BriefIconNMRandTopspin3.5UserGuideforBrukerNMRSpectrometers
AvanceIIIHD400MHzNMRwithAutosamplerinChemistryroom93
DISCLAIMER Thisdocumentis intendedtobeabrief,bare-bonesuser’sguideforNMRdatacollectionusingBruker’s
IconNMRAutomationsoftwareforthe400MHzAvance-IIIHDBrukerNMRspectrometerlocatedinChem93managed by the UC Davis NMR Facility. For detailed help with both routine and advanced NMRexperiments,pleaseconsultBruker’sUserGuides,whichcanbe foundwithin theResources tabonourwebsite,nmr.ucdavis.edu.
CONVENSIONSSomeusercontrolwillbedoneinBruker’sTopspin3.5interface.ForTopspininteraction,keyboardinputisshownasboldfacetypeinthismanual.NotethatinTSthe“enter”keymustbeusedafterthecommandis typed; this is assumed through-out this manual and “enter” key strokes are not given explicitly.Commands inTSaretyped inontheTScommand linenear thebottomof theTSwindow;againthis isassumedandwillnotgenerallybestatedexplicitlyherein.LMB,MMB,andRMBareusedtoindicateactionsoftheleft,middle,andrightmousebuttonrespectively.OnaPCthemousewheelactsastheMMB.Click,anddoubleclickrefertopressingtheLMB.
GENERALPROCEDURE YouwillfindthatthegeneralprocedureforacquiringNMRdataonallNMRspectrometersisessentiallythe
same.IconNMRhandlesthemajorityofthetaskslistedbelow.Thegeneralprocedureisasfollows:1 SamplePreparation2 LoginandStartup3 SetupInitialParameters4 Check/EditAcquisitionparameters5 InsertSample6 LockontoSolvent7 TunetheProbe8 Shim9 CheckReceiverGain10 Acquire11 ProcessData12 RemoveSample13 Logout,SignLogbook
Experiment: RoutineProtonNMRParameterSet: PROTONInstrument: ChemBruker400usingIconNMR
SamplePreparation1. DissolveyoursampleinanappropriatedeuteratedNMRsolvent.Makesurethere
isnoun-dissolvedmaterial.Ifthereis,youwillneedtoeithercentrifugeorfilteryoursampletoremovecrystals/debris.
2. Transferabout550-600uLofsolventintoacleanNMRtube.Werecommendhigh-qualityNMRtubes-rated600MHzorhigher,buteconomytubeswillbeOKforroutineworkatlowerfields(400MHzandbelow).Yoursampleheightshouldbeabout4-5cm.
LoginandStartup
1. Logintoyouriconnmruseraccount.Ifaprevioususeriscurrentlyloggedin,youwillneed
toselectChangeUser,thenlogintoyouraccount.
TIP:useasmallamountofKimWipeinaPasteurPipettetoquicklyfilteroutanyundissolvedmaterial
NOTE:IfyourIconNMRaccounthasnotyetbeencreated,pleasereachouttoBennettAddison:[email protected]
SetInitialParameters1. IdentifyanemptyholderintheBACS120autosampler.Westronglyrecommendyouuse
theholdersintheinnerring:holders1-60.2. Placeyoursampleintoanavailablebluespinner,setdepthusingthedepthgauge,and
dropyoursampleoffintheappropriateholder.DoNOTdropoffyoursamplewhilethecarouselorsample-armismoving.
3. IdentifythematchingholderinIconNMRmenuanddouble-clicktoaddanexperiment.4. Enteryourdetails:DataDirectory,ExperimentName,ExperimentNumber,Solvent,
Experiment/ParameterSet.
Directory:YourdirectoryshouldbebasedonyourPI.Itissetautomaticallywhenyoulogin.
ExperimentName.Usersoftenincludeinitials,labnotebookpage,date,andanyadditionalinfoifdesired.Notedonotusespaces,specialcharacters,etc.
ExperimentNumber.Thedefaultisincrementsof10(10,20,30…)foreachsample/holder,orincrementsof1(10,11,12…)ifyouarecollectingmultipleexperimentsonthesamesample/holder.
Solvent:Selectyoursolventfromthedrop-downmenu
Experiment:Selectyourexperimentfromthedropdownlist.Ifthereisanexperimentyouwouldliketorunbutitisnotonthelist,contactBennett.
Useinnerring:Innerringisthelowernumbers,outerringhighernumbers
Check/EditAcquisitionParameters1. Ifdesired,hittheequalsbuttontoeditstandardProtonacquisitionparameters
includingnumberofscans,spectralwidth,acquisitiontime,offsetfrequency,etc.
2. Editthetitleifdesired.Youcanaddanysample/experimentdescriptionin
thistextbox.Youmayfinditusefullaterforyourbookkeeping.
3. EdittheStartTimeifdesired.Theclockissetto24hrtime.Note,ifyousetastarttimebetweenthehoursof8pm–8am(night-timequeue),pleasemakeareservationontheonlinescheduler.
4. Ifyouwouldliketoalsocollectanotherexperimentonthissample(e,g,C13CPD),you
canhighlightthecurrentexperimentandthenhittheAddbutton.Anotherexperimentwillappearbelowwithexperimentnumber11andanemptyexperimenttype.Selecttheappropriateexperimentandeditacquisitionparametersifnecessary.Detailsareprovidedinlaterpages.
Note:Thedefaultacquisitionparametersaregood,butfeelfreetochangethemasdesired.Ifyouwouldliketochangeanyotherparametersnotaccessibleinthislist,youcanselectParameters–EditAll,whichbringsyoutoTopspin.Youmayneedtodothisforsome2Dexperiments.
11pmStartTime
Note:Thisisredonlybecauseaparameter(ns)hasbeenchanged
SubmityourExperiment1. Whenyouaresatisfiedwithallexperimentsandarereadytocollectyourdata,highlight
theappropriateexperimentorholderdirectory,andhittheSubmiticon.
AUTOMATIONPROCESSES:AfterhittingSubmit,theautosamplerwilltakeover.Theautomationsoftwarewillhandlethefollowingprocesses:
• InsertSample,• TunetheProbe,• LockontoSolvent,• Shim,• CheckReceiverGain,• AcquireData,• ProcessData,• RemoveSample,• BackupDatatoGoogleDrive.
CurrentProcess
IfFlashing:inProgressIfGreen:CompletedIfClear:SkippedorNotCompleted
DataProcessing1. Tolookatyourspectra,simplydouble-clickonyourcompletedexperimentinthe
PrecedingExperimentslist.Ifdataacquisitionandprocessingiscomplete,youwillseeacheckmarkunderAcqandProcbyyourexperiment.Whenyoudoubleclick,youwillbesenttoTopspinforspectralviewing.
SpectralProcessingCommandsandTips:
1. NavigatetotheProcesstab,andhitProc.Spectrumbutton.ThiswillperformFouriertransform(efp),autophaseyourdata(apk),andperformanautomaticbaselinecorrection(abs).
2. Clickanddragtozoomin3. Double-clickorhittheFullViewbuttontozoomout.4. Usemiddlemousescrollwheeltozoomupanddown5. ClickandholdtheHandicontoshiftthebaselineupordownorsidetoside6. ReturntoIconNMRwhendoneprocessing/viewingspectrum
Identifyyourcompletedexperimentanddouble-click.Thelistisorderedchronologically.
LogoutProcedure:1. Whentheautosamplerhasreturnedyoursampletotheholder,youcanremoveyour
sampleandspinner.Caution:doNOTremoveyoursamplewhilethecarouselismoving,anddoNOTreachacrossthecenterwherethesensorislocated.Thisisespeciallyproblematicwhenthereisasamplecurrentlyinthemagnet.Trippingthesensorwithyourhandmayresultinshutdownoftheautosampler.Ifthishappens,besuretocallBennettoranNMRTA.
2. Whenyouaredoneandnolongerusingyourchosenholder,returntoIconNMR,selectyourcompletedholder,andhitDelete.Theholdershouldbecomeavailable.
3. Signthelogbook,includingDate,Name/PI,Nucleus,Drop-OffTime,PickupTime,andcheckifyouhavedeletedyourcompletedruninIconNMR.
