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Practicum 5, Spring 2015 Selective pulses: long pw90s, presaturation and shaped pulses !

This!demonstration!develops!practical!applications!of!the!inverse!relationship!between!time!and!frequency.!!We!will!employ!selective!saturation!of!a!narrow!spectral!region!using!a!very!long!pulse,!we!will!use!a!long!pulse!to!achieve!selective!excitation!and!then!use!a!selective!inversion!(180°)!pulse!as!part!of!a!gradient!echo!selectively!retain!one!resonance!while!randomizing!all!others.!

Selective pulses -1- long square excitation As!always,!begin!by!collecting!a!beautiful!1d!and!by!knowing!the!pw90!at!a!given!power.!!Examples!are!given!below!based!on!a!pw90!of!18!us!at!a!power!of!60.!

In!Acquire>Acquisition!click!on!'Display!Pulse!Sequence'!to!see!the!standard!pulse!sequence!(Figure'1'[1]).!!We!will!look!at!the!effect!of!increasing!the!duration!of!the!observe!pulse,!while!retaining!the!use!of!a!90°!tip!angle.!For!a!power!of!59,!we!measured!a!pw90!of!18!us.!!Enter!18!for!both!the!Observe!Pulse!and!the!pw90.!!Enter!59!for!the!Power![2]!(In!practice!you!should!enter!the!pw90!and!power!you!obtained!yourself.)!Click!on!'Arrays'![3].!!In!the!array!panel!(Figure'2),!give!the!parameter!name!pw,!return![1].!Set!an!array!of!9![2],!starting!at!18!us![3],!exponential!incrementation![4]!with!the!increment!=!.6929!(=ln!2)![5]!gives!pulse!widths!that!double!with!each!step!and!end!at!4599!us!or!4.6!ms![6]!!Note!that!only!the!first!of!those!pulse!widths!will!be!a!90°!pulse,!but!since!the!second!pulse!is!twice!as!long!as!the!first,!it!will!be!a!90°!pulse!if!it!is!executed!with!half!the!pulse!amplitude.!To!make!the!second!and!subsequence!pulses!weaker,!click!on!'New!Array'!and!then!(Figure'3)!enter!tpwr'![1]!under!'Param!Name',!return.!!tpwr!is!the!power!used!for!the!pulse.!Make!this!a!9[step!array!too![2],!starting!at!59![3]!(the!power!needed!for!an!18!us!pulse!to!be!a!90!°!pulse)!and!changing!linearly![4]!with!an!increment!of![6![5].!!Note!that!the!'Array!Size'!is!81![6].!!We!currently!have!each!possible!value!of!pw!for!each!possible!of!tpwr.!!Instead,!we!want!the!shortest!pw!with!the!highest!power,!then!the!second!of!each!array!together,!etc.!!!Change!the!value!of!'Order'![7]!so!that!both!twpr!and!pw!are!arraying!with!order=1.!Now!(Figure'4)!the!array!size!should!read!9![1]!instead!of!81.!You!can!also!use!the!result!of!clicking!'Show!Time'![2]!to!give!yourself!a!sense!of!whether!the!array!will!have!81!steps!or!9,!and!thus!whether!the!array!is!set!up!correctly.!!The!set[up!above!ensures!that!each!of!the!pulses!given!will!be!a!90°!pulse,!although!they!have!a!range!of!durations.!!You!can!now!go!to!an!Acquire!page,!check!the!experiment!by!clicking![Sequence]![3]!and![Show!Time],!and!then!click![Acquire]!to!collect!data![4].!

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Display!the!spectra!obtained!as!a!vertical!stack.!!Note!in!Figure'5!how!all!the!pulses!produce!signals!in!the!centre!of!the!spectrum!but!only!the!shorter!pulses!produce!signals!at!larger!frequency!offsets!from!the!centre.!!The!longer!pulses!excite!narrower!portions!of!the!spectrum,!the!frequencies!closest!to!the!carrier!frequency,!those!for!which!ν[νo!is!smallest.!!In!producing!Figure!5!I!used!a!postscript!output!because!this!has!some!advantages!for!publications!and!grant!applications.!In!the!left[hand!side!panel!(Figure'6),!select!the!1D!tab![1],!then!under!'Basic!Plotting'![2]!chose!(•)!File![3],!click!on!'Print!Screen'![4]!!If!your!interface!does!not!have!a!1D!tab,!go!to!the!menubar!at!the!top!and!under!“File”!(Figure'7![1])!draw!down!a!menu!and!select!“Print!Screen…”![2].!Choose!to!print!to!a!file!(Figure'6![5]).!!Give!a!file!name=pw90length![6].!For!Black!and!white!printouts,!that!will!override!all!the!color!choices!and!thus!free!you!from!changing!them,!choose!(•)!Mono!in!'Print!Screen'.!!With!this!setting!you!do!not!even!need!to!set!the!background!to!white!!!Click!'Save'!![8]!then!'close'![9].!You!should!see!a!message!in!the!response!box!(Figure'7![3])!that!says!“Saving!file:!/home/che555/pw90length.ps”!telling!you!that!the!plot!operation!succeeded!and!giving!you!the!location!of!your!file.!!PLEASE!remember!to!move!this!to!your!own!directory!before!logging!out.!!(Side!note!on!arrays!of!arrays!(all!values!of!tpwr!for!each!value!of!pw)!vs.!arrayed!pairs!of!variables!(each!value!of!tpwr!is!used!in!combination!with!the!applicable!pw90).!!You!can!distinguish!between!the!two!in!Acquire>Overview,!where!the!array!dimension!arraydim!is!9![1]!and!the!array!is!over!(tpwr,pw)![2]!for!the!array!of!paired!variables,!vs.!81![3]!and!twpr,!pw!for!the!array!of!arrays![4].!Figure'8)!

Selective saturation: presat Another!implementation!of!long!pulses!is!'presaturation'.!!In!this!case,!a!long!low[power!pulse!is!applied!continuously!for!a!very!long!time,!long!enough!to!actually!saturate!the!resonance!to!which!it!is!applied.!!Because!the!pulse!is!very!long!(in!time)!it!is!very!selective!in!frequency!space.!!This!method!is!therefore!useful!for!suppressing!a!single!line,!such!as!that!of!a!solvent.!!Our!solvent!is!deuterated,!and!therefore!not!a!big!contributor!to!the!spectrum,!but!we!can!demonstrate!the!method!on!a!line!of!the!sample!molecule.!Starting!from!your!beautiful!1d!.!.!.!!Under!Experiment,!use!Convert!current!parameters!to!do....!(not!Setup!NEW!parameters!for!...)!!Solvent!Suppression![!Select!peaks>!PRESAT!(Figure'9).!!You!will!see!the!long,!low!presat!pulse![1]!immediately!preceding!the!observation!(‘read’)!pulse![2]!!In!Acquire>PRESAT![3]!note!that!there!is!a!second!offset!now![4],!for!the!frequency!at!which!presaturation!will!be!applied.!!Right!above!this!is!the!duration!of!presaturation.!!Since!spectra!collected!in!water!place!the!water!signal!on!resonance!(on!the!carrier!frequency),!the!default!is!on[resonance!presaturation,!when!the![√]!Presaturation!box!is!checked![5].!

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You!can!effect!presaturation!of!a!peak!that!is!not!‘on!resonance’!by!one!of!two!ways.!!Either!you!can!type!in!a!different!Offset![4]!and!the!pulse!sequence!will!use!this!for!the!presaturation!pulse.!!!If!your!beautiful!spectrum!was!correctly!referenced,!you!can!see!what!ppm!your!frequency!corresponds!to!and!adjust!as!needed.![6]!!For!saturation!at!4.17!ppm,!I!used![359!Hz,!and!a!power!of![3![7].!!Because!presaturation!is!applied!over!quite!long!times,!do!not!use!more!than!a!power!of!4.!!The!minimum!power!is![16.!!!A!tricky!way!of!employing!the!cursor!to!determine!the!frequency!corresponding!to!a!resonance!is!to!go!to!Acquire>Channels!and!set!the!decoupler!to!be!H1!(not!C13).!!Then!in!Acquire>PRESAT!(Figure'10![1])!place!the!cursor!on!the!line!you!want!to!saturate![2].!type!sd!(set!decoupler)![3].!!The!response!text!will!tell!you!what!frequency!your!line!corresponds!to![4]!and!you!can!type!that!value!into!the!Offsets!box![5].!!!!The!selectivity!of!presaturation!is!illustrated!in!Figure'11.!!**satmodeYN**!!Alternately!you!can!activate!'Off[Resonance!PRESAT'!([1]!Figure'12).!This!time!we!replace!a!long!low!pulse!with!a!pulse!that!is!shaped![2].!!Its!amplitude!and!phase!vary!during!the!course!of!its!application.!!This!enables!the!pulse!to!be!selective!with!better!off[resonance!properties!(eg.!less!sinc!wiggles).!!Type!in!a!carrier!frequency![3]!and!the!corresponding!chemical!shift!will!be!calculated,!as!above.!!Figure'13!shows!the!effect!of!presaturating!or!not.!!To!make!this!comparison!we!activate!the!‘Arrays’!GUI![1]!and!for!the!parameter!name!type!satmode![2].!!Give!it!array!size!2![3]!and!in!the!second!position!for!the!value!type!‘n’![4].!!!!!

Pbox and a shaped excitation pulse: sh2pul Just!as!a!shaped!weighting!function!can!be!applied!to!a!FID!to!alter!the!shapes!of!the!frequency[space!lines!that!result!upon!Fourier!transformation,!we!can!apply!pulses!that!are!shaped!in!time!(ie!grow!gradually!instead!of!abruptly,!and!shift!between!X[axis!and!Y[axis!delivery)!to!alter!the!shape!of!the!frequency[domain!excitation!band.!This!is!EXTREMELY!powerful!and!permits!highly!selective!non[distorting!pulses.!We!will!use!Varian's!"Pbox"!module!to!facilitate!generation!of!shaped!pulses.!!Starting!from!your!beautiful!1d!for!which!you!know!the!pw90!at!the!power!in!use!.!.!.!In!the!menu!bar!at!the!top,!select!'Edit>New!Pulse!Shapes!...>Pbox!!(Figure'14).!Select!the!Make!Waveform!tab![1].!In!'select!waveform'![2]!choose!excitation![3],!eburp1![4].!!Make!sure!that!the!reference!pw90![5]!and!power![6]!are!correct.!In!Process>Display![7],!place!a!pair!of!cursors!around!the!peak!you!want!to!selectively!excite.![8]!Back!in!the!Pbox!window,!click!on!"Select!from!spectrum"![9].!!!The!software!calculates!the!corresponding!bandwidth!and!frequency!offset!from!the!cursor!positions.!!From!the!reference!pw90!and!power!it!calculates!a!pulse!length.!!!

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Click!on!'Add!Waveform'![10].1!Next!to!'Shape!file!name'!type!in!your!pulse's!name![11]!(for!example!exc6ppm_18Sep2012)!then!click!'Make!!It!!'!![12]!which!becomes!active!only!after!you!have!given!a!name.!A!numerical!description!of!the!shape!is!written!as!a!shape!file!in!your!'shapelib'!directory!in!vnmrsys.!!!Click!on!'simulate'!(Figure'15![1])!to!see!a!simulation!of!the!excitation!bandwidth![2]!superimposed!on!the!spectrum![3].!!The!simulation!shows!that!X!magnetization!is!created!for!spins!near!6!ppm![4]!,!and!that!this!is!at!the!expense!of!Z!magnetization!in!the!same!region!(Figure'16![1]).!!!!Pbox!can!also!help!you!set!up!your!experiment,!for!simple!cases.!!!Use!Browser!to!select!/che555/vnmrsys/data/SelectiveExcitation_chloropropenylbenzenemeth_24Feb2015'!and!drag!it!into!your!experiment.!!You!should!see!the!shaped!two[pulse!experiment!(=sh!2!pul)!appear!in!your!exp!(Figure'17![1])!Use!edit>new!pulse!shapes!...!(Pbox)!and!the!Update!Parameters!tab![2].!!Type!in!the!name!of!the!shaped!pulse!you!want!to!use![3]!!!You!may!need!to!click!on!‘Read!Parameter!Values”.!!Note!the!length!of!your!pulse![5]!and!the!power!it!requires![6].!Now!provide!the!parameter!names!that!the!current!pulse!sequence!uses!for!those!parameters![7]!and![8],!as!well!as!the!parameter!that!points!to!the!shaped!pulse!name![9].!!This!can!be!accomplished!by!clicking!"Set!parameter!values!into!the!experiment"![4].!!Note!that!the!duration!of!the!shaped!pulse!is!given!to!the!experiment!at!pw,!and!the!power!is!changed!to!be!that!of!the!shaped!pulse![10].!!Alternately,!you!can!enter!the!correct!pulse!width!and!power!by!hand!in!Acquire>Acquisition!and!the!pulse!name!in!"Acquire>Pulse!Sequence"!(Figure'18![1])!which!provides!a!second!opportunity!to!enter!the!pulse!width![2]!(but!not!the!power).!!Enter!the!power!in!Acquire>Channels!or!Acquisition.!!!!Be!sure!that!the!host!experiment!you!are!about!to!run!has!the!same!transmitter!offset!(tof,!the!centre!of!the!spectrum)!as!the!experiment!in!which!you!created!the!pulse!(the!one!in!which!you!placed!cursors!and!employed!Pbox!to!make!new!pulse).!!!!In!Start>Standard!turn!off!"Lock!Autoshim!"!and!set!Temperature!to!25.!In!Acquire>Channels,!make!SURE!that!you!use!the!same!transmitter!offset!(and!solvent)!as!was!active!in!the!experiment!upon!which!your!shape!is!based.!!!!!You!are!ready!to!go!now,!after!the!usual!safety!checks:![Display!Sequence]![3],![Show!Time]![4]!and![Acquire]![5].!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!1!!!If!you!want!to!excite!additional!peaks,!choose!pulse!type,!move!the!cursors!and!click!'Select!from!spectrum'!and!then!Add!Waveform'!again.!

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Go!to!Process>Default,!click!'Transform'.!!View!the!entire!spectrum,!use!MM!to!adjust!vertical!scale,!phase!up!the!big!signals.!Figure'19!shows!and!example!of!selective!excitation!vs.!non[selective!excitation,!although!not!with!the!6!ppm[selective!pulse!used!as!an!example!above.!!!!The!'wet'!method!exploits!selective!excitation!pulses!followed!by!destructive!gradients!to!scramble!the!magnetization!of!the!resonances!that!were!selectively!excited.!

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pw=4608 2304 1152 576 288 144 72 36 18

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Saving file: /home/che555/pw90length.ps”

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non-selective excitation

selective excitation

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