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:jbaddison@ucdavis.edu

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.