500 MHz NMR Operation Instructions - Haverford College (Agilent) 500 MHz NMR Operation Instructions (Haverford College) ... • If you are a research student, enter your research

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    Varian(Agilent)500MHzNMROperationInstructions(HaverfordCollege)

    PreparingyourNMRSampleTube

    1. Dissolve(i.e.noparticulates)yoursamplein1mLofdeuteratedNMRsolvent(CDCl3,D2Oord6-DMSOarerecommended).

    2. Placesolutionintoa9longNMRtubeandcapit. 7tubesarehardtoremovefromthecarousel,

    andareolderandoflowerquality.

    3. Findagrayspinnerforyoursample. Seefigure1. Theseareusuallykeptinthetopdrawerright

    behindtheNMRcomputer. TheyshouldnotberemovedfromE107.

    4. Placethegrayspinnerintothedepthgauge(Figure2)andthencarefullypushtheNMRtubeintotheopeningatthetopofthespinner. Itisatightfit;holdthefragileglassNMRtube

    closetothebottomwhilepushingthetubestraightdown.

    5. Pushthetubedownuntilittouchesthebottomofthedepthgaugewhilethespinnerisstillseatedfirmlyatthetop. Besurethattheliquidsamplecoverstheentire

    dottedrectanglemarkedontheinsideofthedepthgauge(ifyouused1mLofsolvent,itwill).

    TherectangleindicateswheretheRFcoilwillfitaroundyoursample

    6. Holdingeitherthetopofthetubeorthetop(black)ringofthespinner,removethetubeandspinnerfromthedepthgauge.UseaKimwipetoremovefingerprints,etc.fromtheoutsideofthetube(belowthespinner)andthespinneritself. TheNMRtubemustextendbelowthespinner

    bytheproperlength,sodontletthetubemoveupordown(withrespecttothespinner)afterremovingitfromthedepthgauge.

    Insertingatubeorspinnerthatisdirty(ontheoutside)willdegradetheNMRspectraoffuturesamples(aswellasyourown).

    Figure1:spinners

    Figure2:NMRtubeinspinner,properlypositionedindepthgauge

    spinner

    topofNMRtube(cap)

    depthgauge

    bottomofNMRtube

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    PlacingyourSampleintheCarouselandsigningin

    CAUTION:Donotapproachthemagnetifyouhaveapacemakerorothermedicaldevicethatmaybeincompatiblewithstrongmagneticfields.Youmaywishtoremovecellphonesandwallets(creditcards)fromyourpockets.

    7. Withthespinnerinhand,climbtheladderandlookatthetopofthecarousel.Selectanyfreeslotexceptforslot#1ortheactivesampleslot(theoneclosesttoyou)(seeFigure3). Explanation:thereisalreadyasampleinthe

    magnet,anditneedstomoveupintothisactivesampleslotbeforeyourtubecandropin.

    8. HoldthetopoftheNMRtubeandcarefullylowerthetube(+spinner)straightdownintotheslot Donotleanagainstthemagnetifyoudo,it

    willwobblebackandforthsinceitissupportedonacushionofair,toshieldagainstvibrations.

    TheNMRtubewillstickupabout1.5abovethetopofthecarousel.

    Notethenumberoftheslotyouused.Unfortunately,thesamplenumbersareatthebottomofthecarousel.

    9. Signintothelogbookwiththedate,yourname,solvent,andtypeofexperimentyouplantodo.Alsoincludethecarouselslotthatyouareusing.

    Thatissowecancomefindyouifyouforgettoremoveyourtubefromthecarousellateron.

    Figure3:NeveraddaNMRtube+spinnertoslot#1orthecarouselslotthatisovertheyellowcautiontriangle(theactivesampleslot).Whenthispicturewastaken,slot#1WAStheactivesampleslot,butthisisnotalwaysthecase.

    StartingtheVnmrJsoftwarewiththecorrectoperatorname

    10. OntheNMRcomputer(youmayneedtomovethemousetowakeit),ifauserisalreadyloggedinandtheVnmrJsoftwareisrunning,clicktheStarttab(Figure4,#6)toseetheoperatorname(Figure4,#7).Ifitiscorrect,youmayskiptothenextsection(SettingupanewStudy). ItIsimportanttobeloggedinasthecorrectuserandtobeusingthecorrectoperatorname

    sothatyoucanfindyourdatafilelater.

    11. Tochangeoperatorname,exitfromtheVnmrJsoftware(usingtheFilemenu)andlogoutofthesystem(usetheSystem:LogOutoptionfromthelinuxdesktop).

    12. Loginwiththecorrectloginname(researchorsuperlaborclasses)andpassword(passwordscanbefoundinthepurplerunlognotebook).

    13. StarttheVnmrJprogram(itsiconwillbeonthedesktop).Youwillbepromptedtoentertheoperatorname: Ifyouarearesearchstudent,enteryourresearchgroupnameforoperatorname

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    Ifyouareinsuperlaboranotherclass,chooseyoursemester.Filesassociatedwiththeseoperatornameswillgenerallydisappearaftertheendofthesemester(researchgroupfilesmaystayslightlylonger,butdontcountonlongtermstorage)

    Figure4.VnmrJscreenshot.Numbersareusedintheinstructions.

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    SettingupanewStudytorununderAutomation

    Theautomationroutineallowsyoutosetupastudyforeachsampletubepositioninthecarousel.EachstudywillconsistofoneormoreNMRexperiments;forinstance,obtaininga1-DprotonNMRspectrumisanexperiment,andobtainingaseriesof13CDEPTNMRspectraisanotherexperiment.

    14. Clickonthesmallcircleatposition#4(Figure4)todisplaythesampleslotnumbers(aringof12numbereddotsFigure5).

    15. Ifyouarerunningthefirstsampleoftheday,orifyoursampleslotnumberisshowingupasacirclewithacolorotherthangray(indicatingtheslotnumberhasalreadybeenusedbysomeoneelse),chooseAutomationRun[autodir]>NewAutomationRunfromtheAutomationmenu(Figure4,#1).

    16. Iftheyarentalreadyselected,clickontheProtocolsandCommontabs(Figure4,#2and#3). DoNOTusetheStd1Dtab

    17. ClickonNewStudyin(Figure4,#10)tocreateanewstudy. Astudyisoneormoreexperiments

    donebacktobackonthesamesample

    18. Clickonthecirclewiththeslotnumberforyoursample(seeFigure5)

    19. Typeinasamplenameandselecttheappropriatesolvent(Figure5,orFigure4,#8and#9). Itisusefultoincludeyournameorinitialsinthesamplename,butyoudonotneedto

    includethesolvent,dateortypeofexperiment.

    20. Clickonyourexperiment(i.e.PROTON;Figure5orFigure4#3). Ifyouwish,youmayclickonmultipleexperiments.Alongerlistofexperimentsisavailable

    undertheLiquidstab.

    Optional:ChangingAcquisitionParametersforanExperiment

    ThefirstfewtimesyoucollectNMRspectra,skipoverthissection.Butbychangingacquisitionparameters,youmaybeabletogetbetterqualityspectrawithmoreaccurateintegrations.

    21. Doubleclicktheexperimentwherelistedinthetobesubmittedstudyqueue(itwillhaveanamelikePROTON_001_day[0:24]upperleftredcircleinFigure6).Waitabout10-15secondsasthedisplayontherightsidechangestoshowtheacquisitionparameters.

    22. Ifitisntalreadyselected,clickontheAcquiretabtotherightoftheStarttab(Figure4,#6).Changeparametersasdesiredforyourspectrum.Someparametersyoumaywishtochangeforaprotonspectrumareasfollows:

    Figure5.Thesamplechangerslotdisplayduringsetupofanewautomationstudy.RedcirclesshowbuttonsthatmustbeclickedorfieldstobefilledinwhensettingupanewstudythatincludesaprotonNMRexperiment(seesteps1820,and24).

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    SpectralWidth(intheDefaultH1list):Bydefaultthisis-2to14ppm,butifyouknowthatallyoursamplessignalsarebetween0and5ppm,thenarangeof-1to6ppmwillsuffice.Warning:donotattempttoexcludeimpuritypeaksbycuttingdownthespectralrange;ifyoudo,thosepeaksmayshowupasFourierfold-overpeaksatthewrongppm.

    Acquisitiontime(ontheleftsideoftheAcquisitionlist):Thedefaultis2-3seconds(itwillchangeifyouchangethespectralrange),buttogetthesharpestpeaks,increasethistoatleast5seconds.

    RelaxationDelay(ontherightsideoftheAcquisitionlist):Theacquisitiontime+therelaxationdelayshouldbeatleast15secondstogetthemostaccuraterelativeintegrations.

    Numberofscans(ontheleftsideoftheAcquisitionlist):Bydefaultthisis8,whichIsusuallysufficientforprotonspectra.Butifyouhaveaveryweaksample,youcanincreaseyoursignaltonoiseratiobyafactorof4byincreasingthenumberofscansbyafactorof42=16(i.e.numberofscans=128).Thisofcoursewilldramaticallyincreasethetimeittakestorunyourexperiment(toatleast32minutes,ifyoualsoincreasedtherelaxationdelayasdescribedabove).

    Youmayalso,ifyouwish,changesomeoftheprocessingparameters.Butthesecanbechangedafteryoucollectyourdata,soitisnotcriticaltochangethemnow.

    23. Onceyouaredoneeditingtheacquisitionparameters,clickSave.onthelineofbuttonsabovetheparameters.Youmaynowaddorchangeparametersforasecondexperimentifyouwish.

    SubmittingyourStudyforAutomation

    24. ClickthegreenSubmitbutton(lowerleftofFigure5).Yourstudyhasnowbeenaddedtotheautomationqueue.Thesampleslotnumberonthedisplayshouldturnyellow.

    25. Ifyoursisnotthefirstsampleoftheday,dataacquisitionmaystillbeinprocessonsomeoneelsessample.Butotherwise,withinafewseconds,expecttoseeandhearsomeactivity: Afterafewseconds,thesamplechangershouldejectthesampleinthemagnetbefore

    rotatingtoyoursampleslotanddroppingyourtubeintothemagnet.Thesampleslotnumberonthedisplaywillturnpurpletoindicateithasbecometheactivesample

    Figure6.Modifyingparametersforanexperimenttobeincludedinanewstudy.

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    Ifnothinghappensafter30seconds(orerrormessagesappearbelow),tryrightclickingonthesampleslotnumberandselectDeleteStudy.ThenchooseDeleteDay&NightQueue.Then,makesurethatthecorrectsampleslotisstillselectedandsubmityourjobagain.

    Ifstillnothinghappens(andyouaresurethatnobodyelseiscurrentlycollectingdataontheirsample),youmaytryAutomationControls>AbortAutomationatthebottomoftheAutomationmenu.Thengobacktostep15andstartaNewAutomationRun.

    Ifstillnothingishappening,seekhelp.

    AftersubmittingyourStudy

    TheadvantageofusingtheAutomationQueueisthatyoucansetupadditionalstudieswhiledatacollectionisinprocess.

    26. ToensureefficientuseoftheNMRtime,dontwaitfordatacollectiontobedonebeforesettingupthestudyforthenextsample.

    27. Ifanotheruseriswaitingtosetuptheirsample,letthemdoso.Iftheyareusingadifferentoperatorname,theymaycloseVnmrJandrestartittochangetheoperatorname.Datacollectionwillcontinueonyoursample. Unfortunately,ifyouchangeloginnames(research,classes,superlab),youcannotaddnew

    studiestotheautomationqueue.

    28. Afteraddingstudiesforallsamplestoberun,addastudyconsistingofjustaprotonexperimentforthelocksample,keptinsampleslot#1.UsesamplenameLockandsolvent=D2O. ThelocksampleisjustatubecontainingD2O.Itisbesttoleaveasampleinthemagnetat

    alltimes(exceptduri