and the indicator is a green check mark you can 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 the indicator is a red X there is a problem with the quality of the spectrum After correcting the pr
46. you switch to a different detector on either model spectrometer or beamsplitter on a Nicolet 6700 only OMNIC automatically resets the default spectral range in the Experiment Setup dialog box Be sure to check the range and set the velocity to a value that is appropriate a Nicolet FT IR User s Guide 71 Using the filter wheel Spectrometer Options This chapter explains how to use these optional spectrometer features The automated filter wheel available for the Nicolet 6700 only moves optical filters supplied by you into the beam path The energy screen wheel moves an energy screen into the beam path to reduce the energy reaching the detector The polarizer allows you to control the orientation of the electric field vector of the infrared beam entering the sample compartment The optional filter wheel accessory available for the Nicolet 6700 only lets you automatically insert optical filters band pass low pass or high pass into the beam path This lets you reduce the amount infrared light that reaches the detector in a spectrally selective way This is particularly useful for studies of small spectral regions or for blocking noisy spectral regions that contain no data of interest Energy from other regions does not reach the detector thus improving the signal to noise ratio in the region of interest 72 Thermo Electron Corporation ui 4 The accessory has two wheels wheel A is closest to the
47. 73 5015 worldwide Fax 608 273 6883 worldwide E mail techsupport analyze thermo com World Wide Web http www thermo com spectroscopy Nicolet FT IR User s Guide 3 4 System requirements If you are supplying your own computer be sure that it meets the following requirements for hardware and software Thermo Electron Corporation One of the following versions of Windows software Windows 2000 latest Service Pack recommended Windows XP Professional latest Service Pack recommended Microprocessor Intel Pentium III 1 0 GHz recommend Intel Pentium II 400 MHz minimum Random access memory RAM 256 megabytes recommended 128 megabytes minimum If you plan to use a microscope 1 gigabyte recommended 512 megabytes minimum Disk drives 5 0 gigabytes recommended hard disk drive 2 0 gigabytes minimum hard disk drive 1 44 megabyte floppy disk drive for 3 5 inch floppy disks Quad speed CD ROM drive Video 15 inch SVGA 4 megabytes of video RAM 16 bit video card capable of displaying at least 256 colors with 1024 by 768 resolution Installing OMNIC e IO devices and card slots Sound card and speakers for listening to the audio portions of tutorials Keyboard and serial USB or PS 29 style mouse Printer port USB parallel and or serial if you plan to print on a local printer One USB 2 0 connector not a hub for data transfer Ethernet port if you plan to connect the system to a
48. GaAs MCT A MCT B InSb PbSe PbS TEC with SabIR InGaAs MCT A MCT B InSb 8 PbSe DTGS KBr DTGS TEC InGaAs 62 Thermo Electron Corporation Spectral Range cm 13 000 2 800 25 000 8 600 13 000 2 000 14 500 8 600 11 700 2 800 11 700 2 800 11 500 2 800 13 000 2 800 10 000 4 200 12 000 3 800 11 700 1 200 11 700 1 200 11 500 1 850 13 000 2 000 10 000 4 200 12 000 3 800 11 000 600 11 000 400 11 000 1 850 11 000 2 000 11 000 375 11 000 375 12 000 3 800 Source ETC white light White light ETC white light White light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light ETC white light Light Range Beamsplitter Detector Spectral Range cm Source mid IR KBr DTGS KBr 7 400 350 ETC MCT A 7 400 600 ETC MCT B 7 400 400 ETC DTGS TEC 7 100 350 ETC DTGS CsI 6 400 350 ETC CsI DTGS CsI 6 400 225 ETC MCT A 6 400 600 ETC MCT B 6 400 400 ETC ZnSe DTGS KBr 4 000 650 ETC MCT A 4 000 650 ETC MCT B 4 000 650 ETC DTGS TEC 4 000 650 ETC DTGS CsI 4 000 650 ETC far IR Solid Substrate DTGS PE 700 50 ETC Si bolometer 700 20 ETC Notes
49. MNIC Help Topics find extended search in the Index and go to Using extended search What is the easiest way to collect sample spectra and add them to a spectral library If you are using OMNIC use the Collect Spectrum button on the Library Names tab of Library Manager available through the Analyze menu to collect a spectrum and add it to a user library The software automatically sets the experiment parameters for example Resolution so that the spectrum will be compatible with the selected library This allows you to collect and add a compatible spectrum in one step instead of three using Experiment Setup to set the parameters Collect Sample to collect the spectrum and Add To Nicolet FT IR User s Guide 105 Opening saving and deleting spectra 106 aM m a J Library to add the spectrum to the library What does the search expert do It determines the search algorithm to use searches the spectral region from 2600 to 450 wavenumbers and then displays the specified number of library spectra that best match the unknown spectrum plus comments about the search results For example the search expert may tell you that the best match is excellent but the second best match is also similar to the unknown You will be able to display the list of matches to see their match values and index numbers How do I open a stored spectrum Choose Open from the File menu locate the spectrum or spectra you want to open sel
50. R single beam spectrum is typically found near 2 000 cm 4 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 a The distorted signal may cause problems with photometric accuracy For good quantitative data the sample and background interferograms should be about the same size Scattering samples and very dense samples produce very small signals that when compared with much larger background signals can distort quantitative data Check the background and sample interferograms If you see a substantial difference in their sizes photometric accuracy could be a problem To solve these problems you can use the following options to modify the infrared beam e Use a bandwidth limiting filter e Use an energy screen e Adjust the aperture on a Nicolet 6700 In Spectrometer Help Topics view Setting up experiments for instructions for using filters and energy screens In some cases system performance improves if you use a filter or screen The filter or screen that you should use for your application depends on the samples being measured and other experimental conditions Try using various filters or screens to determine which give the best results Nicolet FT IR User s Guide 65 When to use bandwidth limiting filters When to use energy screens Use bandwidth limiting filters to improve
51. a green check mark In OMNIC Help Topics find quality checks in the Index and go to Quality checks Thermo Electron Corporation Converting spectra to other units Which Y axis unit should I use for a spectrum 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 Kubelka Munk units are useful for searching diffuse reflectance spectra against libraries of absorbance spectra Use photoacoustic units for spectra collected using a photoacoustic accessory Percent reflectance units are mathematically equivalent to transmittance units but using them for spectra collected using a reflection technique serves to identify the technique Using log 1 R units for spectra collected using a reflection technique is useful for quantitative comparisons since there is often a linear relationship between the concentration of a component and its log 1 R value Collecting a Spectrum available through Learning OMNIC Typical IR Transmission Spectrum In the OMNIC Help Topics Index Find absorbance and go to Converting spectra to absorbance Find transmittance and go to Converting spectra to transmittance Find Kubelka Munk units and go to Kubelka Munk units Find photoacoustic units and go to Photoacousti
52. above a specified height or find label and go to Annotation tool How can I close a task window such as the Find Peaks window Click the Close button if available in the upper right corner of the window You can also double click the button at the left end of the window s title bar if the window is not maximized or the button at the left end of the menu bar if the window is maximized In OMNIC Help Topics find task window in the Index and go to Task windows How can I select a spectral region for an operation Use the region tool to drag across the region in the pane In OMNIC Help Topics find spectral region in the Index and go to Region tool 120 Thermo Electron Corporation 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 in the Index and go to Collection and processing information If you want this kind of information displayed in a spectrum s pane choose Display Setup from the View menu turn on Sampling Information and then specify the types of information you want displayed by turning on options in the Sampling Information box In OMNIC Help Topics find displaying sampling information in the Index and go to Displaying sampling informa
53. absorbance units In the next section you will label a peak in the absorbance spectrum using the annotation tool The palette contains six tools that let you select a spectrum or spectral region change how spectra are displayed in a spectral window find the height or area of a peak or label a peak The names and appearance of the palette tools indicate their functions Region Peak height Annotation Selection Spectral cursor Peak area Only one tool can be used at a time To use a tool first select it by clicking it A tool remains selected until you select another tool 40 Thermo Electron Corporation 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 X 3427 273 2 504 Follow these steps to label a peak in the polystyrene spectrum 1 Select the annotation tool by clicking it The annotation tool lets you label peaks with their frequency locations X values or other information When the annotation tool is selected and you move the pointer into the spectral display the pointer looks like this VT You can label a peak by clicking above it with the annotation tool This displays the label text above the peak wit
54. agnostics from the Collect menu You can also close OMNIC click the Start button in Windows point to Programs All Programs in Windows XP point to the Thermo Nicolet folder and then choose Bench Diagnostics This gives you access to advanced features of the software including the performance test that are not available if you run the diagnostics from OMNIC Thermo Electron Corporation 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 EE Click this button to return to the main Diagnostics window E To exit the Bench Diagnostics software click the Close button at the far right end of the title bar Nicolet FT IR User s Guide 149 XO Troubleshooting Applications Problems If you have turned on OMNIC s spectral quality checks feature the software automatically checks the status of collected interferograms and background and sample spectra When OMNIC performs a check and detects a problem with data collection or spectra the Collect Status indicator is displayed as a yellow circle or a red X You can click the indicator or click the View Collect Status button at the end of data collection to see a summary of data collection problems encountered during the collection and other information about the collection Th
55. apr SISA The information in this publication is provided for reference only All information contained in this publication is believed to be correct and complete Thermo Electron Corporation shall not be liable for errors contained herein nor for incidental or consequential damages in connection with the furnishing performance or use of this material All product specifications as well as the information contained in this publication are subject to change without notice This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under our patent rights nor the rights of others We do not assume any liability arising out of any infringements of patents or other rights of third parties We make no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose Copyright 2004 by Thermo Electron Corporation Madison WI 53711 Printed in the United States of America All world rights reserved No part of this publication may be stored in a retrieval system transmitted or reproduced in any way including but not limited to photocopy photograph magnetic or other record without the prior written permission of Thermo Electron Corporation For technical assistance please contact Thermo Electron Corporation 5225 Verona Road Madison WI 53711 4495 Telephone 800 642 6538
56. asure liquids powders and pliable solids Smart DuraScope The Smart DuraScope combines the benefits of a diamond ATR element with video enhancement to create an analysis tool for a wide range of sample types from large hard materials to small inclusions and contaminants You can position the sample while looking through the diamond ATR element This helps you manipulate micro samples to achieve optimum contact with the crystal resulting in superior quality spectral data Smart Endurance This single reflection diamond ATR accessory is rugged and versatile It stands up to highly corrosive caustic intractable or abrasive samples making it a good choice for almost any sample type Smart Golden Gate This is a horizontal single reflection ATR accessory that features an extremely durable diamond crystal It handles a wide range of sample types including hard or brittle solids corrosive liquids and hard powders Thermo Electron Corporation 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 A complete line of fiber optic probes is available for sampling a wide range of sample types Smart MIRacle This is a single reflection h
57. at is the difference between the Display Setup parameters and the Window options The parameters in the Display Setup dialog box affect the currently active spectral window only The options in the Window options in the Options dialog box available through the Edit menu affect all the new spectral windows that you create After you create a new spectral window you can change the way spectra are displayed in it by using Display Setup in the View menu In OMNIC Help Topics find display parameters in the Index and go to Setting the display parameters or find Window options and go to Window options Nicolet FT IR User s Guide 111 112 What can I do with the Scale commands in the View menu By using the appropriate command you can display spectra so that they are easier to see or compare Full Scale displays the spectra so that they perfectly fit their panes vertically Automatic Full Scale does this automatically when you change the display with the view finder or selection tool The Y axis displayed corresponds to the selected spectrum Common Scale displays all the spectra so that they are not cut off at the top or bottom and use the same Y scale This allows you to compare the band intensities of different spectra Match Scale changes the Y scale of the spectra to be the same as that of the selected spectrum The selected spectrum s scale is not changed This allows you to compare the band intensitie
58. available in the toolbar or in the Collect menu it OMNIC Window E File Edit Collect View Process Analyze Report Window Help sis Default Transmission Plo eS No spectra selected Laa Nicolet FT IR User s Guide 25 Bench Status indicator X Note Toolbar To the right of the Experiment drop down list box is the Bench Status indicator JBench Status If the indicator is a green check mark the spectrometer has passed all of its diagnostic tests If the indicator is a yellow circle a cooled detector in the spectrometer has become warm A message appears explaining the problem and allowing you to access information about correcting it If the indicator is a red X the spectrometer has failed a diagnostic test and requires corrective action A message appears explaining the problem and allowing you to access information about correcting it If you want to view the on line videos to help troubleshoot a problem put the spectrometer s Tutorial CD into the computer s CD ROM drive 4 At the left side of the window is the toolbar You can use Edit Toolbar in the Edit menu to position the toolbar at the top or right side of the OMNIC window as well Each button in the toolbar represents a command or other feature To see the name of the command or feature point to the button and wait a moment To initiate the command or feature click the button with the left mouse button In OMNIC Help Topics find toolbar
59. b of the Experiment Setup dialog box The detector cable is loose at the accessory connector on the rear of the spectrometer or on the back wall of the sample compartment Thermo Electron Corporation Click the source indicator on the Diagnostic tab of the Experiment Setup dialog box to verify that the source is burned out Call Thermo Electron to order a replacement source In Spectrometer Help Topics view Replacing your source in Replacing parts to find part number ordering and installation instructions If you suspect your detector has a vacuum leak view Detector does not stay cooled in the Troubleshooting book in Spectrometer Help Topics Set Detector to None on the Bench tab of the Experiment Setup dialog box Check and tighten the cables The Scan status The spectrometer is turned off indicator does not flash the system is not The spectroscopy software has scanning not been started The spectrometer is out of Note After 1 hour alignment without data collection activity the interferometer stops scanning and the Scan light stays on This is normal Any data collection activity will cause the interferometer to begin scanning The electronics module needs to be reset The laser is flickering The laser is off Continued on next page Turn on the spectrometer power Start OMNIC or other software you are using Align the spectrometer using the Align button on th
60. c units topic Find reflectance and go to Reflectance units Find log 1 R units and go to Log 1 R units Nicolet FT IR User s Guide 101 Using How do I search a spectral library Sp ectr al libr ares First prepare the spectrum as explained below and display or select the region you want searched Then set up the search using Library T e Setup in the Analyze menu and start the search by clicking the r T Search button in the Library Setup dialog box or by choosing Search from the Analyze menu 5 In OMNIC Help Topics find library in the Index and go to J Setting up a library search or Searching a spectral library How should I prepare my spectrum before searching it against a spectral library There are several corrections you can perform on a spectrum to obtain the best search results e If the baseline of the spectrum is sloped curved or shifted E vertically correct it using Baseline Correct in the Process menu In OMNIC Help Topics find baseline in the Index and go to S Correcting a baseline manually Ifthe spectrum has totally absorbing bands eliminate them by UN using Blank in the Process menu Be careful not to blank regions that contain other important spectral information In OMNIC Help Topics find blanking spectral region in the S Index and go to Blanking a spectral region You can also use the region tool to select a reg
61. ckground spectrum How do I specify the Y axis unit for collecting spectra Choose Experiment Setup from Collect menu and then set Final Format on the Collect tab You can change the format of a collected spectrum by using Absorbance Transmittance or Other Conversions in the Process menu See the question and answer in the next section for a description of the available units Collecting a Spectrum available through Learning OMNIC Typical IR Transmission Spectrum In OMNIC Help Topics find units in the Index and go to Selecting the final format 98 Thermo Electron Corporation S 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 We recommend using this setting to ensure the best spectral quality In OMNIC Help Topics find gain in the Index and go to Setting the gain When should I save interferograms with my spectra Save interferograms if you think you may want to restore the original data after it has been processed or if you want to keep an archive of your original data Collecting a Spectrum available through Learning OMNIC Preparing the Software In OMNIC Help Topics find saving interferograms in the Inde
62. colet FT IR User s Guide 49 50 3 Thermo Electron Corporation 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 Choose OK The report is printed on your system printer A 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 The back panel and Inside the spectrometer for complete descriptions of your spectrometer s internal and external components Spectrometer The following illustration identifies some major components visible p on the outside of a typical Nicolet 6700 spectrometer Some components components may not be present on your spectrometer Status indicators Sliding door yA Data collection Ys buttons Beamsplitter Detector fill ports 2 and desiccant 2e M compartment Y Teo a E Detector compartment Emission port for external source Sample D External beam port compartment Nicolet FT IR User s Guide 51 For more information about the Auxiliary pass through connectors see the How to cable an accessory section of the Accessories
63. connector cccceccccccceeeeesceccccceceusssesseceesseees 95 Quick Answers to Your Questions About Using OMNIC 97 Collecting spectra s aisi o MER IR MVP ER IRMN A Scie 97 Converting spectra to other units eee 101 Using spectral Bbtari s a ees ete S emt Se eob eigen pa eee v uctus 102 Opening saving and deleting spectra sess 106 Printing ga os ca sates oun odii reu laf ed Ea QURP Oe NE PN EU fis 109 Displaying Spectra ee e toit cerca eed aae eee lade aUo Oo da 110 Correctie spectra coupe p cas edi Edd A E Ont ean 116 Subtracting adding multiplying and dividing spectra 116 Customitzinp OMNIC codo e a dann cea odas foa ds 119 Other questiols osos sore ee ideae iet eeepc tsi iie re 120 Quick Answers to Your Questions About Using the Spectrometer ists aaarabsid IE PAN aana en 123 Maintenance and Service seii te siio codec bots pieds tua 128 Running diagnostic tests on spectrometer components 129 Maintaining your spectrometer sseeeseeeeeeeeene nene 130 Aligning the spectrometer eee eese ences 130 Aligning an accessory eese esee es eene eene tne tnnt tanen 132 Checking spectrometer performance eese 132 Servicing your spectEOImeter eese eeyveuze sees hee da Pese SURE eae de aer PRe s iR 134 Troubleshooting Software Problems esses 135 Troubleshooting Hardware
64. ctors complies with the voltage and current limitations given in the following Warning Improper or unsafe cabling can cause damage to your accessory and may create a safety hazard Only qualified persons should cable a custom accessory using these connectors Do not pass signals that exceed 15 VDC through these connectors You must also limit the current to a maximum of 800 mA Thermo Electron is not responsible for damage or injury resulting from improper or unsafe cabling a The following diagram shows schematically which pins of the Auxiliary connector inside the sample compartment are connected internally to pins of the Auxiliary 1 and Auxiliary 2 connectors on the front of the spectrometer Since none of these connected pins are assigned by the Nicolet 4700 or Nicolet 6700 they are available for use with custom accessories Sample Compartment Front Panel Connector Connectors e e e oe eo 15 14 13 12 11 10 Thermo Electron Corporation Detector Motors connector A Caution You can use the Detector Motors connector on the rear wall of the sample compartment to connect your own detectors accessory motors and other custom hardware eee E E E a eee0e080 5 14 13 12 11 10 1 Detector Motors Make sure your use of the connector complies with the voltage and current limitations given in the following Warning Improper or unsafe cabling can cause damage to your accessory and may create a safety hazard
65. ctron Corporation 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 How can I find the height of a peak Use the peak height tool to click the top of the peak Then drag the baseline handles to adjust the baseline used for the measurement The corrected measured above the baseline and uncorrected height values appear in the readout above the palette In OMNIC Help Topics find peak in the Index and go to Peak height tool How can I find the area of a peak Use the peak area tool to drag across the peak Then drag the baseline handles to adjust the baseline used for the measurement The corrected measured above the baseline and uncorrected area values appear in the readout above the palette In OMNIC Help Topics find area in the Index and go to Peak area tool Nicolet FT IR User s Guide 115 Correcting spectra Subtracting adding multiplying and dividing spectra 116 lefu oe Note Should I correct the baseline of my spectrum If a baseline is sloped or curved or significantly above zero absorbance or below 100 transmittance a likely cause is how the sample was prepared By correcting the baseline you can often avoid having to prepare the sample again and collect a new spect
66. de o pes 90 S SabIR a an n a E a a a 88 Safety dcos UO e Ht E e eeu 14 sample installing 4er teret eet eee 11 29 34 Dot present onset ener nene eee terea rds 152 ovid dH 151 sample button 5 hie etae te ees 53 sample compartment CODDECtOFS og eee tpe ye tr eterne 92 windows fogged sese 143 sample film in ATR experiment eere 152 sample holder installing 2 xoti Uit 28 installing sample or filter in ss 29 sample shuttle ene ett e te 89 sample spectrum adding to spectral library eee 105 adding to spectral window sess 36 collecting deri ene 27 30 53 sample Wheel eene ho ge 85 sampling accessories esee 85 sampling cup missing or tilted 152 sampling techniques eene 6 SaturatiOn 5 ceterae c n e ER 154 detector un stie eerte De 64 65 66 67 saving COBIIBUFAtlOD cie acere eat et ecd 119 InterferOgramis n ooi eg eee 99 duce 107 spectra as Brousse 8 e ie rei id 108 spectra automatically eere 106 centi m 37 Scan indicator sesseeeeeeeeen e 18 56 145 flashing intermittantly eere 143 scans n rmbet 0f ie diee RECEN EEEE 35 SCAMLETING EP 69 Scrapbook library esee 104 sealed and desiccated sss 33 34 sealed and desiccated sy
67. e Diagnostic tab of the Experiment Setup dialog box Turn off the power to the computer and the spectrometer Leave the power off for 15 seconds Turn on the spectrometer and wait until the start up diagnostics finish Then turn on the computer and restart OMNIC Click the laser indicator on the Diagnostic tab of the Experiment Setup dialog box to check the laser operation Call Thermo Electron for assistance Turn off the spectrometer power unplug the power cord remove the spectrometer cover and make sure the laser cable is seated properly See Replacing the laser in the Servicing your spectrometer book in Spectrometer Help Topics for instructions Warning Never open the spectrometer cover without first turning off the power and unplugging the power cord Nicolet FT IR User s Guide 145 The Scan status The laser or electronics module indicator does not flash is defective continued 146 The spectrometer is overheated You can check whether the temperature of the electronics board is within the acceptable range by clicking the electronics indicator on the Diagnostics tab of the Experiment Setup dialog box A component has failed The beamsplitter is not properly seated Thermo Electron Corporation Check the laser indicator on the Diagnostic tab of the Experiment Setup dialog box If there is a red slash through the indicator click the indicator to view information about the laser operation
68. e collecting spectra Nicolet FT IR User s Guide 19 20 Starting OMNIC Follow these steps to start OMNIC 1 Thermo Electron Corporation Start your Windows software Depending on the version of Windows you are using you may be required to enter your user name and password Enter the information when you are prompted Double click the OMNIC shortcut on the Windows desktop b ppa OMNIC Alternatively you can click the Start button on the Windows taskbar point to Programs All Programs in Windows XP point to the Thermo Nicolet folder and then click the OMNIC program Depending on how the program has been configured dialog boxes may appear asking for a user name and password Type the requested information and then choose OK The OMNIC window appears This window is described in the next chapter and in the Getting Started With OMNIC tutorial available through Getting Started in the Help menu Selecting an experiment The parameter settings for collecting spectra are stored in experiment files You load the settings you wish to use when you select an experiment from the Experiment drop down list box below the OMNIC menu bar see the example below Saale Default Transmission ki Default Transmission A number of experiments are included with OMNIC for performing a wide variety of data collections You can open these experiments by choosing Open in the Experiment Setup dialog box Experiment Setup is
69. e collection and processing information for the spectra you collect By controlling which position of each wheel is in the beam path you can collect spectra with no filter just one filter or a combination of two filters For example you could install and select a band pass filter to block out frequencies in both the high and low ends of the spectral range resulting in a spectrum with absorptions only in the middle of the range You also could accomplish mid range data collection using a high pass filter installed in one wheel and a low pass filter installed in the other To specify the filter s to use for an experiment set Filter Wheel A and Filter Wheel B on the Bench tab of the Experiment Setup dialog box available through Experiment Setup in the Collect menu Experiment Setup C My Documents OMNIC Param Default exp E 31 x CEA an MAE EE Max 0 03 Min 0 02 Loc 1024 f MiniMax f Peakto peak Parameter Value Sample compartment Main Detector DTGS KBr Beamsplitter Source Accessory Window Recommended range Max range limit Min range limit T 1000 Data points us 4100 cm 1 low pass lt Filter wheel B 2800 cm 1 high pass Single beam 74 Thermo Electron Corporation em 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 le
70. e controlled flow cell and must be connected to a thermogravimetric analysis TGA furnace You can analyze the evolved gases from TGA experiments using the OMNIC Series software The TGA interface is usually mounted in the sample compartment of an AEM the TGA module is usually installed on the side of the spectrometer leaving the AEM or spectrometer sample compartment free for other experiments and accessories Transmission E S P accessory Transmission is the oldest and most efficient sampling technique in FT IR spectroscopy and can be used for sampling liquids gases or solids A variety of cells and sample holders are available for transmission analysis All can be mounted in the spectrometer sample compartment Thermo Electron s E S P Enhanced Synchronization Protocol technology provides continuous communication between the accessory and OMNIC to ensure that the accessory is operating correctly This accessory or the validation wheel described below is required for using an NPL or serialized polystyrene standard for validation with Thermo Electron s Val Q software Nicolet FT IR User s Guide 89 90 System accessories 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
71. e installed on spectrometers with sample compartment windows a In Spectrometer Help Topics view Installing optional hardware for detailed information about installing the polarizer In these experiments a unique background is required for each polarization position used For example if you are going to collect spectra at 0 and 90 degrees corresponding background spectra are required at 0 and 90 degrees Thermo Electron Corporation 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 Experiment Setup C My Documents Omnic Param default exp 7 2x onec ERI ouai Advanced Dieunostc Configure izz Max 4 62 Min 2 67 Loc 1024 SEWNTNEN WANG Min Max Peak to peak Sample compartment Main Detector MCT A j Beamsplitter KBr m Source IR B Accessory None E Window None Recommended range 4000 650 Max range limit 4000 Min range limit 400 Gain 2 Autogain ha Velocity 0 6329 i Aperture 100 Sample shuttle Ej 1000 Screen wheel Open j Data points Filter wheel A Open Filter wheel B Open X 44 x PA Polarizer angle ES Single beam Tone In OMNIC Help Topics find polarizer in the Index and go to Controlling
72. e spectrometer has not been For best results allow the spectrometer on long enough to reach at least one hour to stabilize after thermal equilibrium turning it on The spectrometer is not Check the system to make sure the properly purged correct purge gas is being used and that the flow rate is correct Nicolet FT IR User s Guide 153 A spectrum is too noisy There were too few scans The resolution was too high The purge gas flow rate or pressure is too high The detector is saturated The moving mirror velocity is set too high for the detector The sample in an ATR experiment is not in good contact with the ATR crystal 154 Thermo Electron Corporation Increase the number of scans on the Collect tab of the Experiment Setup dialog box Reduce the resolution use a higher numerical setting on the Collect tab of the Experiment Setup dialog box Check the pressure regulator it should be set between 0 7 and 1 4 bar 70 and 140 kPa or 10 and 20 psig Check the flowmeter it should read 15 scfh about 0 4 m3 hr Adjust the flow rate if necessary Add a bandwidth limiting filter or an energy screen to reduce the signal strength Set Velocity on the Bench tab of the Experiment Setup dialog box to a lower value Reapply the sample to obtain more consistent contact between the sample and the ATR crystal Index a absolute transmission accessory eene 85 absorbance units
73. ect the filenames of the spectra and then choose OK You can hold down the Control key to select multiple files In OMNIC Help Topics find spectrum in the Index and go to Opening spectra How can I save my collected spectra automatically Choose Experiment Setup from the Collect menu and turn on Save Automatically on the Collect tab Save Automatically is on by default Specify a base name for naming the saved spectral data files in the Base Name box A sequential number will be appended to the base name when the spectra are saved If you want the interferograms saved with the spectra turn on Save Interferograms Individual spectra are saved with the extension SPA Collecting a Spectrum available through Learning OMNIC Preparing the Software Thermo Electron Corporation 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 In OMNIC Help Topics find report notebook in the Index and go to Adding a report to a notebook You can also place spectra in descriptively named user libraries that you create Keeping spectra in libraries allows you to find them by searching for text contained in the information saved with the spectra In OMNIC Help Topics find s
74. er Does my detector need to be cooled with liquid nitrogen Detectors that have a dewar need to be cooled Dewar detectors are fairly large metal cylinders with a hole in the top These include MCT and InSb detectors To determine if your detector requires cooling open the detector compartment cover and see if the detector has a dewar If during a work session you find that the detector signal intensity is decreasing the dewar may need to be refilled with liquid nitrogen Spectrometer Help Topics Cooling a detector in Setting up experiments Nicolet FT IR User s Guide 125 126 When should I change the desiccant in sealed and desiccated spectrometers only If your spectrometer is in use check the performance of the desiccant by using the Check Desiccant button on the Diagnostic tab of the Experiment Setup dialog box If the check indicates that the desiccant is no longer effective replace it Spectrometer Help Topics Checking and changing desiccant in Maintaining your spectrometer If your spectrometer is in storage check the round blue indicator on the desiccant holder under the beamsplitter compartment cover monthly Change the desiccant if the indicator has turned pink See Ordering parts in Spectrometer Help Topics to find the part number for ordering desiccant bags The desiccant holder under the beamsplitter compartment cover holds one bag Which source should I use Use the source
75. er eei eR RR en 115 y PO EL 115 beo EE 112 Z zoom Expand Contract button ssssss 113 in ON spectrum eoe nie oer e eden 113 Zoom button none tte ei 49 Nicolet FT IR User s Guide 163 164 Thermo Electron Corporation
76. esolution y How to collect data in the visible spectral range If you want to achieve higher resolution you may need to use a smaller aperture setting on a Nicolet 6700 and an energy screen that transmits more light or no screen at all Your spectroscopy software will automatically change the aperture setting if a smaller beam size is required Be aware that the smaller beam size will reduce the signal to noise ratio In OMNIC Help Topics find aperture in the Index and go to Setting the aperture size for information about changing the aperture setting The ability of the spectrometer to collect data is affected by the detector beamsplitter combination and any energy screens or optical filters that are installed in the spectrometer For example if you use an optional quartz beamsplitter a silicon detector and a white light source the sampling range is extended to 25 000 cm 1 Since silicon detectors are very sensitive you will also need to install an energy screen or bandwidth limiting filter to prevent the detector from being saturated during the experiment The following table lists a variety of spectral bands in the extended spectral range and lists the filter or energy screen that should be used to obtain data in each range It also lists typical aperture and gain settings for experiments in each range Only the Nicolet 6700 has an aperture Spectral Range Filter or Screen Aperture Gain 16 000 9 000 cm red
77. f your spectrometer has the Smart Purge option Open the sliding door install the sample and then slide the door until it is open about 1 cm When you hear the purge flow rate return to normal close the door all the way and choose OK If your spectrometer is sealed and desiccated Open the sliding door install the sample close the sliding door and then choose OK ui 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 R IEXEREE d Wavenumbers cm1 2000 2 o The progress of the collection is indicated by the gauge below the spectrum The number of scans collected so far and the total number of scans for the collection are displayed to the right of the gauge Nicolet FT IR User s Guide 35 When data collection is finished a message may appear asking whether to add the spectrum to a spectral window Note If Collect To A New Window is selected in the Collect options available through Edit Options in the Edit menu this message does not appear since the spectrum is placed into a new spectral window automatically a 8 Press the OK Enter button to add the sample spectrum to the spectral window Choosing No would end the procedure without saving the spectrum Choosing More Scans would return you to the Collect Sample
78. formation Where a menu command name is given the corresponding toolbar button is also shown Depending on the software configuration you are using a particular button may not be present in your toolbar How do I set the software for collecting spectra You can set the software in one step by selecting a stored experiment from the Experiment drop down list box below the OMNIC window menu bar To set the experiment parameters individually use Experiment Setup in the Collect menu If you install a Smart Accessory the system automatically sets the software parameters or a list of appropriate experiments is made available for your selection and you can begin collecting spectra Collecting a Spectrum available through Learning OMNIC Preparing the Software In OMNIC Help Topics find experiment in the Index and go to Selecting an experiment or Using Experiment Setup Nicolet FT IR User s Guide 97 Sample du I Nx How do I collect a spectrum First set the parameters as explained above Depending on the settings you may need to install or remove the sample before collecting data Then press the Sample button on top of the spectrometer or choose Collect Sample from the Collect menu Collecting a Spectrum available through Learning OMNIC Collecting the Spectrum of a Sample In OMNIC Help Topics find spectrum in the Index and go to Collecting a sample spectrum or Collecting a ba
79. from the effects of water vapor by minimizing the time that the cover is removed a Spectrometer Help Topics Opening the main cover in Installing optional hardware When should I align the spectrometer Align the spectrometer in the following situations The ambient temperature has changed by at least 5 Celsius degrees about 9 Fahrenheit degrees e You are about to perform a spectrometer validation with Val Q or other software This ensures that the validation is run with the best possible interferometer and electronics settings The spectrometer power was turned off for more than a few minutes and has now been on for one hour We recommend that you leave the power on continuously but if you do need to turn it off allow the spectrometer to warm up for one hour and then align it before collecting spectra a 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 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 Maintenance and Service chapter Aligning the spectrometer in Maintaining your spectromet
80. g 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 eh 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 an energy screen to prevent the detector from becoming saturated or producing a distorted signal Spectrometer Help Topics Installing an energy screen in Setting up experiments When do I need to open the spectrometer cover You need to open the spectrometer cover to change sources Also you need to open the cover if you are installing a spectrometer component such as a laser Nicolet FT IR User s Guide 123 124 A Warning gt OP Important Note Do not operate the spectrometer with the main cover removed The cover protects you from exposure to laser light and live electrical connections A If you must open the main cover for maintenance or service reasons always turn off the spectrometer power and unplug the power cord first If you have a CsI beamsplitter protect it
81. gram on the Bench tab of the Experiment Setup dialog box if the interferogram is not present check the beam path and detector Remove the obstruction Check the Aperture parameter on the Bench tab of the Experiment Setup dialog box For an MCT A MCT B InSb PbSe Si or InGaAs detector set Aperture to 32 For a DTGS detector set Aperture to 100 Nicolet FT IR User s Guide 141 Problem 142 continued The spectrometer is overheated You can check whether the temperature of the electronics board is within the acceptable range by clicking the electronics indicator on the Diagnostics tab of the Experiment Setup dialog box A sampling accessory is not installed properly or is not aligned Detector and beamsplitter are not compatible Thermo Electron Corporation Make sure the cooling vents on the back of the spectrometer are not blocked Make sure the ambient temperature is between 16 and 27 C 60 and 80 F Make sure the accessory is installed correctly and if necessary align it See the instructions that came with the accessory Make sure that selected detector and beamsplitter are compatible Change detector or beamsplitter if necessary The signal intensity is low Also the Scan indicator may flash intermittently and the spectrometer alignment may fail The source is glowing unevenly The beam path is obstructed The sample compartment windows are fogged The beamsplit
82. grazing angle accessory eee eet eeee ese eseeeeeeeeeeeeeneeeee 84 h hardware requirements eee 4 Helps 5d tne erede en 6 7 122 i Information button eese 121 infrared SOUEGe i52 ge GEO eR Rhee 58 Inb detector nitor eot ee 125 Nicolet FT IR User s Guide 157 installing ACCESSOLIES cc oceani t D RE ER 6 12 ACCESSOLY ii eiae teo rta tie 85 beamsplitter iei 10 ELECTOR ccce eR Ere DE Td 11 h rdware 2 sei ete eere d p met emer elsi 7 OMNIS Sautdo neon nC 5 optical hilier a aa 29 sample cete WR REESE ER eS 11 29 34 sample holder 2 nate 28 SOULCE i eec bie EUN E PEE EEE 11 interferogram LOCATION trt eR REUS 147 NOt present ise etate avito uteris 141 SAVING zoe uen D qu ng uon 99 interferometer Stand by mode eet 145 IUBAG eei eunuchi eim 64 k KBr pellet improperly pressed 153 Kramers Kronig correction esee 103 152 Kubelka Munk units eese 101 l labeling peak 4 rhe pes 120 laser b rned Qut eR es 147 defectives testis idle ehe aee 146 detector misaligned sese 139 IlCketing none EEUU 141 145 rm 18 NOU OD c eese er ER Ee A ERREUR HR deis 145 not workilg unies eo ueduenes d 138 replacing ute Let eee 134 Laser indiCatot inier ie eee edite 56 156 Thermo Electron Corporation library adding spectrum to eee 47 105 coniimercl
83. h a line connecting the label to the peak The text is selected so that you can immediately edit it When you press Enter the label appears in its final form Nicolet FT IR User s Guide 4 You can more accurately locate the top of a peak by holding down the Shift key when you click near the peak 2 Label a prominent peak by holding down the Shift key and clicking a little above the peak The label appears Here is an example Absorbance n 4000 3500 3000 2500 2000 1500 1000 500 Wavenumbers cm 1 3 Press Enter to accept the label text You could also perform other operations on the label using the annotation tool To modify a newly created label edit the selected text before pressing Enter To modify an existing label click it and then type a new label and press Enter To delete an existing label click it and then press the Delete key gt f In OMNIC Help Topics find tool annotation in the Index and go S to Annotation tool for more information about the annotation tool In the next section you will compare the spectrum with the spectra in a QC library to verify the composition of the sample 42 Thermo Electron Corporation Verifying the composition of the sample Note You can verify the composition of your polystyrene sample by automatically comparing the collected spectrum with the spectra in a QC Quality Control library The software compares the sample spectrum
84. he positive peak and negative peak intensities are shown next to Max and Min above the live display The interferogram location will be shown next to Location unless Single Beam is selected on the Bench tab 6 When the alignment is finished close the Experiment Setup dialog box Nicolet FT IR User s Guide 131 132 Aligning an accessory Note Checking spectrometer performance You can also align accessories that mount inside a sample compartment This practice does not include Smart Accessories which do not require alignment First align the spectrometer without the accessory installed as described in the preceding section Then set Sample Compartment on the Bench tab of the Experiment Setup dialog box according to the accessory location Set Gain to a value that gives a signal intensity that is appropriate for the accessory ATR attenuated total reflection and diffuse reflection accessories typically use a Gain setting of 2 or 4 If you are not satisfied with the signal intensity after alignment you can manually align most accessories to maximize the signal For complete instructions see the manual that came with the accessory When you manually adjust an accessory watch the largest interferogram peak in the live display on the Bench tab The larger this peak the better is the signal intensity The largest interferogram peak can be positive or negative a If you are unable to see the display turn on Tone on the Be
85. heel A 4100 cm 1 low pass Filter wheel B 2800 cm 1 high pass After you have moved a screen into the beam path you can see its effect on the signal intensity in the live display on the Bench tab This helps you select the optimum screen for a particular sample 76 Thermo Electron Corporation 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 In OMNIC Help Topics find energy screen wheel in the Index and go to Specifying the energy screens in the energy screen wheel for more detailed instructions Experiment Setup C4My Documents OMNICParam Default exp BEE Filter Wheel Wheel A Wheel B Filter Type Filter Type Daily Reet mode Open JS BU prs mio mte Bit Nicolet FT IR User s Guide 77 78 Using the internal polarizer Note An optional automated polarizer lets you automatically control the orientation of the electric field vector of the IR beam entering the sample compartment The range of orientation is 0 to 180 degrees in increments of 1 degree At O degrees the electric field vector is oriented vertically perpendicular to the sample compartment base plate This option is useful for performing polarization studies of thin films and other sample types The polarizer cannot b
86. hen use a different filename to save the Spectrum Converting the The sample spectrum you collected is in absorbance units Since many 2 of OMNIC s data manipulation commands work best on spectra in spectr um S UNITS absorbance units it is often useful to convert a spectrum to absorbance by using the Absorbance command In this example you will convert the 1 2 You can also choose Transmittance from the Process menu Thermo Electron Corporation spectrum to transmittance and then back to absorbance Select the spectrum by clicking it Click the Transmittance button in the toolbar ait The spectrum is converted to transmittance units iy OMNIC Window1 lolx EJ file Edit Colect view process Analyze Report Window Help la x Polystyrenemeasuredasaflm OOOO O a fi mm pue NM v 20 QUU UN 701 60 s0 401 lo o E s E a c sS E amp n 2000 Wavenumbers cm 1 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 in the Index and go to the topic that deals with the units you are interested in Nicolet FT IR User s Guide 39 You can also choose Absorbance from the Process menu Labeling a peak with the annotation tool 3 Click the Absorbance button in the toolbar to return the spectrum to
87. ick the QC Libraries tab to display the available QC libraries The available QC libraries appear in the Available QC Libraries And Groups box Library Setup Polystyrene Quality Control Samp 44 Thermo Electron Corporation The libraries listed in the QC Libraries And Groups box are the libraries with which your spectrum will be compared 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 Choose QC Compare in the Library Setup dialog box to start the comparison You can also close the Library Setup dialog box and begin a QC comparison at any time by choosing QC Compare from the Analyze menu When you begin a comparison the QC Compare window appears At the bottom of the window a gauge shows the progress of the comparison When the comparison is finished the sample spectrum and the library spectrum that best matches it are displayed in panes in the upper portion of the window Comments about the comparison appear in the lower portion of the window Here is an example Nicolet FT IR User s Guide 45 i QC Compare amp Fri Feb 20 14 46 18 2004 GMT 06 00 4 Polystyrene measured as a film Match 99 99 7 Close the QC Compare window by choosing Close In OMNIC Help Topics find QC comparison in the Index and go Lum to Performing a QC comparison
88. ifferent 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 zm Setting up experiments in Spectrometer Help Topics If your sample holder is mounted on a Smart baseplate the Transmission E S P experiment is automatically selected when you install the baseplate in the sample compartment 28 Thermo Electron Corporation If there is a sample in the holder remove the sample 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 To install a sample or filter slide the sample or filter into one pair of slots If the accessory support is currently installed in the slot you want to use remove the support before installing the sample or filter see the first illustration in this section Replace the support when you are finished using the slot Do not discard the support it is needed for installing slide mounted accessories Nicolet FT IR User s Guide 29 30 Collecting the In the data collection procedure that follows you will collect a sample spectrum background spectrum and then a spectrum of the secondary polystyrene standard that came with your spectrometer Before collecting the spectra you will open a configuratio
89. ing OMNIC The following wizards and tutorials are available on your system Getting Started With OMNIC This tutorial available through Getting Started in the Help menu introduces you to OMNIC It includes basic information about the OMNIC window using the toolbar and tool palette creating and using spectral libraries creating your own experiment files and using on line laboratory notebooks to create and save reports Spectrometer Tour When you finish this tutorial you will be familiar with the major components in your spectrometer The tutorial is available through Getting Started in the Help menu Beginner s Guide to FT IR Run this tutorial to learn how an FT IR spectrometer works and the theory behind FT IR spectroscopy The tutorial is available through Getting Started in the Help menu Sampling Techniques This item in the Help menu gives you access to the Choosing a Sample Technique tutorial which helps you choose the best technique for your analysis Also available are tutorials describing how to install and use a number of sampling accessories including Smart Accessories Thermo Electron Corporation On line Help Learning OMNIC This item in the Help menu gives you access to tutorials that explain how to use OMNIC to collect spectra and perform a number of other software operations Spectrometer Help Topics This tutorial available in the Help menu contains step by step instructions for installing
90. ing a TepOLE seed ee Deb POR Pep Ud o Rag ba 48 Spectrometer Busto Siess e diode pitur els dq anaes obe poti pd 51 Spectrometer conipoDents 2o nee tetera 51 Using the data collection DUttONS eese 52 MGE S3DSIde Poitou ot ope eee n oA at ASS 54 What is on the rear panel eee tenore toe te erae eio 55 Turning on the spectrometer power eeeeene 56 Using A heht solr Eein ctr oio ctsac oae eiut e dd 58 Using beamsplitters and detectors esses 60 Selecting the right beamsplitter and detector 60 Improving the quality of your spectral data 64 How to collect data in the visible spectral range 70 About the moving mirror velocity eee 71 Spectrometer Options i1 vesieie e se seaesgsvadesnsdesavaaspiacesdnncdevasdens 72 sine the ner wheel ccs tolo meret t dax tte a NU wee 72 Using the energy screen wheel 5o eene tire eres 75 Using the internal polantZet esce er Foie FERE euo die 78 JACCOSSOPIBS edo Dub Deco esi dcbet Qe ee quas EER ens 8l Smart JXOGeSsOPeS caede uestis aba tace iei e asd in tese 8l Other sampling accessories for different applications 85 Systemi dOOe SSUEIeSa eese cote quen HEP ede cna Eee TUS gt aee anne Si 90 How to cable an accessory ie atis terae Papae eR Ee vag i URS 91 Pass through connectors 5 sonder ede eod dp dr Vos e ES 91 Detector Motors
91. ion of the spectrum that does not include any totally absorbing bands or use the view finder to display the region before searching These methods avoid the loss of spectral information that results from blanking 102 Thermo Electron Corporation In OMNIC Help Topics find spectral region in the Index and go to Region tool or View finder e 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 In OMNIC Help Topics find Kramers Kronig transformation in the Index and go to Kramers Kronig dispersion transformation e If you collected the spectrum using ATR attenuated total reflection use ATR correction available through Other Corrections in the Process menu to correct it for variation in the depth of penetration and then search it against a library of transmission spectra In OMNIC Help Topics find ATR correction in the Index and go to ATR correction e If the spectrum has water or carbon dioxide peaks use Other Corrections to remove these peaks In OMNIC Help Topics find water in the Index and go to H20 and CO2 correction Only those portions of the spectrum which are within the selected region or displayed region if no region is selected and within any of the regions
92. is chapter lists some simple troubleshooting measures you can take to solve data collection problems with the spectrometer If the action does not solve the problem call your Thermo Electron service office In OMNIC Help Topics find troubleshooting in the Index and go to Troubleshooting for more information A spectrum contains The sample has parallel Create a new film using a matte press fringes or channeling highly reflective sides that cause the infrared beam to Try roughening the film surface bounce within the sample slightly with silicon carbide paper or when it is placed other suitable abrasive perpendicular to the beam Rotate the sample so that the infrared beam passes through sample at Brewster s angle Do not use this method if you are performing a quantitative analysis of sample 150 Thermo Electron Corporation A spectrum contains totally absorbing peaks A spectrum contains carbon dioxide peaks that interfere with your data A spectrum contains water peaks that interfere with your data The sample in a transmission experiment is too thick The background spectrum is too old The spectrometer is not adequately purged The spectrometer is not purged The spectrometer is purged but the air dryer does not remove carbon dioxide The desiccant cannot absorb any more water vapor The spectrometer is not adequately purged The spectrometer is not purged Solution Use a
93. items is discussed in a section of this chapter By the time you have run through these items once or twice in the course of your work you will know how to check the system and start collecting spectra quickly Check the purge or desiccant Make sure the system components are powered on Cool the detector if you are using an MCT InSb or other detector that requires cooling with liquid nitrogen e Start OMNIC and select an experiment Thermo Electron Corporation Checking the purge Skip this section if you purchased the Sealed and Desiccated option A Warning 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 approximately 30 standard cubic feet per hour scfh The settings for systems equipped with Smart Purge are given in the next section read this section first If you need to adjust the flow rate or if your application requires a different flow rate follow the instructions in Setting the purge gas controls in the Setting up experiments book in Spectrometer Help Topics Never use a flammable gas to purge the spectrometer The purge gas must be free of moisture oil carbon dioxide and other reactive or infrared absorbing materials Use dried air or nitrogen to purge the spectrometer Other gases even inert gases such as argon can damage the spectrometer and should neve
94. k hazard Always power off the spectrometer and disconnect the power supply from the wall outlet or power strip before disconnecting the power supply from the back of the spectrometer In the Spectrometer Tour available through Getting Started view The back panel for complete descriptions of the rear panel components Nicolet FT IR User s Guide 55 Turning on the Follow these steps to turn on the spectrometer power spectrometer power 1 56 J If the external power supply is not already connected connect it In the Spectrometer Tour available through Getting Started view Connecting to AC power in the Powering up unit for information about connecting the power supply Turn on any accessories you plan to use This includes accessories such as a gas chromatograph a GC interface or an infrared microscope A Warning Always follow the safety precautions in this manual and in the Spectrometer Safety Guide that came with your system whenever you use the spectrometer A 3 Turn on the spectrometer by pressing the power switch I O on the external power supply When you turn on the spectrometer the four status indicators Power Scan Laser and Source flash in various sequences as the system runs through its diagnostic routines When the routines are finished the Power Laser and Source indicators stay lighted The Scan indicator flashes with each scan of the interferometer Note After you tu
95. l nude deed 105 comparing sample spectrum with spectra in 43 CICatiDgz cer DRE 7 47 104 nicer a tiisielsestaninnavntlian Teclact a asdends 136 not listed eee ee 136 saving spectra In nennen 107 scrapbook 5 necesse cte 104 Searching i i HER tates 102 spectrum cannot be added to 135 library search extended search feature eese 105 Search expert ise deett 106 specifying spectral regions for 103 library spectrum displaydng deed eut 104 rid 64 Liquid Analysis System eene 87 liquid nitrogen for cooling detectors 125 log IR units nectit e e a 101 m MAT cosas o eo or RR ERA NR TR 53 Ma crto button enrera UR Ere Dium 53 maintenance stein tede E rer eee Tre 13 128 130 matched scale ote tee 112 math SUDUMACHT Ss oec come etit p tere 116 when to use subtraction esee 117 math operations eorr rieuses ener 118 MCT detectors iie ona a E 125 menu Daria ace ea n E E eet 25 menu Tames 5e nei eee bo re i eren 25 Microplate accessory sseseeseeeeeenenenen 87 microscope deSCEIDUIODS z uestre pet eee temet e ee 88 in viewing mode 152 Mirror velocity 5 nieder et re e PEE 71 moving spectrum in pane eee eeeseeeeseeceneeeeneeteteeeeeeeenes 114 spectrum to another window 114 stacked spec
96. lity spectra with minimal sample preparation The accessory uses a wide variety of low cost crystals that are easy to install and remove Smart Refractor This is top loading accessory is designed for fast analysis of coatings on reflective substrates using the grazing angle specular reflection technique Smart SAGA This advanced accessory is designed for the analysis of thin films on reflective substrates The 80 degree angle of incidence for this reflection absorption accessory allows sensitive measurements of films as thin as 0 1 nm Smart SpeculATR This single bounce horizontal ATR specular reflection accessory allows versatility in measurement where a range of sample morphologies may need to be analyzed Smart SplitPea This horizontal ATR microsampling accessory is designed for fast analysis of solids liquids and powders It is ideal for analyzing hard materials small samples or samples where only minute quantities are available In OMNIC Help Topics find accessory in the Index and go to Specifying the accessory for instructions for setting up and saving experiments for custom accessories Thermo Electron Corporation Other sampling accessories for different applications Note You can install many of the sampling accessories yourself After you install an accessory you may have to align it Instructions for aligning the spectrometer are included in the Maintenance and Service chapter of this ma
97. manual to draw your attention to the on line documentation and other important information This symbol tells you that you can find more information in the on line tutorials To access a tutorial click the Help menu in OMNIC This symbol tells you that you can find more information in the on line OMNIC Help system Choose OMNIC Help Topics from the Help menu This symbol tells you that you can find more information in this manual Thermo Electron Corporation Note Important A Caution A Warning A Danger Questions or concerns Notes contain helpful supplementary information a Follow instructions labeled Important to avoid damaging the system hardware or losing data a 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 A Indicates a potentially hazardous situation which if not avoided could result in death or serious injury a Indicates an imminently hazardous situation which if not avoided will result in death or serious injury a In case of emergency follow the procedures established by your facility If you have questions or concerns about safety or need assistance with operation repairs or replacement parts use the information below to contact Thermo Electron Outside the U S A contact the local Thermo Electron sales or service representative Phone 1 800 642 6538 U S A or 608 2
98. msplitter or detector There are two considerations when selecting a beamsplitter detector combination compatibility and spectral range Combinations are considered compatible if they provide a detector signal that is large enough to allow the beamsplitter to be aligned This does not necessarily mean a particular combination will provide the maximum capable sensitivity range of each component The following table shows which beamsplitter detector combinations perform best and which are compatible 60 Thermo Electron Corporation BEAMSPLITTER Near IR Mid IR Far IR DETECTOR Quartz CaF XT KBr KBr Csl Solid Substrate DTGS X OK Best Best OK X KBr window Csl window DTGS PE window MCT A MCT B InSb PbSe Si PbS InGaAs Best Optimum beamsplitter detector combination OK Compatible beamsplitter detector combination X Incompatible beamsplitter detector combination A ZnSe beamsplitter may also be used as a mid IR beamsplitter in extremely humid environments Valid for room temperature and thermoelectrically cooled versions Nicolet FT IR User s Guide 61 Light Range Beamsplitter visible quartz CaF near IR quartz CaF XT KBr Continued on next page The next table lists the spectral ranges of compatible beamsplitter detector combinations Detector PbSe Sit PbSe Sit MCT A MCT B InSb 5 PbSe PbS TEC with SabIR In
99. n dioxide removing peaks due to sees 103 Channeling in spectrum 150 cleaning purge filter esee 130 closing window esee 120 Collect Sample window sss 99 Collect Status indicator eeesssss 37 150 collecting background 13 3 52 died deep 53 background spectrum eeeeeneene 32 sample spectrum esee 27 30 53 SPEU i ete rre 12 14 23 27 30 98 color of spectrum 111 commercial library finding compound in eee 105 common sc le 2 ccr ero et ett 112 components separating with subtraction esses 117 computer saving spectra on hard disk 107 when to turn On eeeeeeeeee nnne 19 56 configuration default aa esce de e eae 30 ODEeHmg aod su ene ete i lt dre te its 30 SAVING hip au etd eode eed 119 connector Auxiliary 1 2 sien een o a qr 93 Awabhaty 2 eet ree Rn 93 detector nter eC A E DII 92 Detector Motors eese 95 Pass through sessseeeeeeeeeneenee 91 connectors Auxiliary pinouts ee eeeeeeeeeeeeeeeeeeeeeeeeeeeeees 94 for custom ACCESSOTICS esecesceseeseeseeeeeeeeeeeeaeees 94 P ss throu ghnis ninna niea i 94 sample compartment esee 92 contaminants identifying with subtraction ssssse 117 cooled detector
100. n that sets a number of software options for this procedure f You can also learn how to collect spectra by viewing Collecting a f Spectrum available through Learning OMNIC Follow these steps 1 Thermo Electron Corporation Choose Open Configuration from the File menu The Open Configuration dialog box appears listing the available configuration files Opening one of these files lets you quickly set a number of software options Select the DEFAULT CON file and then choose OK This file was provided with your OMNIC software for setting the options for this procedure If it is not already selected select the Default Transmission experiment or the Transmission E S P experiment Both of these experiments set the parameters correctly for collecting a polystyrene sample spectrum The currently selected experiment is shown in the Experiment box near the top of the OMNIC window To select the Default Transmission or Transmission E S P experiment first click the arrow button at the right end of the Experiment drop down list box The Default Transmission or Transmission E S P experiment appears in the list Select the Default Transmission experiment by clicking it Experiment Default Transmission Default Transmission 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 Experimen
101. n the Index and go to Creating a user library and Adding spectra to a user library How can I display a library spectrum in a spectral window If you are using OMNIC locate and select the spectrum in Library Manager available through the Analyze menu and then click the Add To Window button or go to the Library Spectra tab of Library Manager display the desired spectrum on the tab and then double click the spectrum In OMNIC Help Topics find library in the Index and go to Working with libraries Thermo Electron Corporation 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 Type the text to search for in the Text In Selected Item box and then choose Search The search results appear in the table based on the options you have set To see information about a found spectrum double click its row in the table In OMNIC Help Topics find library in the Index and go to Searching a library for text You can use the extended search feature available on the Extended Search tab of the Library Setup dialog box to find library spectra by searching for text in any field included in the library For example some libraries have fields for molecular weight boiling point or manufacturer In O
102. nch tab before adjusting the accessory The tone reaches its highest pitch when the signal is maximized You can use the performance test to track long term spectrometer performance Run the test after you have installed the system and then weekly Keep a record of the actual values obtained When you run the test the software measures the response of the spectrometer optics and atmospheric absorptions inside the spectrometer and then collects a sample spectrum with no sample in place The result is a 100 line a display of system noise that appears as a generally flat line at 100 transmittance Thermo Electron Corporation Note Follow these steps to perform the performance test 1 Make sure the main sample compartment is empty Remove any samples and sampling accessories except a transmission sample holder Exit OMNIC This ensures that the Bench Diagnostics software will run correctly Start the Bench Diagnostics software To do this click the Start button on the Windows taskbar point to Programs All Programs in Windows XP point to the Thermo Nicolet folder and then choose Bench Diagnostics See Performing advanced diagnostic tests in the Troubleshooting Hardware Problems chapter for more information about running the diagnostics software Click the Performance Tests button and then follow the instructions that appear on the screen If the noise readings are greater than normal or ha
103. nformation about ordering replacement parts In OMNIC Help Topics find diagnostics in the Index and go to Checking bench components How do I replace parts in the spectrometer Spectrometer Help Topics Replacing parts Nicolet FT IR User s Guide 127 128 A Warning Maintenance and Service This chapter describes maintenance and service routines that you can perform on the spectrometer We define maintenance as an occasional procedure you perform to keep the spectrometer running efficiently We define service as a procedure to replace a failing part in the spectrometer Perform only those procedures described in this chapter If there are other problems contact Thermo Electron at one of the numbers below Outside the U S A call your local sales or service representative Telephone numbers for all Thermo Electron Customer Support offices are provided with your system Phone 1 800 642 6538 U S A or 608 273 5015 worldwide Fax 608 273 6883 worldwide E mail techsupport analyze thermo com World Wide Web http www thermo com spectroscopy A See Spectrometer Help Topics for instructions for diagnosing spectrometer problems and ordering and replacing parts Thermo Electron Corporation Running diagnostic tests on spectrometer components Note If your system is not performing properly you can use the Diagnostic tab in the Experiment Setup dialog box to check the performance of spectr
104. ng up Before You Collect Spectra chapter Turning on the system components How do I start the software Before You Collect Spectra chapter Starting OMNIC How do I prepare the software for data collection Collecting a Spectrum available through Learning OMNIC Preparing the Software How can I learn how to use the software View the tutorials listed when you point to Getting Started or Learning OMNIC OMNIC Help Topics includes complete instructions for all the OMNIC features Use the Index tab or Contents tab to find the information you need Nicolet FT IR User s Guide 9 10 Using the spectrometer and changing parts j What s inside the spectrometer Spectrometer Tour available through Getting Started Inside the spectrometer How does the spectrometer work Beginner s Guide to FT IR available through Getting Started How do I purge the system Spectrometer Help Topics Installing purge controls in Installing optional hardware How do I use Smart Purge Spectrometer Help Topics Setting the Smart Purge controls in Installing optional hardware How do I change beamsplitters Spectrometer Help Topics Changing beamsplitters in Setting up experiments Selecting a beamsplitter detector and source in Setting up experiments Thermo Electron Corporation Collecting spectra J How do I change detectors Spectrometer
105. ns are available for use 92 Thermo Electron Corporation Connectors on the The illustration below shows the optional connectors on the front of front of the spectrometer the spectrometer that you can use to pass signals to and from the sample compartment Note These connectors are available only on systems that do not include the SabIR accessory or the microplate accessory a Auxiliary 1 This connector passes power or other signals for the accessory to three pins on the Auxiliary connector inside the sample compartment This connector could be used for example to attach the DC output of an AC to DC converter to provide DC power to an accessory in the sample compartment Auxiliary 2 This connector passes signals to three pins on the Auxiliary connector inside the sample compartment This connector could be used for example to allow an accessory in the sample compartment to be controlled through your computer s serial RS 232C port See the next section for information about which pins are available for use Nicolet FT IR User s Guide 93 94 Using the pass through connectors for custom accessories A Warning By connecting custom cables that use the pins on the pass through connectors you can provide power and communication or other signals for your custom accessories The power and signals pass through the spectrometer from the front to the sample compartment and vice versa Make sure your use of the conne
106. nual Instructions for aligning an accessory are provided in the documentation that came with that accessory Some accessories fit into the sample compartment and require that you remove the Snap In baseplate before installing the accessory For information about using Snap In baseplates view Removing the Snap In baseplate in the Setting up experiments book in Spectrometer Help Topics Additional Snap In sample compartment baseplates are available for use with each accessory to make changing accessories easier a Call Thermo Electron if you are interested in ordering any of the following sampling accessories Absolute transmission accessory This accessory allows for the measurement of absolute transmission of samples with reflective surfaces The design prevents energy reflected from the sample from entering the interferometer for remodulation Using this accessory involves replacing pinned in place mirrors before and after the sample compartment Automatic sample wheel This accessory holds multiple samples and rotates them into the beam path for data collection The sample wheel is commonly used to measure multiple polymer or pressed powder samples automatically Nicolet FT IR User s Guide 85 86 Auxiliary experiment module AEM The AEM provides you with an additional sample compartment You can position it on the right or left side of the spectrometer With an AEM installed you can run routine analyses with the
107. oblem collect the spectrum again To view information about the collection including a list of any problems that have occurred click the Collect Status indicator during or after the collection You can also click the View Collect Status button in the message that may appear when the collection is finished see step 7 of the procedure in the preceding section For each listed problem an Explain button is provided to let you access troubleshooting information You can save your spectrum on the hard disk by using either of two commands in the File menu Use Save when you want to save a spectrum using the current filename and path Use Save As when you want to save a spectrum using a new filename or path Follow these steps to save the spectrum you just collected 1 Select the polystyrene spectrum by clicking it 2 Choose Save As from the File menu The Save As dialog box appears Nicolet FT IR User s Guide 37 38 3 Type a descriptive name such as POLY SPA following the directory path in the File Name box Here is an example C My Documents OMNIC Spectra POLY SPA The text can be either upper or lower case The default directory path for saving files is determined by the settings on the File tab of the Options dialog box available through Options in the Edit menu Choose OK If you typed a filename that already exists in the directory a message appears asking whether to replace the existing file Choose No and t
108. ometer components and determine the source of the problem OMNIC continuously monitors the operation of the spectrometer hardware and shows its status with the Bench Status indicator below the menu bar of the OMNIC window See The OMNIC window in the Your First Experiment chapter for more information a Follow these steps to run the spectrometer diagnostic tests 1 Make sure the main sample compartment is empty Remove any samples and sampling accessories except a transmission sample holder 2 Choose Experiment Setup from the Collect menu or the toolbar The Experiment Setup dialog box appears 3 Click the Diagnostic tab The Diagnostic tab appears showing icons for the major components of the spectrometer with a live display of the signal from the detector Nicolet FT IR User s Guide 129 Maintaining your spectrometer j Aligning the spectrometer 130 Note 4 Torun 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 appears in the Status column If the value is outside the acceptable range an X appears in the Status column 5 When you are finished viewing the information choose OK This section describes how to use the OMNIC software to align the spectrometer and accessories and run performance tests View Maintaining your spectrometer
109. optional hardware changing replaceable parts maintaining your spectrometer and setting up the system for a variety of experiments If you ever have a problem with your spectrometer use this tutorial to access troubleshooting information and get part number and ordering information Technical Support This tutorial available in the Help menu outlines the many support training and custom application services available from Thermo Electron It includes Technical Support telephone and fax numbers as well as e mail and web site addresses The Library Creation Wizard prompts you step by step through creating a user library of spectra The wizard appears when you click the Create Library button in Library Manager available in the Analyze menu in OMNIC Choose the Help Topics that interest you from the Help menu to display that Help system It lets you quickly find answers to your questions about using the software There are several other ways to enter a Help system You can see information about many features in OMNIC such as a parameter in a dialog box by clicking the feature using the right mouse button If the active dialog box or window includes a question mark button near the upper right corner you may need to first click that button and then click the feature of interest using the left mouse button A brief description of the item appears and in most cases one or more buttons that you can click to display more detailed
110. or the report Then use Preview Print Report to view the report as it will appear on paper Click the Print button to print the report View Creating Reports available through Learning OMNIC to learn about OMNIC s report features In OMNIC Help Topics find template in the Index and go to Selecting editing or creating a report template or find report previewing or printing and go to Previewing or printing a report Nicolet FT IR User s Guide 109 You can also use Add To Notebook to add the report to a report notebook You can then print the report with the Print button when you view the notebook using View Notebook In OMNIC Help Topics find report in the Index and go to Adding a report to a notebook How can I preview spectra or other information before printing Use Preview Print Report in the Report menu to view a report as it would appear on paper The report is displayed using the current report template that is the template you specified with Template or the one you are viewing and working with If the report is displayed as you want it to appear on paper you can print it by using the Print button In OMNIC Help Topics find template in the Index and go to Selecting editing or creating a report template or find report previewing or printing and go to Previewing or printing a report How can I select more than one spectrum at a time After selecting the first spectrum by clicking i
111. ore You Collect Spectra iiie tib Cont ci Seve b peste peg 14 Checking the D FSEO eder obire eames acti A itd 15 Smart Purge settings cost vA du TQU TI UDIR Made Ds P Rt IUE 16 Checking th desiccant srira AN ENDE IR bU US NINE 17 Turning on the system components esee 18 Cooling the detector cosas verse aos PME t REM DRE neiise Mo PA Doe 19 Staruns 2 du Ld 20 Selecting an experiment gsi sa2cscadasesacsceasdocersnssecdaaadastaceasncecsannoendes 21 Your First Experiment MN T 23 Th OMNIC window cadere odii aa aE Ea eus 24 Spectral WINdOW P iiare i Fit 24 s oco 25 Experiment drop down list BOX ettet trenta 25 Bench Status indicator Lieu ei In Haie tributa tese ADD 26 Ec E M E 26 Collecting a sample spectrum eee 27 Installing the standard sample holder 28 Collecting the sample spectrum tren teritur 30 How do I know if my spectrum is good sseeesss 37 SAV UNS the SPC CHUM si scudo ous METUENS SER URINE Ape QD RUE 37 Converting the spectrum s Ubtts uoce eb euet dots ie ues ee RR 38 Labeling a peak with the annotation tool 40 Verifying the composition of the sample sse 43 Creating a user ibrary oet DRE ae estote ies RE ENSURE RUE 47 Adding a spectrum to a user library sees 47 Creating and print
112. orizontal ATR accessory with exceptional throughput and sensitivity It can use several crystal types and has a micrometer screw for precise control of applied pressure Smart Multi Bounce HATR This multi reflection horizontal ATR accessory has a shorter pathlength and higher throughput than traditional HATR accessory designs It is the best choice for routine analysis of strong infrared absorbing samples This accessory is ideal for rapid quantitative and qualitative analyses since sample preparation is usually not necessary Smart OMNI Sampler This single reflection ATR accessory features a spherical crystal that lets you measure a wide variety of sample types The unique tower design automatically applies the optimum pressure while protecting the crystal The accessory is ideal for analyzing very small samples or sample areas and provides high reproducibility Smart OMNI Transmission This easy to install transmission accessory lets you sample liquids gases and solids using a wide variety of transmission cells and infrared cards Smart Orbit This single reflection ATR accessory features a durable diamond crystal and a swivel pressure tower that ensures consistent pressure from sample to sample You can use the accessory to perform analyses from the near IR to the far IR Nicolet FT IR User s Guide 83 84 Smart Performer This single reflection ATR accessory features a horizontal sampling surface for collecting high qua
113. ost of the energy from the source which means you should use a large aperture size Detectors that require cooling with liquid nitrogen are very sensitive and require a small aperture size or the use of an energy screen see the preceding section for more information Nicolet FT IR User s Guide 67 66 Note On a Nicolet 6700 the setting of the Aperture parameter determines the area of the aperture opening Doubling the setting approximately doubles the area The light energy is proportional to the aperture area A setting of 100 gives a nominal aperture diameter of 8 mm and an approximate area of 0 50 cm2 a The following table lists recommended aperture settings for different detectors with the appropriate energy screen installed See the preceding section for information about the correct energy screen to use for each detector type The settings in the table are based on the physical size of the detector elements and maximize the amount of infrared energy that reaches the sample To correct linearity and photometric accuracy problems you can reduce the setting but you will pay a price in terms of the signal to noise ratio Detector Aperture Setting DTGS 100 MCT A MCT B InSb PbSe Si InGaAs 32 In OMNIC Help Topics find aperture in the Index and go to Setting the aperture size for information about changing the aperture setting Thermo Electron Corporation How to improve the signal to noise ratio Note If you
114. pectrum in the Index and go to Adding a spectrum to a user library When you add a spectrum to user library whose resolution is lower the spectrum is deresolved For this reason it may be better in some cases to save your sample spectra as files on the hard disk and consider the copies of them added to a user library to be for searching purposes only a We recommend that you create descriptively named folders directories on your hard disk for different categories of spectra For example you could have a folder for each project you are working on for each of your clients for each laboratory application or for each sample type See your Windows documentation for information about creating directories You can specify which folder to use when you use Save or Save As in the File menu to save spectra This will make it easier to find a spectrum in a particular category when you Nicolet FT IR User s Guide 107 108 use Open in the File menu to open a spectrum In OMNIC Help Topics find spectrum in the Index and go to Saving spectra using new filenames How can I save several spectra in one file as a group Select the spectra and then choose Save Group from the File menu To select more than one spectra hold down the Control key and click each spectrum you want to select with the selection tool and then release the Control key Spectral groups are saved with the extension SPG In OMNIC Help Topics find saving spectra
115. primarily analyze qualitative data you may wish to optimize the system for a better signal to noise ratio This can be particularly important when you are working with scattering samples and samples that absorb more infrared energy These samples produce smaller signals that can be lost in the noise There are several ways to improve the signal to noise ratio The most commonly used method is to increase the number of scans This both reduces the noise level and makes small absorptions easier to distinguish You can also improve the ratio by reducing the resolution that is using a higher Resolution setting Another method is to use an energy screen that transmits more light or no screen at all In this case the resulting spectrum might be distorted and accuracy and stability could be reduced Checking the single beam baseline in the region below the low end cutoff will give you a rough idea of how much distortion is occurring If the distance from the baseline to 0 is more than 15 of the spectrum s maximum intensity value you may have difficulty reproducing the results 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 A In Spectrometer Help Topics view Setting up experiments for instructions for installing filters and energy screens Nicolet FT IR User s Guide 69 How to improve the r
116. r be used for this purpose 4 We recommend that you leave the purge on at all times This keeps the spectrometer free of undesirable gases protects the optics and improves the system s thermal stability Nicolet FT IR User s Guide 15 16 Smart Purge settings In Spectrometer Help Topics view Installing optional hardware for information about installing purge equipment and setting the controls for the first time Maintaining your spectrometer contains information about inspecting and replacing the purge filter In the Spectrometer Tour available through Getting Started view Sample compartment for information about using Smart Purge The Smart Purge option increases the purge gas flow rate when you install or remove samples If you have this option set the pressure regulator to 80 psi The auxiliary tank may be required depending on the flow rate supplied by your purge gas source See the following table for details Flow Rate Tank Required Comments less than yes Some purge gas and pure air 50 scfh generators provide a flow rate of less than 50 scfh 50 99 scfh optional Using the tank will improve performance 100 scfh or no A flow rate of 100 scfh gives the greater best results Flow rates greater than 50 scfh cannot be measured with the flowmeter installed by Thermo Electron See your air dryer manual or contact the department that maintains your purge equipment if you don t know the flow rate of
117. rces simply by changing the Source setting on the Bench tab of the Experiment Setup dialog box This option lets you collect spectra in the mid IR to far IR range or in the visible to near IR range The spectral range is determined by the source beamsplitter and detector you are using Nicolet 6700 spectrometers with the emission accessory can use an external source if one is available The beam from the external source passes through the emission port on the right side of the spectrometer In OMNIC Help Topics find source in the Index and go to Specifying the source type for instructions for using different sources in your spectrometer Nicolet FT IR User s Guide 59 Using beamsplitters and detectors J Selecting the right beamsplitter and detector A number of beamsplitters and detectors are available for use in the Nicolet 4700 and Nicolet 6700 spectrometers You can change the detector type in either model but the beamsplitter type can be changed only in the Nicolet 6700 Not all beamsplitters and detectors can be used together Some detectors can accommodate only a portion of the energy from the source and require changing the aperture size on a Nicolet 6700 or installing an energy filter This section explains how to select and optimize the performance of beamsplitters and detectors In Spectrometer Help Topics view the appropriate lesson in Setting up experiments if you need to install or change a bea
118. rdering parts book for power cord descriptions and part number information The ground prong on the power Replace the power cord In cord has been removed or is Spectrometer Help Topics see defective Miscellaneous parts in the Ordering parts book for power cord descriptions and part number information 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 140 Thermo Electron Corporation System does not scan The system scans normally but gives very low signal intensity Laser is flickering The spectrometer is out of alignment The moving mirror velocity is set too high There is no interferogram The beam path is obstructed The aperture is set incorrectly on a Nicolet 6700 Continued on next page Click laser indicator on Diagnostic tab of Experiment Setup dialog box to check laser operation Call Thermo Electron for assistance Align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box Set Velocity on the Bench tab of the Experiment Setup dialog box to a lower velocity If the Source status indicator 1s off click the source indicator on the Diagnostic tab of the Experiment Setup dialog box to check the source current and voltage If the Source indicator is on check the interfero
119. re it to enter Turbo or Rest mode at specific times or the spectrometer is in sleep mode Turbo mode Use this mode if you are analyzing a sample such as a thick film that requires greater infrared energy This increases the output of the source especially in the frequency range around 2 500 wavenumbers To turn Turbo mode on or off use the Source parameter on the Bench tab of the Experiment Setup dialog box available through Experiment Setup in the Collect menu So long as you are collecting data the source remains in Turbo until you turn that mode off Whenever the spectrometer is in stand by mode the source returns to Normal mode When the spectrometer enters sleep mode the source shifts into Rest mode This extends the life of your source In OMNIC Help Topics find source in the Index and go to Specifying the source type for details Thermo Electron Corporation El 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 Po nattivi ze StITIBde DailyRestmode When you resume data collection activity the source automatically re enters Normal mode In OMNIC Help Topics find source in the Index and go to Extending the life of the source with rest mode for details You can switch between different internal sou
120. riment Setup C My Documents OMNIC Param N2_2 exp Poteet Bench Qual Advanced E Zero filling None Automatic blanking of regions Apodization Happ Genzel Blank Start Region End Region Phase correction Mertz zl 0 00 0 00 fV Set sample spacing based on spectral range Sample spacing 4 7 Set filters based on velocity Macro for Macro button Browse Low pass fiter 1 L MEENENENEENEMENMAHENNNENEN High pass filter IEA Single sided interferogram Reset bench at start of collection M Start collection at extemal tigger 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 FA Smart 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 In addition to traditional accessories a variety of Smart Accessories are available for your spectrometer Nicolet FT IR spectrometers identify each Smart Accessory as it is installed and set the software parameters for data collection Also a series of spectral quality checks are performed to ensure that the accessory is installed and operating
121. rn on the spectrometer let it stabilize for 15 minutes one hour for best results before collecting data Leave the spectrometer on at all times unless the building is subject to power outages or you need to perform a service or maintenance procedure Leaving the spectrometer on increases stability and consistency of performance a 4 Thermo Electron Corporation Turn on the printer and then the computer Note Reverse the order given in the preceding procedure when you turn off system components 1 Turn off the computer 2 Turn off the printer 3 Turn off the spectrometer Press the power switch on the external power supply to O 4 Turn off the accessories In the Spectrometer Tour available through Getting Started view Powering up for complete instructions for turning on your system The spectrometer enters stand by mode 10 minutes after data collection activity has ceased This mode continues for 1 hour After 1 hour the interferometer stops scanning and the spectrometer enters sleep mode The Scan light stays on continuously Any data collection activity will cause the interferometer to begin scanning Exiting OMNIC also activates stand by mode 4 If the Power Laser or Source indicators flash or will not light at all or if the Scan indicator will not light the Bench Status indicator will show a red X and troubleshooting tips will appear on the screen If you cannot resolve the problem by following the
122. rum Correcting a baseline will give you better results when you search the spectrum against a library subtract the spectrum from another spectrum find peaks in the spectrum or quantify components in the spectrum Collecting a Spectrum available through Learning OMNIC Common Problems with IR Spectra In OMNIC Help Topics find baseline in the Index and go to Correcting a baseline manually How can I subtract a spectrum from another spectrum Use Subtract in the Process menu whenever you want to subtract one spectrum from another Subtract is commonly used to remove spectral features of solvent residues or pure components from the spectrum of a mixture of compounds Select the spectrum from which you want to subtract spectral features this is the sample spectrum Then hold down the Control key and select the spectrum with the features you want to subtract from the sample spectrum this is the reference spectrum Subtract is available only when two spectra are selected a Thermo Electron Corporation 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 In OMNIC Help Topics find spectrum in the Index and go to
123. s reflected from instead of penetrating a flat shiny sample measured using a specular reflection accessory Thermo Electron Corporation Check the sample compartment or accessory to make sure the sample is properly positioned in the beam path Make sure the cup is properly positioned in the diffuse reflection accessory For more information view the appropriate tutorial available through Sampling Techniques in the Help menu Put the microscope in infrared mode and collect the spectrum again Make sure the sample is held evenly and has good contact with the crystal Set Resolution on the Collect tab of the Experiment Setup dialog box to a value that lets you see small peaks Use a lower numerical setting to achieve higher resolution Correct the spectrum by using Other Corrections in the Process menu Select Kramers Kronig Try using a less reflective sample 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 an empty sample holder in the infrared beam The spectrometer is not Use the Align button on the properly aligned causing a Diagnostic tab of the Experiment sloped baseline Setup dialog box to align the spectrometer Th
124. s of different spectra Offset Scale shifts the spectra vertically so that they overlap less making them easier to see When you use these commands keep in mind that the current Y axis is always accurate for the currently selected spectrum but may not apply to other spectra in the window In the OMNIC Help Topics Index For information about Full Scale or Automatic Full Scale find spectra and go to Displaying spectra full scale or Displaying spectra full scale automatically Thermo Electron Corporation 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 How can I zoom in on an area of a spectrum Draw a box around the area using the selection tool and then click inside the box You can also use the Expand Contract buttons at the left end of the view finder or drag the regions markers in the view finder to display a smaller spectral region You can press and hold down the mouse button during these operations to continuously expand or contract the display To expand and contract the spectra horizontally about the center use the view finder s Horizontal Expand Contract buttons left most To expand and contract the spectra vertically about the center
125. se Rely on the indicator only when the spectrometer is in storage A See Ordering parts in Spectrometer Help Topics to find the part number for ordering desiccant bags Nicolet FT IR User s Guide 17 18 Turning on the We recommend that you keep your spectrometer on at all times unless the building is subject to power outages or you need to system components perform a service or maintenance procedure Leaving the system on keeps it stable and gives you the most consistent results If you must turn the spectrometer off allow it to stabilize for at least 15 minutes one hour for best results before collecting spectra Follow these steps to turn on the system components 1 If the external power supply is not already connected connect it In the Spectrometer Tour available through Getting Started view Connecting to AC power in the Powering up unit for information about connecting the power supply Turn on any accessories you plan to use This includes accessories such as a gas chromatograph a GC interface or an infrared microscope A Warning Always follow the safety precautions described in this manual and in the 3 Thermo Electron Corporation Spectrometer Safety Guide that came with your system a Turn on the spectrometer by pressing the power switch I O on the external power supply to l When you turn on the spectrometer the four status indicators Power Scan Laser and Source flash in
126. se tips or by turning the spectrometer power off and then on contact Thermo Electron at one of the numbers below Outside the U S A call your local sales or service representative Phone 1 800 642 6538 U S A or 608 273 5015 worldwide Fax 608 273 6883 worldwide E mail techsupport analyze thermo com World Wide Web http www thermo com spectroscopy a Nicolet FT IR User s Guide 57 58 Using a light source A Caution 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 In Spectrometer Help Topics view Installing a new source in Setting up experiments if you need to install or change a source Even after the spectrometer is turned off the external housings of working IR sources remain hot for up to 15 minutes To avoid being burned allow the source to cool before touching it a The ETC infrared source can be operated in the three modes of operation described below Normal mode In this mode the temperature of the source is maintained at an optimal level for normal spectral data collection This improves the consistency of your spectral data by ensuring that the infrared energy level reaching your samples is constant The source operates in Normal mode unless you configu
127. search esee 102 preparing to collect eene 14 previewing before printing esee 110 quality cutem aeneo a iege 37 SAVING ingen dete eu dc RH dH 37 162 Thermo Electron Corporation spectrumj continued selecting o Re eter ere 110 tle z s ees erepto et 31 totally absorbing peaks in sesss 151 DEIN TES 38 98 101 water peaks in isisi rte dte 151 ZOOMING in on area Of seese 113 specular reflection esee 152 specular reflection accessory eese 84 89 starting OMNIC sess 9 20 status indicators not lit seeeeeee 140 Subtracting spectra 116 System accessories nebenbei 90 t technical SUpport itte e tetris 7 telephone numbers see 3 7 temperature eeeeeeeeeeeeeenneenn 138 142 146 153 outside allowed range sss 139 TGA interface eee oaa etg 89 TGA module 5t tro oret 89 tool annotation cd et pere eee 120 peak area x een eR enel 115 peak height 2 emere 115 TESION E 120 SelectiOD s 4 ec b re e et 114 spectral GUrSOF iere ree eh 115 LOOM DAL 55i Rente ere se Rege een 26 tools id ente eh onte esee aen metet 40 totally absorbing bands blanking eee 102 HPAI Goce oud HEN IE 7 transmission accessory eeeseeeeeeeeeeee 83 89 troubleshooting esee 7 applications
128. sing the filter wheel in the Spectrometer Options chapter for complete information Thermo Electron Corporation 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 A variety of short and long pathlength gas cells are available Cells include built in transfer optics that fit into your spectrometer The cells are suitable for use in both ambient and elevated temperature conditions Gas cell heating transfer optics purge gas manifold and sample window options are available to accommodate a variety of sample gases and sampling conditions GC interface This interface attaches to the right side of the spectrometer and must be connected to a gas chromatograph GC You can then analyze IR spectra from GC experiments using the OMNIC Series software Liquid Analysis System This system lets you collect and process quantitative analysis data for liquid samples It uses OMNIC Integra software which contains methods for quantifying components in specific types of liquids Microplate accessory This accessory allows you to collect transmission or diffuse reflectance spectra of multiple solid or liquid samples consecutively All the samples are loaded into the sample
129. sly checks the status of your system If a problem is found a message automatically appears giving you access to more information This chapter lists some simple troubleshooting measures you can take to solve software problems with OMNIC If the action does not solve the problem call your Thermo Electron service office gt In OMNIC Help Topics find troubleshooting in the Index and go S to Troubleshooting for more information You cannot add a The resolution of the spectrum Collect the spectrum at the same resolution spectrum to a user is lower higher numerical as the library first set Resolution on the library value than that of the library Bench tab of the Experiment Setup dialog box and then add it to the library The spectrum is from a Only spectra you collect can be added to a commercial library user library Commercial libraries cannot be altered and the spectra contained in them cannot be copied to other libraries The Quantify No quantitative analysis Select a quantitative analysis method using command is dimmed method is selected Quant Setup in the Analyze menu No spectrum is selected Select a single spectrum The quantitative analysis Select an appropriate method for the method is not appropriate for selected spectrum the selected spectrum Nicolet FT IR User s Guide 135 After data collection a message says the sample and background spectra have the wrong resolution An experimen
130. 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 Each position accepts one 1 mm thick or one 4 mm thick filter that is 1 inch in diameter Spacers are provided to secure mm filters in position In Spectrometer Help Topics view Installing an optical filter in the automated filter wheel in the Setting up experiments book for instructions for installing filters in the wheel Once you have installed your filters enter their descriptions into OMNIC using the Filter Wheel table on the Configure tab of the Experiment Setup dialog box Be descriptive Experiment Setup C My Documents OMNIC Param Default exp Filter Wheel Wheel A Wheel B Filter Type Filter Type Dally Reetriodel Open Open A filter 20khz B filter 20 A filter 30 khz B filter 30 A filter 40 khz B filter 40 Irractivityfse Str de In OMNIC Help Topics find filter wheel in the Index and go to Entering descriptions of the filters in the filter wheel for more detailed instructions Nicolet FT IR User s Guide 73 Your filter descriptions will be saved in the experiment file and are available for selection through the Filter Wheel A and Filter Wheel B parameters on the Bench tab of Experiment Setup Your descriptions of the filters used during data collection also are saved in th
131. spectra 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 OMAN ISS IN dew I ese SSS SSS SSS SSS SSS SSeS ES Ez Ele Edt Colect view Process Analyze Report Window Hep 8l x po A No spectra selected o S656 5 3 u os bai minl ul ee Em s E 24 Thermo Electron Corporation Menu bar Experiment drop down list box 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 All of the menu commands are explained in detail in the on line tutorials or the OMNIC Help system yy OMNICG Window1 E File Edit Collect View Process Analyze Report Window Help Below the menu bar is the Experiment drop down list box It lists all of the experiment files you have opened plus the default experiment file and an experiment file for any Smart Accessory module you have installed By selecting an experiment with this feature you can quickly set the software parameters for the type of experiment you want to perform You can see the parameter settings for the selected experiment by using Experiment Setup
132. stem 17 126 search specifying spectral regions for 103 search expert ose eias eee eee edi 106 searching preparing spectrum for 102 spectral library teet 102 selecting experirment 5 Reese 21 30 report template sess 109 spectral regions eere eene 120 rsen 110 SerViCe EET E E E TA 13 128 134 Signal antensity 5g viene 131 lowi dote ee Sed 141 142 143 signal to noise ratio 66 69 increased by bandwidth limiting filter 65 Silicon detector oie eA E etes 70 Smart Accessories ssesssseseeeeeeenenee enne 6 81 Smart ACCeSSOTIY eite Aa ee ip eR ed 97 Smart baseplate sisipin ecis 28 86 Smart Puree ueste reus 10 16 33 34 Smart Purge Kites ee oan eire 9 Snap In sample compartment baseplates 28 software le rmng z ie ERR ERE Mes 9 not started 2 2 2 e tee iet eoe 145 preparing for data collection sss 9 TequUirements i e seii RERO HERE 4 SCATUTIB iot RC ER died RU eU Eee 9 troubleshooting sissioni 135 SOUICE 2 5 dst etie deo ret ei ns 58 burned out dece Fd endi 144 external asin hss taces eo eee 59 glowing unevenly esee 143 1nstallilig nero GS s 11 DOE WOFKIIg ico ete es taie eve e en ne Ten RUN 147 IODpl Cmg iiei dne ERR RH RES 134 WHICH to Use tee Rr HER RU 126 Source indicator eeeeeeeeee 18
133. t Setup dialog box After you have selected one of them the first time the experiment will appear in the Experiment drop down list for future selection You can also set up and save your own experiments Press the Sample button on top of the spectrometer to start sample data collection You can also click the Collect Sample button in the toolbar or choose Collect Sample from the Collect menu The Collect Sample window appears and then a dialog box showing the default title for the sample spectrum Collect Sample Enter the spectrum title Fri Feb 20 14 46 18 2003 GMT 06 00 Nicolet FT IR User s Guide 31 32 5 Thermo Electron Corporation Type a title in the text box and choose OK or just press the OK Enter button on top of the spectrometer to accept the default OK Enter Since the experiment you are using specifies that a background be collected before every sample a message appears asking you to prepare to collect a background spectrum Confirmation Background Please prepare to collect the background spectrum This means that you need to remove any sample from the sample holder so that the beam path is clear When you then collect a background spectrum the result is a measurement of the response of the spectrometer alone that is without absorptions due to a sample 6 Look through the sliding door to make sure there is no sample in the sample holder and then press the OK Enter bu
134. t hold down the Control key while you click each additional spectrum You can also choose Select AII from the Edit menu to select all the spectra in the window that are not hidden In OMNIC Help Topics find spectra in the Index and go to Selection tool or Selecting all the spectra in a spectral window 110 Thermo Electron Corporation o uu 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 To specify the color for selected spectra click the color next to Selected Spectrum and then click a color Typically red is the color reserved for displaying selected spectra In OMNIC Help Topics find spectra in the Index and go to Specifying colors for spectra and other features You can also specify colors for displaying spectra in a particular spectral window Start by selecting the spectra for which you want to specify a color and then choose Display Setup from the View menu Click the desired color in the color array and then choose OK When the spectra are no longer selected such as after you select a different spectrum they will be displayed in the color you clicked In OMNIC Help Topics find spectra in the Index and go to Selecting a color for the currently selected spectra Wh
135. t provided with OMNIC does not produce good results The desired experiment does not appear in the Experiment drop down list box Libraries created with previous version of OMNIC are not listed in the Library Setup dialog box 136 The resolution of the current background spectrum does not match the resolution selected for the sample spectrum collection The parameter settings in the experiment file have been changed so that the experiment is no longer useful The experiment was installed with the software but has not yet been opened The libraries are not in one of directories listed in the dialog box typically LIBS within the OMNIC directory Thermo Electron Corporation 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 Restore the experiment to its default settings First open the experiment using Experiment Setup and save it using a new filename if you do not want to overwrite it Then open the experiment in the FACTORY directory whose filename is same as the original experiment and save it in the OMNIC PARAM directory If the experiment was designed for a Smart Accessory install the accessory the experiment will be opened automatically and will appear in the Experiment drop down list box If the experiment was not designed for a Smart Accessory open it using Experiment Setup it will
136. te 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 e Open a configuration e Select an experiment Collect a sample spectrum e Save the spectrum Convert the spectrum to other units Label a peak in the spectrum Verify the composition of the sample by comparing the spectrum with spectra in a QC library Create a user library e Add the spectrum to a user library Create and print a report containing the spectrum You can learn all these things and more by running the on line tutorials provided with OMNIC Start with the Spectrometer Tour and Getting Started With OMNIC available through Getting Started Follow the instructions in the preceding chapter to prepare the system and start OMNIC before using this chapter If you have a dedicated system such as an ECO RS that normally uses a software package other than OMNIC skip this chapter See the special documentation that came with your system for instructions for using that software If you need information about using the spectrometer see the chapters that follow this one a Nicolet FT IR User s Guide 23 The OMNIC window The large window that appears on the screen when you start OMNIC is called the OMNIC window Spectral window Within the OMNIC window is a spectral window which you can use to display and manipulate
137. ter is fogged The spectrometer is out of alignment A sampling accessory is not installed properly A detector that was just installed is not seated properly Check to see if the source element is glowing evenly Order a replacement source if needed Remove the obstruction Replace the windows In Spectrometer Help Topics view Replacing sample compartment windows in Replacing parts to find part number ordering and installation instructions Check the laser signals by clicking the laser indicator on the Diagnostic tab of the Experiment Setup dialog box For a Nicolet 6700 replace the beamsplitter if necessary For a Nicolet 4700 contact technical support Align the spectrometer using the Align button on the Diagnostic tab of the Experiment Setup dialog box Make sure the accessory is installed according to the instructions that came with it Make sure the hole and slot in the detector plate fit over the pins on the spectrometer baseplate See Replacing the detector in the Servicing your spectrometer book in Spectrometer Help Topics Nicolet FT IR User s Guide 143 The source status indicator is off There is frost on the outside of the detector You encounter problems when selecting external detectors on an AEM GC interface or microscope 144 The source is burned out The insulating vacuum chamber of the dewar has begun to leak A custom detector 1s selected on the Bench ta
138. that is appropriate for the spectral range of your experiment determined by the ranges of the beamsplitter and detector Thermo Electron offers a mid IR to far IR source ETC and a near IR source white light In OMNIC Help Topics find source in the Index and go to Specifying the source type Spectrometer Basics chapter Selecting the right beamsplitter and detector in Using beamsplitters and detectors Thermo Electron Corporation J Should I turn off the spectrometer when I m not using it 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 If a problem occurs a troubleshooting message appears See the Troubleshooting book in Spectrometer Help Topics for instructions for diagnosing spectrometer problems and ordering and replacing parts If you want to view the on line videos to help you in troubleshooting a problem put the Spectrometers Tutorials CD in the computer a You can also make a more thorough check on a spectrometer component by choosing Advanced Diagnostics from the Collect menu This starts the Bench Diagnostics program which provides information about the status of the component as well as troubleshooting information replacement procedures and i
139. the polarizer for more detailed instructions Begin you experiment by collecting backgrounds as single beam spectra at each polarizer angle required by your experiment Save each background spectrum with a unique descriptive name such as Background 0 Background 90 Once the background spectra are collected and saved you can begin to collect sample spectra Sample data may be collected and saved as single beam spectra Once data collection is complete use the appropriate background file to reprocess the data into your final format Sample data also may be collected and saved as ratioed spectra T A R etc using the corresponding stored background Use the Background Handling parameter on the Collect tab in Experiment Setup to specify the Nicolet FT IR User s Guide 79 80 background file name Click the Use Specified Background File checkbox and then enter the background spectrum filename If you have OMNIC Macros Basic or OMNIC Macros Pro you can create a macro that changes the angle incrementally with each successive set of background and sample spectra Then use Experiment Setup to specify that the Macro button start the experiment and run the macro Use the Macro for Macro button field on the Advanced tab in Experiment Setup dialog box available through Experiment Setup in the Collect menu to specify the macro to run You may browse to locate the macro file or type the full path and file name into the text field Expe
140. 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 An optional filter wheel available for the Nicolet 6700 only lets you automatically move a filter into the beam path before collecting data See Using the filter wheel in the Spectrometer Options chapter for more information In Spectrometer Help Topics view Setting up experiments for instructions for installing filters in the sample compartment or optional filter wheel Depending on the types of detectors you use your system may include a set of four energy screens These metal screens help prevent detector saturation and signal distortion by blocking out a portion of the energy at all frequencies of the infrared beam If your experiments deal with information from a broad range of frequencies these screens may be the most effective means of reducing the light level The energy screens are labeled A B C and D The following table shows the percentage of the infrared energy that each screen passes It also lists the detectors typically used with each screen as a starting point for correcting linearity problems Screen Transmitted Detectors Typically Used With Screen None 100 DTGS A 30 MCT A B 10 C 3 D These are nominal values that may vary due to diffraction and detector variations 66 Thermo Electron Corporation What aperture size to use for
141. tion How can I copy a spectrum and paste it into a text document Select the spectrum and choose Copy from the Edit menu This places the spectrum on the Clipboard in the form of a Windows metafile this is the file format with the most flexibility for pasting into other programs You can then paste the spectrum into a document by using a word processing program In OMNIC Help Topics find copying spectrum in the Index and go to Copying items Nicolet FT IR User s Guide 121 122 How can I get on line Help while using the software The OMNIC on line Help system lets you quickly find answers to your questions about using the software There are several ways to enter the Help system To see information about a particular feature in OMNIC click the feature using the right mouse button A brief description of the feature appears and in most cases one or more buttons that you can click to display more detailed information Click the Discussion button to display a complete discussion of the feature or the dialog box or window that contains the feature Click the How To button to display a step by step procedure for using the feature or the dialog box or window that contains the feature e You can press the F1 function key at any time to see a discussion topic for the currently displayed or selected feature dialog box or window e Ifa dialog box or window contains a Help button click it to see information about the dialo
142. too high sess 139 154 BAS ioni tice e ORIG EHE Ie eterna 15 inadeguate iier eot et etes 151 153 when to USE naisesse srpa isserrat airs 15 purge filter cleaning a R 130 purge gas gerierator een di e reo e E hei 90 q QC comparison Set ng Up iet edes RE 43 QC Tlibrary ette ec tee 43 quality of spectrum eese 37 quality standatds 2a ree eese 100 Quantify 2 een bao Re ee 135 quantitative analysis seseeees 64 65 66 135 r LEAL Panel esac ves sok Weds e tbe a teta 55 region selecting 3 dau duree gus 120 regions specifying for library search 103 remote diagnostics 90 Remote Start accessory sese 88 replacing parts in spectrometer 127 report CI eAlDnBz axe tete ta eed 48 109 previewing oce cerei essences 49 109 printing armed hei 50 report notebook delent ipei UR 109 SAVING SD C T IIb n ett ep egit 107 report template CICatIDg uideor ed ueque 49 selecunp rettet ud 48 109 requirements of system 4 160 Thermo Electron Corporation TESOlUM ON 2s udi Rd 135 affected by aperture sese 67 70 affected by energy screen sese 70 and aperture etr r EER REA 67 IMPLOVING rogat nO UR eed 70 iie i e RENE theta Laesboese been 136 152 too high zudem eeu eob ades 154 Roll Zoom window eeseeeeeeennee 113 114 RSVDB z iue ganan de
143. trum einer rerit 114 moving mirror velocity limitations eese 71 n Nicolet Centaurjis 2 eoo rit feit 88 Nicolet Continuum niisiis 88 MOISE 32305 ER 65 69 number of scans signal to noise ratio affected by 69 LOD OW ees teteen 154 0 offset SCale 2 cede i e et e opes 112 OKJEnter button tee eni 53 OMNIC CUSTOMIZE dude tede i RC eines 119 Helps eo EP CREER RS 7 122 1stallimig i e EE 5 learning Ee PLE 6 7 preparing for data collection 97 Starting dee eite t reped 9 20 wizards and tutorials eene 6 OMNIC window itte es 24 Open Configuration esee 30 opening configurato sii iae t ees 30 spectrometer COVET Sietas a aS 123 Spectr eire 106 optical layouts pa a orara aaen aissa 54 ordening parts act R R a 7 p J reflectance units sese 101 transmittance units sese 38 palette eet eR HE Ue 40 parameters SOUT Go rere b eee i er eee eine deas 21 part numbers 45 dene eben 7 parts orderme iuo ae moedures esa a rei 7 feplacing iis tune eR ERR 7 pass through connectors eese 91 94 jon T EE 94 password n 2 ete ete rta Pede ee tbe SERE 20 pasting spectrum sse 121 peak ALC Ais invio ie eiecit ree kes 115 height c tu arin Rees 115 l beling oe ede pede eem 120 peaks carbon dioxide
144. ts book in Spectrometer Help Topics to find part number and ordering and installation instructions Check the source indicator on the Diagnostic tab of the Experiment Setup dialog box If necessary replace the source Check and cool the detector Align the spectrometer If the interferogram is still not located correctly call Thermo Electron for service Remove the obstruction Turn off the spectrometer power and check the data cable connections Change the detector or beamsplitter Nicolet FT IR User s Guide 147 148 Performing You can use the Bench Diagnostics program to perform diagnostic tests on the main components of the spectrometer You should run advanced these tests if you have problems with your spectrometer to determine diagnostic tests the cause The diagnostics provide information about the status of the component as well as troubleshooting information replacement procedures and information about ordering replacement parts Use the diagnostics software to e Run the spectrometer performance test Test specific components of your spectrometer e Get information about replacement parts Check the spectrometer configuration e 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 Di
145. ts you automatically insert an energy screen into the beam path to block out a portion of the energy at all frequencies of the infrared beam This is useful for preventing detector saturation and signal distortion For more information about using energy screens see When to use energy screens in the Spectrometer Basics chapter The wheel can be moved to any of four positions an open position for collecting spectra without a screen in the beam path and 3 screen positions As shipped from the factory the screen positions are populated with 30 10 and 3 screens The Screen Wheel parameters in Experiment Setup to describe the percentage of light transmitted by each screen installed in the wheel Simply select one to move the screen into the beam path Nicolet FT IR User s Guide 75 To specify the screen to use for an experiment set Screen Wheel on the Bench tab of the Experiment Setup dialog box available through Experiment Setup in the Collect menu 7 In OMNIC Help Topics find energy screen wheel in the Index and goto Controlling the energy screen wheel for complete instructions Experiment Setup C My Documents OMNIC Param Default exp Quality Advanced Parameter Sample compartment Detector Beamsplitter Source Accessory Window Recommended ranae Max range limit Min range limit Autogain 0 9494 10 Sample shuttle zi Screen wheel Filter w
146. tton 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 Open the sliding door remove the sample close the sliding door and then wait 1 minute before choosing OK If your spectrometer has the Smart Purge option Open the sliding door remove the sample and then slide the door until it is open about 1 cm When you hear the purge flow rate return to normal close the door all the way and choose OK If your spectrometer is sealed and desiccated Open the sliding door remove the sample close the sliding door and then choose OK A background spectrum appears in the Collect Sample window The spectrum is updated as more data are collected When all the data have been collected a message appears asking you to prepare to collect the sample spectrum Confirmation 2 Sample Please prepare to collect the sample spectrum Nicolet FT IR User s Guide 33 34 7 Thermo Electron Corporation Install the thin film polystyrene sample labeled Secondary Polystyrene Standard 1 5 mil Polystyrene through the sliding door wait if necessary see the instructions below and then press the OK Enter button If your spectrometer is purged but does not have the Smart Purge option Open the sliding door install the sample close the sliding door and then wait 1 minute before choosing OK I
147. 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 Cooling the detector J A Warning 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 Reverse the order given in the preceding procedure when you turn off system components Turn off the computer Turn off the printer Turn off the spectrometer Turn off the accessories qd ES Some detectors such as an MCT or InSb detector require cooling with liquid nitrogen In Spectrometer Help Topics view Cooling a detector in Setting up experiments for instructions Liquid nitrogen is extremely cold and therefore potentially hazardous Avoid contact with skin Wear protective clothing and follow standard laboratory safety practices to prevent injury Liquid nitrogen can be hazardous if handled in an insufficiently ventilated room A After you fill the detector dewar with liquid nitrogen the dewar holds about 750 mL allow the detector to cool at least 20 minutes befor
148. ve 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 a If special performance tests are available for your spectrometer a button labeled Extended Tests or another appropriate name will appear Click this button and follow the instructions that appear on the screen to perform the tests Nicolet FT IR User s Guide 133 134 Servicing your spectrometer Note Some spectrometer components including the detector light source laser and power supply were designed so you can replace them yourself if they fail The diagnostics software will alert you to failing components For instructions for diagnosing spectrometer problems ordering parts and replacing parts choose Spectrometer Help Topics from the Help menu A If the source laser module electronics module or power supply must be replaced refer to the replacement parts list made available when you choose Spectrometer Help Topics from the Help menu Call 800 642 6538 or 608 276 6373 to order the replacement assembly If you are outside the U S A contact your local Thermo Electron office Telephone numbers for all Thermo Electron Customer Support offices are provided with your system Thermo Electron Corporation FA Troubleshooting Software Problems The OMNIC software automatically and continuou
149. with reference spectra in the appropriate category in the library and then tells you whether the sample matches a library spectrum If you were unsure of the composition of the sample you could perform a spectral search using a search library In that case the software would search the library and then display a list of the library spectra that best matched the unknown spectrum a Follow these steps to perform a QC comparison 1 Select the spectrum by clicking it 2 Choose Library Setup from the Analyze menu The Library Setup dialog box appears with the Search Libraries tab displayed Library Setup Aldrich Linked IR Aldrich Vapor Phase Sample Library Ca Georgia State Crime Lab Sample Libre Add s j HR Nicolet TGA Vapor Phase a Hummel Polymer Sample Library 4 PEE emoyg Organics by RAMAN Sample Library Raman Sample Library Nicolet FT IR User s Guide 43 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 your QC comparison 3 Add the LIBS directory within the OMNIC directory to the list of directories if it is not already in the list This is the directory that contains the provided Polystyrene Quality Control Sample library To add the directory to the list choose Add Directory In the dialog box that appears locate and select the LIBS directory and then choose OK 4 Cl
150. x and go to File handling What does the Collect Sample window show The window displays the live spectrum as it is being collected plus a gauge indicating the progress of the collection an indicator showing whether any problems have occurred and other information about the collection Collecting a Spectrum available through Learning OMNIC Collecting the Spectrum of a Sample Nicolet FT IR User s Guide 99 100 In OMNIC Help Topics find spectrum in the Index and go to Collecting a sample spectrum How do I know my spectra are meeting quality standards OMNIC continuously monitors the quality of the data you collect based on the parameters you set The Quality tab in the Experiment Setup dialog box contains parameters for specifying the spectral quality characteristics that you want checked when you collect spectra OMNIC offers four categories of spectral quality checks e Spectrum checks e Parameter checks e Background checks e Interferogram checks When OMNIC performs a check and detects a problem the Collect Status indicator is displayed as a yellow circle or a red X Click the indicator or click the View Collect Status button at the end of data collection to see a summary of data collection problems encountered during the collection and other information about the collection When a collected spectrum passes all of the selected quality checks the Collect Status indicator appears as
151. you specified for the library using the Region Setup tab of the Library Setup dialog box will be included in the search If the spectral range of the spectrum is broader than that of the library spectra use the region tool to select the region of the spectrum that coincides with the library spectra before you start the search You can also use the view finder to display the region to search The Search command operates on the selected region or on the displayed region if a region is not selected Nicolet FT IR User s Guide 103 104 In OMNIC Help Topics find spectral region in the Index and go to Region tool or View finder How do I create a spectral library If you are using OMNIC use the Create Library button on the Library Names tab of Library Manager available through the Analyze menu to create a user library Once a library is created you can add spectra to it with Add To Library in the Analyze menu or by dragging the spectrum to the library s book on the Library Names tab of Library Manager You can use a search library you create just as you would a commercial library to identify unknown spectra You can use a QC library to verify the composition of a sample If you create a scrapbook library you can find spectra in it by searching for text but not by spectral searching When you create a library you determine the kinds of information that will be saved with it In OMNIC Help Topics find library i
152. your detector 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 In Spectrometer Help Topics view Setting up experiments for instructions for installing energy screens in the sample compartment An optional energy screen wheel lets you automatically move a screen into the beam path before collecting data See Using the energy screen wheel in the Spectrometer Options chapter for more information The aperture in a Nicolet 6700 is a variable diameter opening that controls the angular size of the infrared beam and thus the amount of radiation that reaches the sample Using an aperture has these advantages e It lets you use more sensitive detectors e It helps prevent infrared energy saturation so the response of the detector is more linear timproves wavenumber accuracy and resolution by acting as a point source of infrared radiation In general you will find that the larger the aperture the better is the signal to noise ratio of the collected data The smaller the aperture the better the stability and accuracy will be Small apertures are needed for high resolution experiments DTGS detectors can accommodate m

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