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NMR Spectroscopy User Guide

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1. 299 One Pulse OBeDU etse iere ceteri perte rente EIER eva bene etes RR DEP Oei 299 Lese Qelbure CP ee sic tiie Sei eR ene 299 One Pulse with TOSS Onepultoss oreste rite rrt eere arte eet tape ee 300 pwX90 Measurement with CP Tancpxflip eet 300 CP with PSLG Decoupling Ianepxfslg 2 m rere trie 300 AT wu CP Pane pt eisien a Eee rene erts 300 Interrupted Decoupling with CP Tancpxidref ees 301 lH Timo with CP CTanopxterhlio Lectt trente rne 301 CP with TOSS Tanepxtoss terme eet norte rcr ead 301 X Dwobulse Tor TLE POPU siari sr caner t errat 301 X Hahn Echo with CP Tancpxecho 1 ener terrere enr reete detras 302 13 5 HX2D EXPE MEMS oiire er rere eron tore OEE E EE EE E E E TEE EEES 302 2Q 1Q with CP and C7 Mixing C7imad2d esses 302 Heteatlgepad uie pene cp E EE PEERS HDI aie ata eee 302 PES UAE ies 03 occ thts osenkeh ds isthe E R A Raters tienets 303 WISE Wisentancp 2d iss sere ete tre tex aene eaaet eee teo 303 IX HXY Experiments ueni ioo eter E tom at Beasties weitere eee rane 303 One Pulse REDOR with XY8 on X and Y Redorlonepul 303 CP REDOR with XY8 on X and Y Redorltancp eere 304 One Pulse REDOR with XY8 Y and X inversion Redor2onepul 304 CP REDOR with XY8 on Y and X Inversion Redor2tancp 304 13 3 Quadrupole E
2. stdih Display Sequence Arrays dl Pulse Sequence Data Excitation hannels Spectral width 009 6 Hz v Relaxation delay 1 000 sec Flags Acquisition time 503 sec w First pulse us or e degrees Future Actions Complex points 15040 Inter pulse delay sec Observe Pulse 7 75 us or 90 degrees Scans Requested 16 nes a P Receiver Gain Ano Calibration pw90 7 75 at Power 55 Steady State m v off B 1 Set up experimental parameters and post acquisition actions 2 Click the Acquire button to acquire NMR data Process the Data VnmrJ NMR data processing and the functions accessed by clicking on the Process tab are described in Chapter 6 Processing Data page 93 E Process 1 aa Display More 1D Integration iCursors Line Lists Plot Text Output Transform all Transform FID Weighting Interact none Transform Size Acquired Points Linear Prediction Solvent Subtraction Auto LP Ful Clear Display Reference Peak Picking Autoscale By Solvent Peak Autophase By TMS Find Peaks Full Screen c Full Spectrum Reference cursor to Integration Display Text za Find nearest line msg values Baseline Correct Normalized Yalu Vert Scale Absolute w DC Correct Set Norm ta f1 Axis PPM v Find Integrals Clear Integrals Display Mode Phased wr BC Correct Pl
3. B 399 Surayesd Spectra and BID e DURER este tee ER 399 jo MOUSE 402 v 403 16 L0 Applications DIftectOrles seite tete Pert eec mh repe e epi Eee etre antis 404 Applications Directories MOMENTE 404 Using the Applications Directories Interface sese 404 16 11 Setting Colors an Vnmt eae eorpore Pri egt o reU REA 405 01 999343 00 B 1207 NMR Spectroscopy User Guide 1 5 Table of Contents Using Standard Styles and Themes eerte 405 Creating Editing and Applying Styles and Themes sesss 406 Deleting Styles and Themes tenter tet entes 406 Chapter 17 Locator and File Browser eere 407 LS V UTS CAUOL d 407 Locator Statements and Ment 2 esa eret dre eee ania cease dns 408 Usine the LOCAIOE is ion ses ener eee o ees 410 17 2 Locator Statements etie etre EE eter er Peer mE eese ee Tessa veo erra 411 Editable Fielda Me ER 412 Sorne Locator SEMENE Ioco oceni eU EPOR GENERE 412 125 File BIOWSOE Scott eR OE VIberte teneis eines tO RR TET IAE 413 Opa PTE o ep ere ea eee bnc pe 414 rur qo C 414 Appendix A Variable Temperature System eere 415 fcd VI Sep esent Wo Dea td Ue diu 415 WA dlc ME 415 AS Temperature Tray us deemed Gere Grp pe en FEE HE 416 AA O
4. ssssesseeeeeeennenen eere Mapping the 2 LSbum ioi de trot rae REPRE ETE Acquisition Parameters for Standard Two Pulse Sequence sess Interactive FED DIS play erinran eee en Petr th Ee ERE tea sehen ceed i eES Bre ATE DEP P VEHI PES Interactive Spectrum Display ERES UE E R e es SEES Le RYE Een Viewport Tab and Controls osse terrent eenie dente dere ede de ee dete Display Tools and Controls 0 rere toD EEPRREEEEED EORR Creating an Inset Frame eeceieetta bei bee teer there EISER ESEESE ee EE d TD STACK EOS PE Ct 3i scere tre eerie it orit tere n IER 2D Spectra with Overlaid ID S aie eien rti ero do ted etr etit es Stacked Oyerlaid 2D Spectra ees rro peret tese Errare ire ie d Plot Designer with Current Default Template esee Default oneD Template with Imported Data eene Editing a Plot Region Commands sese eene ltem Preferences WIndOoW eteeto nope I OSEE REIR REESE RUIN eet SEIT Text Inp t Wand Wi serere ere Eee eter imet Sehen Fei euo te E EE Plot Saye Window aee aita te bese OV OBERE rede best ue io etes eb ates tags Styles and Themes for Display and 2D Colors sse fami onpasm ble rre rat eee EAEE OE TEESE n Ee LI EIS A Pulse Field Gradient Experiment Pulse Sequences Gradient Stimulated Echo Element enne Doneshot Acquisition Tab and Default Page seen Dbppste Exper
5. CEB RATE A ETA RSET spin Assignment Spin System Make toa ist Mewate iterations 20 AY Use tine tit iterate JAX JAY SS Show simulation o nee 31 Spin system AX2Y Show specum Assign Lines E e Y Y 0 00 ew iea inesi Cear assigned ttl sax 7 4550 EXPERIMENTAL LINES LINES CALCULATED Jay 1 3733 i sifreq i clindex clfreq Xv 0 0000 0 00 1 0 00 line transitions frequency intensity 3 1 4 3800 652 1 000 6 2 7 3799 279 1 000 i 3 8 3793 197 1 000 32 13 15 3793 197 1 000 EUH ad se iA 2E Close Figure 98 Spin Simulation Spin Assignment Tab The Spin Assignment Tab has the following buttons and fields refer to Figure 98 as needed Button or Field Description Spin System Show simulation button Show spectrum button Make line list button Use line list button Use fitspec button Show assigned lines button Clear assigned lines button Iterate button Iterations field Iterate field Displays the spin system selection Display simulated spectrum Fourier transform and display the spectrum Create a line list from the current spectrum and threshold and copy the list into the spin simulation line assignment file Copy the current line list into the spin simulation line assignment file Copy the fit spec line list into the spin simulation line assignment file Display the spin simulation line assignment file spini la Clear the line assignments Iteratively fit the simulated transition
6. Figure 67 HMQC Pulse Sequence Showing Movement of Attached Protons 3 Next the 180 proton pulse places the b proton magnetization along the y axis but does not affect the a and c proton magnetization 4 The next pulse has the following effect a The 90 490 x carbon pulse is effectively a null pulse All rotational directions are maintained b The 90 490 y 180 x carbon pulse reverses the 13C which makes the a proton magnetization attach to the down 3C and the c proton magnetization attach to the p P C essentially reversing their rotational direction 01 999343 00 B 1207 NMR Spectroscopy User Guide 251 Chapter 12 Indirect Detection Experiments 252 5 After another period A 1 2J the following occurs a Thea b and c proton magnetization are refocused along the y axis b Theb proton magnetization are still along the y axis and the a and c proton magnetization are refocused along the y axis Subtracting the signal resulting from step 5b and 5a by changing the receiver phase oph results in cancellation of the b proton magnetization while the signal for the a and c proton magnetization doubles To create a 2D experiment with information about heteronuclear chemical shifts we introduce an evolution time t that occurs between the two X nucleus 90 pulses as shown in Figure 68 90 180 x oph x x X Figure 68 Evolution Time Added Between X Nucl
7. Sram Acquire Process MEETS sequence show Time Arrays way Defaults Acquisition C13 Sequence ancpx Environment MMM 0 2 00 0e oe Se TF Channels Acquisition Time 0 01984 sec M Temperature 1f hd Pulse Sequence Mere Complex Points 2D Increments Future Actions Recycle Delay Spectral Width Receiver Total Scans Complex Paints Block Size Phase Tables Steady State Receiver Gain po el Figure 82 Acquisition Parameters Solids Field Parameter Description and Settings Spectra Width sw Spectral width menu select units Hz kHz MHz or ppm Acquisition Time at Data acquisition time menu selections sec ms or us Complex Points np Total number of points collected during the acquisition time Recycle Delay di First delay in the sequence menu selections sec ms or us Total Scans nt Total number of transients collected Block Size bs Enter number of scans for block size and place a check in the check box to enable Remove the check from the box to set bs n not used and the block to Total Scans nt Steady State ss Number of dummy scans run before starting data acquisition Receiver Gain gain Gain of the receiver Set the value from 0 to 30 in the field Place a check in the box to turn off the autogain function Do not use autogain with solids MAS Rate srate Rotor spin rate menu select units Hz kHz MHz or ppm srate identifies the spin rate for automatic calculation of synchronized delays in some sequen
8. eese re en eene 230 Heteronuclear Spin Echo Difference Experiment sese 251 HMQC Pulse Sequence Showing Movement of Attached Protons 251 Evolution Time Added Between X Nucleus Pulses sseseee 252 HMQC with BIRD Pulse Nulling Effects 253 Verifying Cancellation with Pwx 0 90 255 Optimizing the BIRD Nulling TIME ssrin eo oeisio eeit 255 Coupled HMQC Spectrum of 3 Heptanone nicsen eiaeia 256 Expansion of Coupled 3 Heptanone HMQC Showing Multiplets 257 Decoupled HMQC Spectrum of 3 Heptanone eese 257 Basic HMQC Pulse Sequence nurse territi etin Ee deer Perg de desee de 260 HMQC Pulse Sequence with nu11 0 and mbond n sess 260 Solids Protocols Tabs 35i Heo hore ete eere obs ha ecu st EHE E HERE AE 269 Solids Experiments and Menus ss e rte PR eiae TEET ERE ENRERE 269 Channels Page and Basic Calibrations 200 0 ce ecee eeeeeeseceseeseceeeeseeeeeeeeseeeeseeeaeeaeenaees 271 Solids Spin Temp page with spintype Ma8 oo eee cee eeeeeeeeeeeeeeeeaeeeeetneenaees 272 Tancpx Pulse Sequence page of the Acquire tab 276 Acquisition Parameters Solids sss 278 Receiver Page of the Acquire tab Solids sese 2779 Tune Panel Solids i osten et teur RU de e MEO A AESA 281 Tuning Pattern Solids ceri ror tanga teeta eec eR RE ERER ERN eee 282 Adamantane Reference Sp
9. Wesco Fitting Routine analyze option linear poly1 quadratic poly2 cubic poly3 exponential curve exp The program expfit is called by this usage of the analyze command expfit creates the files analyze out used by exp to display the results and analyze list a table of results 4 Enter exp1 to see the results as a graph Figure 101 shows quadratic fittings for the data given in the example of the regression inp file in the next section 5 Enter pexpl page to plot one data set or enter pexp1 index index to plot multiple data sets Both exp1 and pexp1 set the scale automatically to show all points if possible 6 Optional Enter the scalelimits macro to set limits for the scales using one of the following Enter scalelimits with no argument to start an interactive process that prompts for the four scale limits Enter scalelimits x start x finish y start y finish with limits for the x axis and y axis as arguments The limits are retained as long as an exp1 display is retained Enter autoscale to return to automatic scaling by expl 7 Enter cat curexp analyze list to show the results of the analysis in the Text Output panel Contents of analyze out File The data input file is analyze out except for regression when the input file is regression inp The file exp1 out saves certain display and plot parameters Values can be 2048 points maximum from a data set 2
10. eee 69 Displayime Che IHIIBHD o ee ettet t rH n p ote Ebr ette ERA 69 Lose ASDA c erre tercer ertt eaten E EER EEEE 70 cine rci ELE 70 Shimmap Piles and Parameter Sets reete ie 70 4 7 Gradient Shimming for the General User see 71 6 NMR Spectroscopy User Guide 01 999343 00 B 1207 Table of Contents Testing SOUVEMS Me ME 71 4 8 Deuterium Gradient Shimming Procedure for Lineshape sese 72 SGU WP e M 72 Makine tbe SD M osuere erret Ph D RRRHERER 72 Siring Z Gradient SMODE eon eet rette ho rete rents 73 Optimizing Nonsspinmning ShWlg erroe perse iere ette rh eee certe eret 73 Evaluatine TROIS BEM TY eoi rrt ERR RR 73 9 Calibrating BZWIDG eter creer tto er Sess np prse Ee SE Les Pret a EE eges 73 4 10 Varying the Number of Sbims 1 retener tp rper Perret aiaei 74 Changing the Number of Shims Used for Gradient Shimming 74 Selecting Optimization of Z1 Through Z4 Shims First eeseesss T5 4 11 Variable Temperature Gradient Compensation sese 75 4 12 Spinning During Gradient Shimming esee 3 4 13 Suggestions for Improving Results waise necia E E eene 76 4 14 Gradient Shimming Pulse Sequence and Processing sse 77 Chapter 5 Data Acquisition cscsesscscsesasscsstssunasesensstesatnonatsnusececrstsansannasassannerasnae 8
11. States Haberkorn or TPPI experiment has been performed in a particular dimension This assumes that the pulse sequence has been written to perform standard phase cycling as described above If the data are reflected along a particular dimension it is possible or probable that different coefficients are required for data processing In this case the t3d nocoef formis used to allows coefficients to be specified which are found in a text file named coef in the 3D experiment directory unlike in t 2d where they are given as arguments to the command By default t 3d calls the make3dcoef macro to create a coefficient file using the 1coef and f2coef string parameter values The format for the 3D coefficient file is an extension of that used for 2D coefficients The coefficient file contains four rows of eight coefficients used to construct the t hypercomplex interferograms and a final row of eight coefficients used to construct the t4 interferogram The actual values of the coefficients depend on the order in which the States Haberkorn components of the 3D FID data set were collected This order depends in turn on the values of the parameters phase phase2 and array If TPPI phase cycling is used to collect data along one or both of the indirectly detected dimensions instead of four data sets per ni ni2 increment there are only two or one data sets respectively per ni ni2 increment If there are only two data s
12. Figure 20 Viewport Tab and Controls 01 999343 00 B 1207 NMR Spectroscopy User Guide 113 Chapter 7 Displaying FIDs and Spectra 114 Display Region Tools and Controls Orsptay Ades Aw The display region see Figure 21 of the viewport tab has the following tools button and check boxes Vaga Delete allat Z Ads Viewport Tools page 114 Fullsize Frame border Inset Frame Buttons page 114 Figure21 Display Tools and Display Check Boxes page 115 Controls Viewport Tools Icon Function Default mode left mouse click moves the left cursor and right mouse click moves right mouse cursor R Zoom mode left mouse drag across a region zooms in the region Q Left mouse double click on a peak or any point center the point and zoom in Right mouse double click on a peak or any point center the point and zoom out Exit zoom mode click any button on the panel graphics toolbar or redraw button Left mouse double click centers the point Right mouse drag up expands the spectrum Right mouse drag down contracts the spectrum Exit pan mode click any button on the panel graphics toolbar or redraw button Jj Pan mode left mouse drag moves the spectrum n d Inset mode left mouse drag a box over a spectrum region creates an inset frame of the region A viewport can have multiple inset frames Exit inset mode release mouse button Al Zoom out to
13. Command line Drag down the advanced function bar to open a command macro and parameter entry field and a text output field The default settings make the click and dragdown feature display the command line available see VnmrJ Installation and Administration manual for changing this default Open or close the field by clicking once on the button which restores it to its most recent view Error and information messages are displayed in the scrolling text window above the command line in addition to the hardware bar Click on the arrow with the left mouse button to view the command history Select a command from the command history by highlighting it and pressing Return to execute it Hardware Bar HCN123 Acquisition status Message history Trash can ardware robe Acquisition message Message 01 999343 00 B 1207 NMR Spectroscopy User Guide 381 Chapter 16 VnmrJ Experimental Interface 382 The hardware bar contains the following Trash Can page 382 Hardware Monitors page 382 Probe Selection page 382 Acquisition Status Details page 383 Acquisition Status Display page 383 History of Acquisition Messages page 383 History of All Messages page 383 Message Display page 383 Click on the bar to the left of the trash can with the left mouse button to hide or show the hardware bar Ihe current state of the acquisition system and system messages are displayed on the right side of the
14. 01 999343 00 B 1207 NMR Spectroscopy User Guide 103 Chapter 7 Displaying FIDs and Spectra Figure 18 Interactive FID Display The normal spectrum display enables interactive manipulation of a single 1D spectrum A spectrum is displayed by clicking the 1D Spectrum graphics control button y or by transforming a data set A spectrum displays in the graphics window similar to Figure 19 Figure 19 Interactive Spectrum Display 7 2 Display Tools VnmrJ provides interactive tools for creating highly individualized displays of NMR data Interactive Display Tools page 104 Display Parameters page 105 Controlling Cursors and Vertical Scale page 106 Display Limits page 107 Interactive Display Tools These tools are described below Mouse buttons The mouse buttons correspond to the display parameters shown on the lower right part of the graphics window The display parameter change as different graphics control functions are selected Typically the left button controls the left cursor position the middle button controls vertical scaling and the right button controls the right cursor or delta between the two cursors Graphics control The graphics control bar next to the graphics canvas provides buttons graphics control buttons for cursors zooming scales grab amp move threshold phasing and refresh Different functions appear for FID or spectrum display 104 NMR Spectroscopy User Guide 01 999343 00 B
15. Acquire and process data post acquisition using current weighting functions and values go Acquire and process data post acquisition using the current settings including active wbs wnt wcxp and werr func tions an Abort data acquisition for the current sample Sample handlers systems remove the sample insert the next queued sample in the magnet and start data acquisition The Process menu selections are Menu Items Process and Display 1D Full Process Drift Correct Spectrum Automatically Set Integrals Baseline Correct Set Spectral Width between Cursors Set Transmitter at Cursor NMR Spectroscopy User Guide Descriptions Process and display the 1D data Process and display the 1D data using the processing and display parameters and setting set in the Process tab panels Apply drift correction along both axes of a 2D data set Apply baseline correction Mark new spectral width on the graphics screen using the left and right cursors then select this option to set the new spectral width Mark new transmitter location on the graphics screen using the cursor then select this option to set the transmitter 01 999343 00 B 1207 16 2 Main Menu Bar Menu Items Descriptions Add and Subtract 1D Results are shown displayed in experiment 5 Data Sub menu items Clear Buffer and Add Current Spectrum Clears buffer experiment 5 or creates experiment 5 and places current spectrum in e
16. Correcting Systematic Gradient Errors 1 Set the display threshold parameters to select a few strong well resolved signals known to arise from single species i e the signals are not composites of overlapping signals from species with different diffusion coefficients Click Recall Original NMR Data Check the Calibration Flag checkbox The analysis uses the shapes of the decay curves in the first analysis to correct for systematic errors Set calibflag back to n to stop using the internal gradient calibration Click Calculate full DOSY Spectrum with dialog or type undosy calibflag y dosy If the initial DOSY run was used with a dialog prune argument the same increments must be deleted in the second run using Calculate full DOSY with dialog undosy calibflag y dosy prune and specifying the same increment number s Extracting Spectra Extract spectra of the mixture components separated along the diffusion axis as follows 184 NMR Spectroscopy User Guide 01 999343 00 B 1207 10 9 Processing 2D DOSY Experiments 1 Select the region of interest using the two cursors in the interactive 2D display dconi mode 2 Click on Proj projection 3 Click on Hproj sum horizontal projection 4 Plot using the Plot menu Displaying Integral Projection Displays the integral projection of a DOSY data set onto the diffusion axis as follows 1 Copy the data to a second experiment 2 Jointhe experiment with
17. Drag a protocol experiment into the graphics canvas to load the experiment DragaFID from NMR data to retrieve the FID The process macro can also be invoked so that the FID is transformed Double click a workspace to join that workspace Dragging and dropping a workspace into the graphics area also joins the workspace j exp Double click a parameter set to load that set in the current workspace or drag and drop a parameter set Double click a shim set to load the shims Dragging and dropping a shim set to the current shim buttons also loads the shims into acquisition Drag either data or shims and drop them in the trash can in the lower left portion of the hardware bar to move the item to the trash can Retrieve an object from the trash can by double clicking on the trash can selecting it and then clicking the Restore items button Editing File Names from the Locator A new file added to the locator from within VnmrJ appears in its appropriate spot in the Locator and it appears in green at the top of the locator window If one of the columns in the Locator is filename click on the green file name to change it Change the file name press Return or click on another line to remove the old name from the Locator and add the new one The Locator redisplays to show the new name Locator Statements Varian supplies a number of Locator statements with VnmrJ Add to or edit these statements in the following ways Sav
18. Select a system level probe and active for user Opens window to edit level probe probe file X Open the Probe window t Edit Probe Place a check in this box Probe name as shown Parameters Zero leel user iv Probe name entry field Calibration availability Em level Click here to select Se aaa a calibration option is grayed out as shown if no probe is selected Qose L Figure 3 Calibrating a Probe NMR Spectroscopy User Guide 01 999343 00 B 1207 2 5 Tuning Probes on Systems with ProTune 2 5 Tuning Probes on Systems with ProTune This section applies to Varian NMR Systems spectrometers equipped with ProTune Configuring for Operation with Automated Sample Handlers Applies to systems equipped with ProTune The system must be properly configured and ProTune calibrated Refer to the VnmrJ Installation and System Administration manual for configuring the software and calibrating ProTune Data acquisition with an automated sample handler uses the Walkup interface 1 Login or switch operators to the walkup account administrator and start VnmrJ 2 Click on the Tools button on the main menu bar 3 Select Probe Tuning 4 Select Auto tune setup from the pop out menu 5 Specify when ProTune automatically tunes the probe Tune when changing Placing a check in the box next to each change in vise Dm condition results in automatically tuning the pro
19. The new bearing pressure can be read from the display on the automated MAS speed controller Starting the Rotor Manually Start a rotor manually and then put it in regulation as follows 1 Set the Target Hz on the Spin Temp page 2 Set the knobs for the drive and bearing pressure valves on the controller counter clockwise 01 999343 00 B 1207 NMR Spectroscopy User Guide 273 Chapter 18 Solids Experiments Press the Auto Manual button on the controller to put it in manual mode Obtain stable spinning near the desired speed using the knobs Press the Auto Manual button again to put the rotor in regulation Reset the pressure valves counterclockwise D3 49v DA m C09 Stop the rotor as follows Press Stop button on the Spin Temp page It is not possible to return to manual mode while the rotor is spinning The Start Spin and Stop Spin buttons on the MAS automated speed controller have the same function as the Start and Stop buttons on the MAS Spin Temp page Setting the Temperature Starting Temperature Regulation page 274 Stopping Temperature Regulation page 275 Recovering from a VT Fault page 276 The temperature of the rotor is controlled through the VT stack that for wide bore magnets sits in the upper barrel of the magnet and must be installed before starting solids VT operations The VT stack inserts into the liquids upper barrel and mates to the top of the probe for wide bore magnets The VT stack sits
20. The zfs zero frequency suppression option is selected if both bandwidth ssfilter and polynomial ssorder are set to a value The Ifs low frequency suppression option is selected if bandwidth is set to a value and polynomial is not checked The zfs and Ifs options are both turned off if bandwidth is blank Left Shift FID Left Shift Frequency Phase Rotation Use the Linear Prediction panel to adjust the Left Shift FID Left Shift Frequency and the Phase Rotation Check Left Shift FID to left shift the interferogram by the entered number of complex or hypercomplex points before weighting and Fourier transformation are performed The value must be between 0 and number of increments minus 1 Enter a negative value for Left Shift Frequency to shift the peaks upfield to the right or a positive value to shift the peaks downfield to the left The Left Shift Frequency values operate only on complex np FID data t dimension in a 2D experiment To phase rotate the interferogram check the appropriate box and enter a value in degrees zero order phase rotation This causes zero order phase rotation before weighting and Fourier transformation are performed 2D Processing of 3D Data Acquisition and full processing of 3D data requires the parameters ni2 and sw2 d3 is the delay increment in the ni2 dimension 2D processing of slices of the 3D data matrix is accomplished using the following commands ft2d ni2 transforms
21. Add Subtract Tools Menu for Add and Subtract page 326 Interactive Add Subtract Toolbar page 326 Menu for Add and Subtract Access the Add Subtract experiments from the Main Menu as follows 1 Click on Process on the Main Menu 2 Select Add and Subtract 1D Data The following sub menu items are presented Clear Buffer and Add Current Spectrum Clears buffer experiment 5 or creates experiment 5 and places current spectrum in experiment 5 Add Second Spectrum into Buffer Adds current spectrum algebraically to data in experiment 5 Interactive Add Subtract Toolbar The Interactive Add Subtract toolbar has the following buttons the labels on some buttons change depending on the current mode NMR Spectroscopy User Guide 01 999343 00 B 1207 14 4 Addition and Subtraction of Data Each button name tool tip and function is listed in Table 32 Table 32 Add Subtract Toolbar Buttons Button Name Description Box Box is shown when the display is in the cursor mode Click to change to the box mode with two cursors Cursor Cursor is shown when the display is in the box mode Click to change to the cursor mode U E E Select Selects the current addsub or result mode Text in the field next to active matches the color of the spectrum Arrow colors Green current mode spectrum is selected Yellow addsub mode spectrum is selected Blue result mode spectrum is selected a Expand The third but
22. GR PEN P hyw Figure 58 DOSY Gradient Compensated Stimulated Echo HMQC Phase Sensitive Table 22 Dgcstehmqc_ps Parameters Parameter Description del the actual diffusion delay gtl total diffusion encoding pulse width gzlvll diffusion encoding pulse strength gstab gradient stabilization delay pwx 90 deg X pulse pwxlvl power level for pwx jixh one bond H X coupling constant c180 flag to make the 180 deg X pulse a composite pulse satmode flag for optional solvent presaturation ynn does presat during satdly yyn does presat during satdly and the diffusion delay satdly presaturation delay before the sequence part of d1 satpwr saturation power level satfrq saturation frequency alt grd alternate gradient sign s for odd scans lkgate_flg flag to gate the lock sampling off during the diffusion sequence sspul flag for a GRD 90 GRD homospoil block gzlvlhs gradient level for sspul hsgt gradient duration for sspul phase 1 2 for States Haberkorn acquisition The diffusion gradients gt 1 must be synchronized with sample spinning when using a nano probe gt121 0 srate trunc gtl srate 40 5 where srate is the sample spinning speed Run the phase sensitive 2D HSQC spectra in separate experiments and process the data with the dosy3Dps macro 01 999343 00 B 1207 NMR Spectroscopy User Guide 1 93 Chapter 10 DOSY Experiments Dbppste ghsqcse Bipolar Pulse Pair Stimulated Echo Gradient HSQC Sensitivity Enhanc
23. Mode Rotate rotates the image Zoom zooms in out Translate moves the image Select selects the atoms Measure measures distance angle or dihedral Refer to Measuring a Molecule page 129 Save Image Saves the molecule image as BMP JPEG PPM PNG or PDF The image is saved in the directory username vnmrsys mollib icons with the name entered in the field Refer to Saving a Molecule Image page 129 Measuring a Molecule 1 Select the measure mode distance angle dihedral 2 Click on the appropriate atoms to create the measurement distance click two atoms angle click three atoms dihedral click four atoms 3 Display the measurement by selecting the Measurement display option Saving a Molecule Image 1 Select the file format for the image BMP JPG PPM PNG or PDF 2 Enter a name for the image and add a file extension that corresponds to the file format chosen in step 1 3 Press Enter The file is saved in the directory username vnmrsys mollib icons Jmol Display Options Change the foreground color of the molecule window enter the following command on the VnmrJ command line vnmrjcemd mol foreground color where coloris a color name or a hex value The foreground color by default is set to the most visible color according to the background color Change the font of the labels on 3D molecule graphics use the Edit Display Options window an
24. Panel provides a reduced set of the full 2D process display and plot parameters available on the parameter pages of the process tab Control Basic Process Controls F1 check box F2 check box Weighting Linear Prediction Processing Buttons Description or Function Check box to make F1 FT Data Size dropdown menu active Select the size of the F1 data set F1 Acquired points are shown to the right of the menu Check box to make F2 FT Data Size dropdown menu active Select the size of the F2 data set F2 Acquired points are shown to the right of the menu Select a weighting function from the dropdown menu Click on either or both the Auto LP F1 and Auto LP F2 buttons to enable or disable linear prediction during data in process Placing or removing a check mark from a box is the same as clicking on a button Data is processed as stated on the button using the processing parameters in the Basic Processing frame and on the parameter pages FT 1D 1st Increment FT ID All Transform F2 Full 2D Transform More Processing Parameter Pages button Basic Display Display 2D 2D Vertical Panel 9 x Basic Processing FT Data Size Acq Pts wiri ik 256 eF2 ik w 1024 Weighting mee E Linear Prediction OFI Awtelf k L F2 utei Fi FT 1D ist increment Fut 2D Transform More Processing Parameter Pages J Basic Display Dsplay 20 Display Trace Prowchong Ful
25. Sample Tubes Buy the best quality NMR sample tubes and clean the outside of each tube with a solvent such as isopropyl alcohol followed by a careful wiping with a wiper tissue before placing the tube in the probe Sample Changes and Probe Tuning Probe tuning is required when there is a significant change in the polarity of the solvent Changing from a non polar organic solvent to a more polar organic solvent or aqueous solvent generally requires retuning the probe Changes in the ionic strength of the solution e g low salt to high salt also require retuning of the probe 2 3 Ejecting and Inserting the Sample The spectrometer is equipped with hardware and software to provide computer control of sample ejection insertion spinning locking and shimming This section covers computer controlled sample ejection and insertion Insert Sample Find 20 Notebook Page _ Gradient Shim 3 Solvent cpcis zl Spin jatfo Hz amp SPin Temp comment Temp a NOMS STANDARD 1H OBSERVE Lock Status Off Level Shim method z122 Ejecting a Sample Always eject first even if no sample is in the magnet to start airflow to carry the sample The eject air is turned on and under computer control the sample if present rises back to the top of the upper barrel Remove the sample and replace it with another sample Using the Start Tab The Insert and Eject buttons are on the St
26. sssseeeeeeneen 317 Add Spectra and Display Result eese 328 Display of Regression Fittings sesionin isetende nre tnn ntn t E E n 334 Pbox Make WayefOotEm 2 ree tete teste er rE ET E 342 Shaped Pulse Simulations Reference Spectrum see 342 Pbox Update Paramelers uoo pe Eier rete fec d eed 343 Pulsetool Spin Simulation Window esee 355 biu x 364 Graphics Canvas ioco t HP RN PER HE ORO EE ar caceps cp HERR PUREEESEE 384 Miewport settings WIDdOW ireeeter otro teet Cree eae na obe eek to gavencoteyseveousesees 389 Setting Display Colors recte rete emet fo septi here ei pre NES 390 Viewport Tab and Controls er e teet e hr o eR eer intres 390 Setting Spectra Colors by Viewport sssssessseeeeeeeeeenren nemen 393 Contour Controls e ie tte ote eter PEE ndeubes 394 Text Panel Controls and Text Editor sese 395 Creating an Inset Frame o ert ter rete SEE cH ES ECHTE TE ERUIT C TRUE SE 398 Applications Directories Interface for Users 405 Setting Display Clos te e REO Lee testeretin ie ite Certe et teep eiu eh 406 hA I V M 407 Locator Menus and Controls cseteris tente tone tet En SEs rS Tesei isin 408 Generic Locator Statement cie rr EP PE ERR perire E Era 412 Approximate Shape of Axial Gradients sese 421 Theoretica
27. 01 999343 00 B 1207 NMR Spectroscopy User Guide 159 Chapter 10 DOSY Experiments 10 2 160 A a0 x exp D x C0 Cl x grad pli C2x grad pli x grad p1i a2 x exp al x D x C0 Cl x grad pli C2x grad plix grad p1i The diffusion coefficient D is available from the separate reference integral region The constants CO C1 and C2 are defined in Equation 2 The fitting parameters are a0 al and a2 In order to perform the non linear least squares analysis of Equation 3 the pge results macro is supplied with two arguments e g pge results 1 3 The first argument is the region on which to perform the analysis just as for the single component analysis case and the second argument is the integral region used to get the value of D The fitting parameter a0 corresponds to the time zero integral amplitude of the reference component a2 corresponds to the time zero amplitude of the other component al corresponds to the ratio of the two diffusion coefficients DOSY Experiments 2D DOSY Experiments Dbppste DOSY Bipolar Pulse Pair Stimulated Echo Experiment page 166 DgcsteSL DOSY Gradient Compensated Stimulated Echo with Spin Lock page 167 Oneshot page 168 2D DOSY Experiments for Biological Samples DgcsteSL dpfgse DOSY Gradient Compensated Stimulated Echo with Spin Lock page 169 Dbppste wg DOSY Bipolar Pulse Pair Stimulated Echo page 170 Dbppsteinept DOSY Bipolar Pulse Pair Stimu
28. 189 10 11 Processing Absolute Value 3D DOSY data see 190 10 12 Phase Sensitive 3D DONS Y siirros raehri e ret ttr fei Pee ebrei eee 192 Setting Up Phase Sensitive 3D DOSY Experiments eene 192 Dgcstehmqc ps DOSY Gradient Compensated Stimulated Echo HMQC 193 Dbppste ghsqcse Bipolar Pulse Pair Stimulated Echo Gradient HSQC Sensitivity Enhanced uoce tree cet eet unire te eter e rece tria eer i 194 10 13 Processing Phase Sensitive 3D DOSY Data eee 195 Pie Processing M E 195 Processme Data from 3D DOSY Experiment 22er 196 10 14 IDOS Y Inclusive DOSY J mespresa ets cet ee erben nie eoi es ne eene es 196 Deosysdosy COSI DOSY iriri tereti ete tue tea rette terrere ent 197 Dhom2djidosy Homonuclear 2D J resolved IDOSY 198 Dghmacidosy Gradient HMQC IDOSY eese 199 10 15 Processing FDOSY data erro a OE RR aa oem 201 10 16 Sample FIDs to Practice DOSY Processing eee 201 ossi son EE E A M 201 NMR Spectroscopy User Guide 01 999343 00 B 1207 Table of Contents Ibi eroi Pur Dr 202 Deocste5E dpi Dl Luisa oth oo nmreteo memet detti 203 Dbppsteinept fid 1 eie aee er tee roto ertet terrere etr tette 203 PBC ECOG c 205 Desstehingulid ues EE reet tse rey 207 5129 T1H Dehimuqcidosy Hd 1 ederet ertt ERR p reies 208 ID IT Refe
29. 2D F1 and Windowed PMLG N Wpmlg2d 372 NMR Spectroscopy User Guide 01 999343 00 B 1207 Acquisition Menu 16 2 Main Menu Bar The Acquisition menu selections are Menu Items Descriptions Parameter arrays Array definition Open Array Parameter window Array Parameter Description Sze Order Onom region ni Number of increments in Ist indir 128 0 On Arrayed j hase Ss STE ee cav un parameter fields Array Size 256 Total Time 0 0 1 UnArray New Array E Active Param phase Current Value E o o o o Status region ue Position value Array limits a 1 7 Array Size 2 m 2 2 region First Value i Increment 1 0 Last Value 2 hne Style Linear Randomize Array elements window Window controls close Abandon Array Parameter Window Regions Array definition Arrayed parameter field columns Parm Name enter name of arrayed parameter Description displays text description of array Size displays number of steps or increments in the array Order displays precedence for running the array double click in the field and enter the array order Arrays with sequential numbers create a full matrix array A x Array B and each array can be a different size Arrays with the same order number and the same size create a diagonal array On Off
30. A1ray is used array not used Fields and buttons Array Size field shows size of selected array Total Time field shows estimated time to complete the array UnArray button remove selected parameter from the list of arrayed parameters NewArray button add new row to list of arrayed parameters Status show active parameter during acquisition and parameter s current value Array limits 01 999343 00 B 1207 Array Size field enter the size of the array and press return NMR Spectroscopy User Guide 373 Menu Items Chapter 16 VnmrJ Experimental Interface Descriptions First Value enter the starting value of the array and press return Increment enter the array increment and press return Last Value enter the ending value of the array and press return Inc Style button click and select linear or exponential Randomize button click to create a random array Array elements Change the value of the array element by double clicking on the value of the array element associated with the array position entering a new value and pressing Enter Window buttons Acquire Data Acquire and WFT Acquire and Process Abort Acquisition Process Menu Edit Not active Undo Click to undo click again to restore the change Close Closes the window Abandon Closes the window and makes no changes Acquire data only No post acquisition processing go
31. Introduction to Spin Simulation The software includes an iterative spin simulation program based on the FORTRAN program LAME also known as LAOCOON with magnetic equivalence added LAME calculates the theoretical spectrum for spin 1 2 nuclei given the chemical shifts and the coupling constants Up to eight closely coupled non equivalent spins ABCDEFGH can be handled Equivalent spins can be treated by magnetic equivalence factoring to extend the simulation to systems such as A3B2CD3 The X approximation can be used to handle different types of nuclei Nuclei are treated as different types if there is at least one spare letter in the alphabet between their groups e g ABD and ABX are both systems using the X approximation Frequencies intensities energy levels and transitions can be listed and simulated spectra can be displayed and plotted Parameters can be adjusted by iteration to approach a given experimental spectrum One or several parameters can be kept constant for iterative runs and one or several parameters can be set equal to each other and held equal during the course of the iteration A worked through example is provided in Spin Simulation Step by Step page 311 The menus and dialog windows simplify the procedure A number of specialized commands and parameters are also available Table 29 lists these commands and parameters References for the spin simulation algorithms 01 999343 00 B 1207 NMR Spectroscopy User G
32. Not all pulse sequences have the TPPI method incorporated The acquisition status window displays a count of the current FID and the number of completed transients ct in that FID The current FID number is the total count of completed FIDs to this point including all arrays Since the phase parameter is cycling the most rapidly and since typically phase is an array of two values the current FID number is typically twice the number of the current increment For example when the counter reads FID 54 this means that 27 FIDs of the first type of experiment have been completed 26 of the second type and the system is working on the 27th experiment of the second type 11 3 Weighting This section describes weighting functions for processing 2D experiments 2D Weighting Parameters this page Interactive Weighting page 219 218 NMR Spectroscopy User Guide 01 999343 00 B 1207 2D Weighting Parameters 11 3 Weighting The 2D weighting parameters used for processing the ty domain the interferogram or first indirectly detected dimension ni are set on the Process page in the Process panel and are analogous to weighting parameters for 1D experiments mx Start Acquire Process Transfoi Full Clear Screei TT AutoSelect Weighting Transform F1 only Both F1 amp F2 Weight Parameters F1 F2 FT Data Size Acq Pts panera exponential exponential line broadening v F1 256 v 128 Integration gaussian
33. There is now a series of spectra each consisting of an absorptive and a dispersive part formed as linear combinations of the original real and imaginary parts Complex interferograms then form out of corresponding points along the frequency axis from each of the spectra and transform to produce the final 2D spectrum The real and imaginary part of the interferograms can be formed from any linear combination of the real and imaginary parts of one or more spectral sets after the first Fourier transformation Refer to these coefficients below according to the following scheme RR1 is the coefficient used to multiply the real part first R of spectra in set 1 the 1 before it is added to the real part second R of the interferogram IR2 thus represents the contribution from the imaginary part of spectra in set 2 to the real part of the interferogram and so on Another set of complex interferograms are formed from these two sets of f spectra for some experiments This set of interferograms is 90 out of phase in f to the previous set and can be constructed without any additional coefficients Different experiments require different coefficients Some such as heteronuclear 2D J experiments consist of only one FID and spectral set and hence there will be a total of four coefficients Others including hypercomplex 2D experiments consist of two original data sets and hence a total of eight coefficients Other experiments are possible with thre
34. 1 Choose fn preferably with n gt 2 np and n1 2 Enter ft to transform the raw data as mentioned earlier if there is significant signal left at the end of at it might be necessary to use w t with gf set 3 Display the first increment with ds 1 adjust the phase of the reference signal and use r1 to select the reference signal In earlier versions of f iddle it was necessary to create a parameter phinc to anticipate the changes in the reference signal phase with increasing evolution time The current algorithm automatically adjusts the phase unless the noaph option is selected Deconvolution will set the reference signal phase as a function of t 1 to place the reference signal at frequency rfp1 in 1 Therefore remember to set rf11 and rfp1 before using fiddle2D or the 1 frequencies might unexpectedly change 4 Define the reference region with the two cursors and then enter the command fiddle2D writefid file or fiddle2Dd if a 2D difference spectrum is required as with corrected HMBC The writefid option is essential because iddle2D alone does not store the corrected time domain data If phase sensitive gradient enhanced 2D data is to be processed alternate FIDs will have opposite phase modulations i e the experimental array will alternate N type and P type pathways in such a case use the alternate option The corrected 2D FID data can be read into an experiment and processed as normal after
35. 12C bound proton magnetization to relax back to equilibrium If t is adjusted so that the 12C bound proton magnetization are approximately at a null then when the remainder of the pulse sequence the normal HMQC sequence is executed cancellation of the 12c bound proton magnetization is enhanced since those proton magnetization had very little magnetization at the start of the HMQC sequence Obviously not all proton magnetization will have the same relaxation time so the choice of t must be a compromise generally NMR Spectroscopy User Guide 01 999343 00 B 1207 12 8 Experiment Manual Setup 90 180 90 X 90 180 x oph x x t 1h D D t D 12 to D 180 x 90 x 90 X BIRD Pulse Figure 69 HMQC with BIRD Pulse Nulling Effects unless only one proton is involved the additional suppression from the BIRD nulling will be a factor of two to five For systems that exhibit a negative NOE such as macromolecules cross relaxation between the inverted proton magnetization on 12C and the noninverted proton magnetization on 3C will decrease the intensity of the desired proton signal The extent of this decrease can vary between 0 and 100 For this reason omission of the BIRD part of the sequence is advised for macromolecules BIRD pulse nulling is also not possible when long range indirect detection experiments Heteronuclear Multiple Bond Coherence or HMBC are performed In this c
36. 146 experiment library 145 exponential curves 151 FID 104 file of line assignments for iteration 315 grid lines 234 integral reset points 126 integrals 121 388 line assignments file 315 modes 106 next plane 244 numerical integral amplitudes 126 peaks on top of spectrum 239 polynomial curves 151 previous plane 244 projection of data on plane 246 second cursor 106 238 shaped rf pulses 355 simulated spectrum 314 simulation parameter file 315 spectra with whitewashing 234 spectrum 97 104 01 999343 00 B 1207 Index spectrum from array 148 Dpfgdste 165 stacked 3D spectra 234 Parameters 180 subset of 3D planes 244 dpir command 126 theoretical spectrum 321 dpirn command 126 trace at cursor position 238 dplane macro 244 246 traces 239 dprofile macro 345 353 Display button 240 dproj macro 246 Display color map 109 236 387 dpwr parameter 87 display command 125 Dqcosy 370 Display contour map 109 236 387 dres parameter 87 349 Display image map 109 236 387 dres2 parameter 87 display limits 234 dres3 parameter 87 Display Lists of Integrals 123 124 dres4 parameter 87 display parameters moving 367 drift correction 246 display region tools and controls 114 drift correction both axes of a 2D data set 374 Display scale spectrum 108 386 drift correction calculation 222 Display Shimmap button 69 dry nitrogen gas 416 417 Display stacked spectra 109 236 387 ds command
37. 210 reference position 112 referencing solids 282 referencing clearing in 2D spectra 235 refofs parameter 350 refrigerating device 417 region command 126 region selective 3D processing 243 regionx results file 159 regression 332 376 regression analysis 332 analyze out file 335 commands 339 curve types supported 336 regression inp file 338 window 332 regression inp file 332 333 334 335 337 338 Relaxation Measurements 370 relaxation times measurement 151 Remove Hadamard 230 removing systematic errors 185 reps parameter 350 Reset button 241 reset integral to zero 125 reset parameters 246 reset pisema 303 resetf3 macro 246 resolution enhancement 95 219 220 resolution enhancement function 93 94 restore spin system to before last iterative run 316 Return to previous tool menu 107 385 review papers DOSY 212 RF calibration flag for Hadamard waveforms in ni 232 rfl2 parameter 243 rfp2 parameter 243 right command 234 right phase 96 rinput 339 Roesy 370 ROESY phasing 233 Roesyld 370 rof2 parameter 82 85 room temperature stability 417 room temperature shim coil currents 50 room temperature shims adjustment 61 rotate command 235 rotate homonuclear 2D J data 235 Rotational Echo Double Resonance REDOR CP with XY8 Y and X inversion 304 01 999343 00 B 1207 Index one pulse with XY8 Y and X inversion 304 with constant linear or tangent ramped prep XY8 decoupling 304
38. 417 01 999343 00 B 1207 Index spinner control 432 spinning sidebands 427 spinning sidebands removing 55 spins command 314 315 316 spins inpar file 316 spins list file 316 317 spins outdata file 317 spins stat file 317 spline fitting 222 spsub command 330 sqcosin macro 94 sqsinebell macro 94 squared sinebell function 93 Ssechold 305 372 ssfilter 100 ssfilter parameter 226 sslsfrq 100 sslsfrq parameter 100 ssntaps 100 ssorder parameter 100 226 st parameter 351 Stack Spectrum 119 standard calibration experiments menu 378 standard coil groupings 432 standard two pulse sequence 85 86 Stars 376 starting criterion for shimming 430 starting Plot Designer 133 starting point for a deconvolution 319 States Haberkorn and Ruben 216 225 status concept 36 status 266 stdpar directory 429 stdshm macro 433 steady state transients 85 steps parameter 349 Stepsize for Hadamard waveforms in ni 232 stepsize parameter 350 sth parameter 315 316 Stop acquisition 379 store line assignments 315 storing Locator items 399 Styles and Themes 405 Styles and Themes for viewports 390 Styles and Themes window 379 su command 37 417 sub button 327 sub command 329 subexperiments 146 subtract FID from add subtract experiment 329 sucyc parameter 350 SUN file format 141 superhypercomplex data acquisition 243 Svs parameter 315 sw parameter 351
39. 430 Lorentzian lines 317 Lorentzian lineshapes 94 321 low gamma nucleus and acoustic ringing 279 low order shims 55 low temperature VT calibration 418 Ip parameter 96 97 111 lp1 parameter 232 233 lp2 parameter 243 Isfid parameter 98 329 Isfid2 parameter 243 Isfrq parameter 100 244 Isfrq1 parameter 244 Isfrq2 parameter 244 lvl parameter 122 125 Lyl Tit button integrals 122 M M shimming criterion 430 macromolecules 253 magnetic equivalence factoring 309 magnetization recovery to equilibrium 84 magnitude mode 2D experiment 225 magnitude mode transform 225 make3dcoef macro 245 makedosyparams 165 makeslice 165 making a new protocol 376 a workspace 365 manual locking 47 Manual Tuning software interface 32 mapping the shims 64 Marion and Wuthrich 216 Mark button 241 mark button 316 mark command 322 mark1d out file 316 319 322 MAS Speed Controller 42 MAS spin rate 272 MAS Spin Temp page probe file contents 272 MAS Spinner panel 42 match experimental and calculated lines 314 NMR Spectroscopy User Guide 443 Index maximum intensity 234 maxincr parameter 349 measured line frequencies 315 medium shimming criterion 430 menu bar 365 methanol for VT calibration 418 method parameter 429 MIFF file format 140 min button 327 mixing patterns creation 341 MLEV 16 decoupling 87 Molecular Structures 379 motion artifacts 64 mouse button labels 104 Mqm
40. Every Experiment Shims before the start of data acquisition for each new experiment Every FID Shims before the start of data acquisition for each FID Shim on Lock options menu next to Shim method zi1z2 Low non spins Allz s Hi res Z s Fine z1z2 Fine z1 z3 Autoshim is controlled by the selection made from the Shim method menu This is a complete background Autoshim method that provides no interaction with the operator The type of automatic shimming to be done during routine sample changes depends on the level of homogeneity required on any particular sample the change in sample height and the maximum time desired for shimming 7172 shimming average homogeneity needs with long samples of identical height e all z s variable sample heights More time is required The method shims first Z1 Z2 and ZA then Z1 Z2 and Z3 and finally Z1 and Z2 3 8 Selecting Shims to Optimize 52 Which Shims to Use on a Routine Basis page 52 Shimming Different Sample Geometries page 53 Which Shims to Use on a Routine Basis The following suggestions assist in routine shimming especially on shim systems with a larger number of shim channels Establish and maintain lineshape Use Z to Z5 possibly Z6 X Y ZX ZY and possibly Z2X and Z2Y The effects of Z7 and Z8 and realistically Z6 are too small to see with the lineshape sample NMR Spectroscopy User Guide 01 999343 00 B 1207 3 9
41. Figure 11 Shimmap Plot of Z1 Through Z6 How Automated Shimming Works The shims must be mapped before gradient automated shimming is used see Mapping the Shims page 65 for details When gradient shimming is run from the Gradient Shim page the curve fit plot is displayed for each iteration The plot shows the raw data as 1 and the curve fit as 2 see Figure 12 Shim adjustments for each iteration are also displayed in the Text Output window see Figure 13 and have converged when the rms error number is less than 1 0 Gradient shimming continues until convergence or until a maximum of 5 iterations are reached T 30000 20000 T T T T T 10000 o 10000 20000 30000 Fit Frequency vs Field Figure 12 Curve Fit Plot If a shim goes out of range the shim is set to maximum and shimming continues with the remaining shims If convergence is then reached shimming is tried once more with all Z shims and continues unless a shim goes out of range again NMR Spectroscopy User Guide 01 999343 00 B 1207 4 6 Shimmap Display Loading and Sharing mapname 5mm Triax 01 shimset 4 gzsize 6 rms err 1 892 Shim Offset Old New Diff Error z1 800 9405 9269 136 48 z2 800 3118 3104 14 13 z3 3200 4356 4321 35 37 z4 3200 4049 4885 836 104 z5 3200 13443 14537 1094 322 z6 3200 15619 12568 23051 467 Z7 3200 0 0 0 0 z8 3200 0 0 0 0 Figure 13 Display of Shim Adjustments fo
42. Interactions of Natural Organic Matter Using Diffusion Ordered Spectroscopy Magnetic Resonance in Chemistry 2002 40 S72 S82 Liu M Tang H Nicholson J K Lindon J C Use of IH NMR Determined Diffusion Coefficients to Characterize Lipoprotein Fractions in Human Blood Plasma Magnetic Resonance in Chemistry 2002 40 S83 S88 Danielsson J Jarvet J Damberg P Gr slund A Translational Diffusion Measured by PFG NMR on Full Length and Fragments of the Alzheimer AB 1 40 Peptide Determination of Hydrodynamic Radii of Random Coil Peptides of Varying Length Magnetic Resonance in Chemistry 2002 40 589 897 Derrick T S Lucas L H Dimicoli J L Larive C K 19F Diffusion NMR analysis of Enzime Inhibitor Binding Magnetic Resonance in Chemistry 2002 40 S98 S105 Camoron K S Fielding L NMR Diffusion Coefficient Study of Steroid Cyclodextrin Inclusion Complexes Magnetic Resonance in Chemistry 2002 40 S106 S109 Monteiro C Maechling C du Penhoat C V Monitoring the Non Specific Interactions of Catechin through Diffusion Measurements Based on Pulsed Field Gradients Magnetic Resonance in Chemistry 2002 40 S110 S114 Regan D G Chapman B E Kuchel P W PGSE NMR Diffusion Study of the Self Association of N Methylacetamide in Carbon Tetrachloride Magnetic Resonance in Chemistry 2002 40 S115 S121 Cabrita E J Berger S HR DOSY as a New Tool for th
43. Join experiment 5 j exp5 and use the normal spectral display e g ds and plotting commands to examine the results Add Subtract Related Commands and Parameters The add subtract experiment related commands are listed in Table 33 and parameters are listed in Table 34 Table 33 Add Subtract Related Commands Commands Description add Add current FID to add subtract experiment addi Start interactive add subtract mode clradd Clear add subtract experiment jexpl jexp9999 Join existing experiment select Select a spectrum or 2D plane without displaying it setvalue Set value of a parameter in a tree spadd Add current spectrum to add subtract experiment spmin Take minimum of two spectra in add subtract experiment spsub Subtract current spectrum from add subtract experiment sub Subtract current FID from add subtract experiment add lt multiplier lt new gt gt add new add trace index select next prev selection index select f1f3 f2f3 fif2 proj next prev plane i setvalue parameter value index tree spadd lt multiplier lt shift gt gt spadd new spadd trace index spsub lt multiplier lt shift gt gt spsub new spsub trace index sub lt multiplier lt new gt gt sub new sub trace index Table 34 Add Subtract Related Parameters Parameters Description arraydim number Dimension of experiment 01 999343 00 B 1207 NMR
44. Mixture at 60 C 183 energy level table 314 dosy prune 186 EPS file format 140 dosy d1 d2 186 error handling control 45 dosy_grad_calib 165 ethylene glycol for VT calibration 418 dosy2d 165 excellent shimming criterion 430 dosy3d 165 exchanger coil 44 dosy3Dps 165 Ex pand button 238 327 Dosy inept DOSY 2D 371 expanded display 238 dot command 150 experiment downfield peak shift 226 library 145 downsampling 100 stop acquisition 89 editing text inside a text frame 396 efficient mode decoupling 87 ejecting a sample 29 elements 01 999343 00 B 1207 NMR Spectroscopy User Guide 439 Index experiment 5 exp5 used with add and subtract 326 Experiment Panel solids protocols 266 experimental frequency index of a transition 315 experiments 2D DOSY setting up 163 accessing 380 acquiring 81 Dbppste 166 175 DgcsteSL 167 176 178 loading 39 oneshot DOSY 168 run unlocked 49 Experiments Menu 370 expfit 339 expfit command 335 expl 339 expl command 151 expl out file 335 explib and viewports 339 explib command 145 exponential curves analysis 151 exponential signal change 152 exponential weighting 93 95 220 extract 2D planes from 3D data set 244 246 F F1 Axial Displacement 260 F1 phase detection 260 F1 F2 and F3 dimensions 243 flcoef parameter 245 fy axis 216 f2coef parameter 245 FAD technique 260 FAX file format 140 fbc 165 fbc macro 184
45. Mow HT pars 20165 Display to exp Peris structures Peak aR Set list into parameters Import curexp htfrg1 il thresholds are adjusted Save HT Frequencies automatically and a line list is created Close The line list is set into the parameter ht rq1 Only frequencies separated by the minimum line width are used Places the cursor on the nearest line Adds the current cursor position to the line list The cursor must be more than the minimum line width from an existing frequency in the line list Removes the line nearest the cursor position from the line list Displays the frequency list If a 1D spectrum is displayed show the frequencies using dpf in units set by the axis parameter Clears all frequencies from the frequency list Save HT Frequencies 230 NMR Spectroscopy User Guide 01 999343 00 B 1207 Line List Hz ppm menu 11 7 Hadamard Spectroscopy Saves the current frequency list as a Hadamard line list for the current nucleus tn It saves the frequency list band width current nucleus spectral width and frequency offset in a persistence file The frequencies and other parameters are loaded from the persistence file when loading a Hadamard experiment Displayed in the editable text entry window under Line List The first column contains the Hadamard frequency list parameter ht frq1 The second column of numbers if present contains the bandwidth in H
46. NMR probe A coil or sum of coils whose field is aligned along the axis of the magnet is called a Z axial shim gradient Z1 Z2 Z3 etc Coils whose fields are aligned along the other two orthogonal axes are called X and Y radial shim gradients X1 XY X2Y2 Y1 YZ etc The field offset coil ZO zee zero alters the total magnetic field Each shim gradient is controlled by its own parameter for example the X1 shim gradient is controlled by a parameter named x1 Depending on the value of the shimset parameter shim values range from 2047 to 2047 or from 32767 to 32767 with a value of zero producing no current Automated Shimming on the Lock Refer to section B 3 Autoshim Information on page 428 for more information about Autoshim 01 999343 00 B 1207 NMR Spectroscopy User Guide 51 Chapter 3 Experiment Setup Like locking shimming can be done by using the controls on the Shim page Automated shimming is often preferred however It can be set up from the Standard page of the Start tab Insert Find zo v NE Gradient Shim Mapname Notebook Page Solvent CDCIS zl Spin at o HR Comment Temp a e STANDARD 1H OBSERVE When Notused Lock Status Off Level Wer Shim method z1z2 Shim on Lock options menu next to When Not used disables automatic shimming Every sample Shims before the start of data acquisition for each new sample
47. S G j S O exp D Y F G A exp 1YSG VA Representing convection by a crude model of equal and opposite flows each of uniform velocity leads to cancellation if the imaginary part above and the result is a cosine modulation S G j S 0 exp D Y E G A cos 1y G 4 VA Observing such an oscillatory behavior of the signal decay see also Figure 51 is a clear indication of convention Assuming convection is constant in time and strictly laminar the effect of convection on diffusion spectra can be efficiently eliminated Figure 43 displays the necessary modifications orange box on a gradient stimulated echo pulse sequence halfway through the diffusion delay the magnetization is moved back to the transverse plane by a 90 pulse and gets refocused by the first green gradient pulse The second green gradient identical in sign duration and length to the previous one phase labels the spins in the opposite direction The magnetization is then converted back to axial for the second half of the diffusion delay The ordered nature of convection assures that the phase evolution due to convection is opposite during the two halves of the diffusion delay and therefore compensate each other while diffusion being a random process does not get affected In order to detect only desired coherences homospoil gradient pulses shown in red are used in both halves of the diffusion delay del Figure 43 Modification of a Dgset SL Addin
48. Select Analyze 3 Select Regression The regression window is displayed The function of the buttons are as follows Button and Button Group Function Display x axis buttons x linear Display output with a linear x axis x square Display output with a quadratic x axis x log Display output with a logarithmic X axis eae close Display y axis buttons y linear Display output with a linear y axis y square Display output with a quadratic y axis y log Display output with a logarithmic y axis Regression fit buttons linear Perform a linear regression analysis quadratic Perform a quadratic regression analysis cubic Perform a cubic regression analysis exponential Perform an exponential regression analysis 332 NMR Spectroscopy User Guide 01 999343 00 B 1207 Button and Button Group 14 5 Regression Analysis Function Output buttons Plot Plot the regression analysis Show fit output Display regression output Create interactive input The program displays a series of prompts requesting input Regression Step by Step Using the Regression Window 1 Click on Create interactive input button The program displays a series of prompts requesting the axis label titles and the data pairs ao cep data entry Enter an X and Y pair separated by a space Enter the next X and Y pair Finish the data set by pressing the Enter key Respond to the prompt and press y to enter another data set o
49. Select an experiment Load the Dgestecosy fid into the current experiment Click on the Process tab Select the DOSY Process panel Click on the Process 2D button Click on the Retrieve peak assignment from FID file button The signal regions for this file were saved with the FID file Place a check in the box to the left of Box Remove any checks in the boxes to the left of Cross Number and Diff Cornst Click on the Redisplay 2D Spectrum button Click on the Process 3D DOSY Spectrum button The cosy spectrum is displayed with the cross peaks labelled with the diffusion coefficient and error bar The crosspeaks of interest are 4 1 4 8 1 3 5 O methylidene mio inosytol 3 6 3 9 methyl alpha D glucopyranosid 2 8 3 1 sucrose the 3 lines between 3 2 and 3 6 D 10 10 m2 sec are overlapping diagonal peaks Rejoin the DOSY experiment Remove any checks in the boxes to the left of Cross Box Number and Diff Cornst Click on the Redisplay 2D Spectrum button Display the following projections Inosytol a Enter 4 1 in the field next to Lower Diffusion Limit b Enter 4 8 in the field next to Upper Diffusion Limit c Click on the Show Diffusion Projections within limits button Glucopyranosid a Click on the Show original 2D spectrum button b Enter 3 6 in the field next to Lower Diffusion Limit c Enter 3 9 in the field next to Upper Diffusion Limit d Click on the Show Diffusion Projections within limits
50. T R Switch Delay rd 4 i m Pulse Sequence imum Value of rd 003 More Future Actions Sampling Delay Adjust ad 4 u DDR Time Correction ddrtc us Transmitter Undlanking Prepulse Delay rof 1 Pp us z Figure 83 Receiver Page of the Acquire tab Solids The Receiver page of the Acquire tab contains parameters that affect the receiver gain the dead time and phase correction see Figure 83 The dead time is the time after the pulse or cross polarization before acquisition of the first data point All solids pulse sequences make use of explicit code for acquisition and avoid using rof 2 and alfa The parameter ddrtc controls the digital receiver time correction and is explicitly defined in solids data sets Solids protocols do not automatically set ddrtc The user must set it manually as described below Field name Parameter Values Description Receiver gain Values between 0 and 60 default is 30 Gain can be as low as 0 for Gain gain very strong signals as for proton experiments A gain greater than 30 is usually of no benefit T R Switch rd Values range from 2 0 and 4 0 us for IH or C to many hundreds of Delay rd microseconds for low gamma nuclei with acoustic ringing The application of rd in solids sequences is analogous to that of the rof2 in other sequences Set rd to avoid probe ring down in the first few points of the FID The delay follows the last pulse or the cross polarization and precede
51. The 2D DOSY display is set up in the same experiment where the data processing takes place The synthesized spectrum contains n1 2 traces in the diffusion domain 1 and n2D real data points in the spectral domain 2 n1 is limited to the range 128 1024 Normally n2D of 16k suffices If n2D n1 is too large spectral synthesis and display slows down and or out of disk space exhausted The variable ni is set to n1 2 this setting is required by dconi after displaying a 2D spectrum ni must be back to zero if more data is to be acquired or the sequence is to be displayed dps The Calculate Full DOSY Spectrum button defaults to uses all the experimental spectra and covers the whole diffusion range seen in the experimental peaks Three auditioning processing buttons are provided Calculate full DOSY with dialog Start a dialog to allow one or more spectra to be omitted from the analysis calls dosy prune Calculate partial DOSY spectrum d1 and d2 are numbers causing the diffusion range of the synthesized spectrum to be limited to d1 10719 m sec and d2 107 9 m sec calls dosy d1 d2 NMR Spectroscopy User Guide 01 999343 00 B 1207 10 10 Absolute value 3D DOSY Calculate partial DOSY with Dialog Combine the previously described arguments dosy prune d1 d2 The message Systematic Gz deviations indicates that the random errors in the data are sufficiently small that it may be worthwhile to correct for the sm
52. This is automatically performed by the ga command Automatically process data from an experiment that acquires data sets after all FIDs are collected A 2D experiment is an example of such an experiment Set the wexp for when experiment parameter e g wexp wft2da Take correct action in the event of an acquisition error Set the werr when error parameter e g werr react 5 7 Acquisition Status Window 90 Click on the black triangle next to the status display to open the Acquisition Status window The display contains fields for acquisition status information Fields are displayed based upon the hardware configuration of the system or the parameters set on the system Table 4 lists the possible fields with a description of each field NMR Spectroscopy User Guide 01 999343 00 B 1207 5 7 Acquisition Status Window Table 4 Fields in the Acquisition Status Window Field Description Status Present status of acquisition The values displayed should be self explanatory e g Shimming with two exceptions Active means that the acquisition computer started but the console is not active yet and Inactive means that acqstat cannot communicate with the acquisition computer or that the acquisition computer is not executing Queued Number of experiments queued by multiple go commands Exp Number of the active experiment e g exp1 exp2 exp3 FID Number of the FID being acquired if in an arraye
53. XY8 decoupling with pulses on Y and a refocusing pulse on X with a choice of SPINAL64 or TPPM decoupling during both acquisition and REDOR evolution Used to measure X Y bond distances for inorganic and organic materials redor2tancp is the favored REDOR sequence if homonuclear coupling or quadrupole coupling is present for the X nuclei Rotationally synchronized pi pulses interfere with the refocusing of these interactions into rotational echoes and dephase the magnetization redor2tancp has only one refocusing pulse on X NMR Spectroscopy User Guide 01 999343 00 B 1207 13 8 Quadrupole Experiments 13 8 Quadrupole Experiments 3Q 1Q MQMAS with Z filter Mqmas3qzf2d page 305 5Q 1Q MQMAS with Z filter Mqmas5qzf2d page 305 Quadrupole Echo Ssechold page 305 3Q 1Q MQMAS with Z filter Mqmas3qzf2d Description Protocol Sequence Apptype Mqmas3qzf2d mqgmas3qzf2d c solidsseqid 3 quantum multiple quantum MAS with a third Z filter pulse and a choice of SPINAL64 or TPPM decoupling Used to obtain a 2D MQMAS spectrum for all spins 3 2 to 9 2 5Q 1Q MQMAS with Z filter Mqmas5qzf2d Protocol Sequence Apptype Mqmas5qzf2d mqmas5qzf2d c solidsseqld Description 5 quantum multiple quantum MAS with a third Z filter pulse and a choice of SPINAL64 or TPPM decoupling Used to obtain a 2D MQMAS spectrum for all spins 5 2 to 9 2 Quadrupole Echo Ssecho1d Protocol Sequence Apptype Ssechold ssechold
54. a problem for the lock experiment since by definition the lock experiment is complete once the autolock operation is completed Full Optimization Full optimization is the most complete optimization of lock parameters A fuzzy logic autolock algorithm automates the parameter control process in order to find the exact resonance and the optimum parameters phase power gain automatically and quickly with high reliability Fuzzy rules are used in the program to find the exact resonance frequency and for adjusting power and phase The fuzzy rules are implemented at different stages of the autolock process First the software finds the resonance If the exact resonance cannot be found phase and power are adjusted and the software looks for the exact resonance again The software then optimizes the lock power to avoid saturation optimizes the lock phase and optimizes the lock gain to about half range RF frequencies decoupler status and temperature are also set during full optimization 3 7 Adjusting Field Homogeneity 50 Refer also to Chapter 4 Gradient Shimming on page 61 if the system is equipped with gradient shimming capabilities Shim coils produce small magnetic fields used to cancel out inhomogeneity in the static field In shimming the current in shim coils is adjusted to make the magnetic field as homogeneous as possible Computer controlled digital to analog converters DACs regulate the room temperature shim coil cur
55. automatic phasing algorithms 96 autoscale 339 autoscale macro 151 335 autoscaling 151 AutoTest 378 av command 97 AVS file format 140 awc button 95 220 axial gradients 421 axial shims 428 Axis 115 394 axis 393 axis labeling 244 axis parameter 126 B B shimming criterion 430 background Autoshim 52 429 background operation 243 Backup File button 242 backwards linear prediction 227 bad shimming criterion 430 bandpass filters 250 bandwidth 100 baseline correction 122 125 186 222 233 374 baseline flatness 82 436 NMR Spectroscopy User Guide baseline spikes 416 bc command 125 233 Bearing Max psi 273 bearing air 30 bearing air supply 417 bearing pressure solids 273 bilinear rotation decoupling 252 binary peak file 239 242 Bipolar Pulse Pair STE with watergate 2D DOSY 371 Bipolar Pulse Pair Stimulate Echo DOSY 2D sorl Bipolar Pulse Pair Stimulated Echo Convection Compensated DOSY 2D 371 bipolar pulse pair stimulated echo experiment DOSY 166 175 BIRD pulse nulling effect 252 Bloch Simulation subwindow 357 359 Bloch simulator 344 350 block size storage 90 BMP file format 140 borders showing and hiding 139 Both button 241 Box button 240 241 327 Box cursors 109 237 387 BR24q 372 Br24q 306 brackets notation 147 broad peak base 427 broadband probes 249 Bruker data processing 98 Bruker data autophasing 97 bscor parameter 350
56. enabled if checked Process data on drag and drop check to enable Set display from plotter aspect ratio wysisyg check to enable Spectrum updating during phasing 0 100 set the percentage of the display that is updated during interactive phasing 100 is recommended Max of pens number of plotter pens to use Show Tooltips check to enable Day Limit of files in Locator neg forever enter an integer value Turn Locator Off check to enable The View menu selections are View Menu Items Command Line Holding Panel Parameter Panel Frame Viewport 1D 2D Cryo 01 999343 00 B 1207 Descriptions Displays the command line if it is hidden default is account owner only Opens the vertical Holding Panel Opens the horizontal parameter panels if they are hidden See Frame Panel page 394 See Viewports page 389 See ID page 402 See 2D page 403 Controls for cryogenic system and probe Refer to the related manuals for instructions NMR Spectroscopy User Guide 369 Chapter 16 VnmrJ Experimental Interface View Menu Items Descriptions Arrayed Spectra See Arrayed Spectra and FIDs page 399 Toolbars Opens a popout menu Place check next to a tool bar to show the tool or remove the check to hide the tool bar System Toolbar teil agio M A g ny v Refer to System Tool Bar on page 40 for a description of the system tool bar functions User Tool bar a
57. number of the heteronucleus of interest for example hmqc 1 for lH the default is Bes Figure 76 is a diagram of this sequence The first 2 pwx pulse on the X heteronucleus is a composite 180 consisting of 90 v9 180 v1 90 v9 90 180 90 90 180 oph x x 1 D D t D Ww 2 D H 1 180 x 90 x x 90 X Figure 75 Basic HMQC Pulse Sequence pw 2 pw pw pw 2 pw v1 v1 v2 v1 v4 oph o ja 1 di D D null D i d2 2 d2 2 D j H i 2 pwx pwx pwx v9 v1 v9 v3 v5 bbd X Figure 76 HMQC Pulse Sequence with nu11 0 and mbond n Phase Sensitive Aspects of the Sequence The parameter phase as in other phase sensitive 2D experiments controls the f phase detection Use phase 1 for 1D setup experiments or a 2D experiment without quadrature detection in fj Use phase 1 2 fora normal 2D experiment using the States Haberkorn Ruben hypercomplex method Use phase 3 to acquire data with TPPI and make sure Sw1 is twice the expected range The FAD for F1 Axial Displacement technique Marion D Ikura M Tschudin R Bax A J Magn Reson 1989 85 393 involves a change of phase cycling that shifts the axial artifacts in a hypercomplex experiment to the edge of the spectrum giving the hypercomplex version the benefit of TPPI with none of the disadvantages It is also refe
58. page 397 Using a Text Template page 397 Deleting Text Template page 397 The supplied default template sampleInfo displays the content of the text file in the current exp directory created from the comment text field in Study panel under the Start tab Creating a Text Template 1 Create one or more text frames on the graphics canvas 2 Entera name in the field next to the Save template button 3 Click the Save template button A template may contain one or more text frames The current text display layout is saved as new template using the name entered in the field next to the Save template button The template will be overwritten if the name already exists in template menu Using a Text Template 1 Click on the dropdown menu next to Select Template 2 Select a named template 3 Click on the a text frame to edit the content The Edit Text window is displayed see Figure 113 D 4 Edit the text or change the type color size and or type face style 5 Click Update to apply and display the changes to the text in the active text frame Deleting Text Template 1 Click on the dropdown menu next to Select Template 2 Select a named template 3 Click on the Delete from menu button Creating a Spectrum Inset Frame Inset Frame Buttons and Tools page 398 Creating the Inset Frame page 398 Zooming in on a Region Within an Inset Frame page 398 Resizing an Inset Frame page 399 Moving an Inset
59. pl s2pul Data run byeveryone on any date f lt gt si sl s Search results are displayed in the list Those a seam a seme a ime saved 8 2pul ems 001 2006 10 19 09 5 items in the white part of the list satisfy the s2pul ODCE f Seog s2pul e 1999 08 search sentence Those in the gray part do lt 2pul NOED x 2pul hol not Three attributes are displayed for each 2pul pis s2pul item that is found by the search The attributes correspond to the three columns in the list Clicking on the attribute name at the top of the list with the left mouse button opens a menu of attribute choices 4 Clickon an item in the Locator list to select that item Drag the selected item to the graphic area or the parameter panel area to load the data into the current experiment For example dragging a data set to the graphic canvas retrieves that data set into the current workspace experiment and displays the spectrum Dragging a workspace to the graphic canvas causes that workspace experiment to be joined with the graphic area Double clicking on an item performs the same action as dragging the item to the graphics canvas 16 5 Advanced Function and Hardware Bars Advanced Function Bar page 381 Hardware Bar page 381 Advanced Function Bar Toggle spectrum or sample tray display Function bar Command history Clear study home walkup4 vnmrsys data tmpstudy hd
60. the previous simulation The effect of a series of pulses can be evaluated by loading the first pulse and performing the simulation with Initialize set to YES loading subsequent pulse setting Initialize to NO and selecting Go after each pulse is loaded 4 Click on the Sweep button and select Freq B4 or Time for the sweep Freq a Enter a value in the B1max for B at the maximum pulse amplitude b Enter a value in the Start Freq KHz field for the starting frequency c Enter a value in the Stop Freq KHz field for the ending frequency Bl a Enter a value in the Frequency KHz field for the how far the magnetization is off resonance b Enter a value in the B1 Start KHz field for the starting B field c Enter a value in the B1 Stop KHz field for the ending B field Time The results are displayed in the form of a projected three dimensional coordinate system showing the path of the magnetization over the course of the pulse a Enter a value in the B1max for B at the maximum pulse amplitude a Enter a value in the Frequency KHz field to see how far the magnetization is off resonance 5 Accept the default values or enter values or for each of the following a Steps not available if sweep is set to Time the number of steps used in the simulation b Phase Enter the phase of the pulse 01 999343 00 B 1207 NMR Spectroscopy User Guide 359 Chapter 15 Pulse Analysis c Index Counter that dis
61. with one pulse prep XY8 decoupling 303 routine shims 55 rp parameter 96 97 110 rpl parameter 232 rp2 parameter 243 running an experiment 378 running 1D 2D experiments 23 S S2PUL pulse sequence 85 258 s2pul c 265 safety circuits on VT controller 419 safety sensor for VT controller 419 sample ejection 29 height 28 52 429 insertion 29 30 naming a 24 position 28 preparation 27 spinning 40 417 temperature 44 tubes 29 sample depth 28 sample spin rate 40 satellite signals 324 saturation of the lock signal 54 save a file save as 414 Save as 365 Save As 379 save button 327 Save data setup 366 Save Data Setup window 26 Save HT Frequencies Hadamard 230 saved data file names 26 location 26 sb button 95 220 sbs button 95 220 sc parameter 149 sc2 parameter 149 scale image to full window 107 scale integral value 126 scalelimits 339 scalelimits macro 151 335 screen position 106 sdp 165 185 sealed samples at elevated temperatures 44 sealed samples caution 419 second cursor 106 second cursor pair 238 second evolution time 243 seeing tool bar 380 Seeing Remaining Experiment Time 383 Select Hadamard 230 NMR Spectroscopy User Guide 447 Index Select button 327 Select zoom region 107 385 selecting items in the holding pen 399 selective excitation 341 using Hadamard technique 227 Selective Excitation 1D Experiments 370 selective Fourier tra
62. 0 part of wave wraparound factor 0 to 1 time reversal flag yes 1 no 0 frequency sweep reversal flag 0 to 1 stretching factor gt 0 dc correction y n Additional parameters are usually data matrices such as Fourier coefficients or square wave parameters e g length phase amplitude etc These matrices are listed without parameter names The size of the data matrix given is defined by cols rows number of columns number of rows Pbox incorporates the following amplitude modulation AM functions Sq sqa gs lz sch hta tra Sc csp wr sed qp ata square constant amplitude square wave amplitude modulation used for composite pulses Gaussian Lorentzian sech hyperbolic secant tanh hyperbolic tangent triangular amplitude ramp sinc function cosine power wurst wideband uniform rate smooth truncation seduce 1 mixture of sech and sin quadrupolar amplitude mod for CA atan frequency sweep pulse 348 NMR Spectroscopy User Guide 01 999343 00 B 1207 15 1 Pandora s Box exa exponential amplitude tna tangential amplitude fs Fourier Series ft inverse Fourier Transform Pbox incorporates the following frequency modulation FM functions ls linear sweep chirp tns tangential sweep tan ht hyperbolic tangent sweep tanh lzs constant adiabaticity Lorentzian sweep ca constant adiabaticity CA sweep frequency modulated frame cas constant adiabaticity sweep phas
63. 0 0 0 0 0 to adjust f phasing note that this argument has nine consecutive zeros in the middle and five zeros at the end 6 Adjust fpf 2D spectrum phase Set trace 1 to adjust the f phasing rp2 and 1p2 then set trace 2 to trim the f phasing if necessary Some pulse sequences are written to result in a 180 phase shift across the spectrum Remember that in VnmrJ the origin for phasing is defined as the right edge of the spectrum however in real terms the actual origin of phasing i e the zero frequency point is at the center of the spectrum If a certain 1p1 or 1p2 value is expected such as 180 simultaneously use a value of rp1 or rp2 equal to 1p1 20r 1p2 2 e g 90 Adjust the weighting functions for the 3D transform by using the wt i command and examine interferograms Do so along either the t or t axes Use the same commands given above to adjust the phasing the commands with the long series of zeros but use w t1d instead of w t2d For the final transformation the specdc3d parameter controls the dimensions in which a spectral drift correction is performed on the data A three letter value of ynn gives drift correction along f3 the first letter but not along f the second letter or f the third letter this value is probably a good starting point for your efforts The pmode parameter is ignored by the 3D transformation no phasing is possible after the 3D transform The
64. 002 gzlvl13 rephasing gradient amplitude for HMQC gt3 gradient duration in seconds 0 002 gzlvl max maximum gradient power 2048 for Performa I 327768 for Performa II IV and Triax gstab optional delay for stability pwx 90 deg X pulse pwxlvl power level for pwx alt grd flag to invert gradient sign on alternating scans default n lkgate_flg flag to gate the lock signal during diffusion gradient pulses jixh heteronuclear coupling for the Xfer delay satmode yn turns on presaturation during satdly yy turns on presaturation during satdly and del the presaturation happens at the transmitter position set tof right if presat option is used satdly presaturation delay part of d1 satpwr presaturation power sspul flag for a GRD 90 GRD homospoil block gzlvlhs gradient level for sspul hsgt gradient duration for sspul lkgate_flg flag to gate the lock signal during diffusion gradient pulses phase 1 2 for phase sensitive data convcomp y selects convection compensated hmqcidosy n normal hmqcidosy 200 NMR Spectroscopy User Guide 01 999343 00 B 1207 10 15 Processing I DOSY data The diffusion gradients gt 1 must be synchronized with sample spinning when using a nano probe gtl 1 0 srate trunc gt1l srate 0 5 where srate is the sample spinning speed Reference M J Stchedroff A M Kenwright G A Morris M Nilsson and R K Harris Phys Chem Chem Phys 6 3221 3227 2004 10 15 Processing I
65. 01 999343 00 B 1207 Chapter 11 Multidimensional NUR 247 NMR Spectroscopy User Guide 01 999343 00 B 1207 Chapter 11 Multidimensional NUR 248 NMR Spectroscopy User Guide 01 999343 00 B 1207 Chapter 12 Indirect Detection Experiments Sections in this chapter 12 1 Probes and Filters this page 22 The Basic HMQC Experiment for UC an page 250 12 3 Experiment Manual Setup on page 253 12 4 Cancellation Efficiency on page 258 2 5 Pros and Cons of Decoupling on page 259 12 6 N Indirect Detection on page 259 12 7 Pulse Sequences on page 259 This chapter describes one indirect detection experiment known as heteronuclear multiple quantum coherence HMQC Indirect detection experiments show correlations between heteronuclei while detecting high sensitivity protons HMQC differs from the older heteronuclear correlation techniques that detect the low sensitivity heteronucleus for example IC or ISN 12 1 Probes and Filters Indirect Detection Probes The most commonly used probes for indirect detection experiments are the Varian Inc indirect detection NMR probes such as the Triple Resonance Penta Tunable Triple Indirect Detection gHX Nano Cold Probes and others Indirect detection probes have a IH coil and an X nucleus coil with the 1H coil positioned closer to the sample for the highest possible sensitivity of the observed nucleus When connecting cables to the probe i
66. 10 4 Gradient Strength Calibration 162 The measurement of accurate diffusion coefficients is only possible if the gradient strengths used in the DOSY experiments are properly calibrated Calibration of gradient strengths using a gradient profile is sufficient for most gradient experiments but not for diffusion experiments Calibrate in a DOSY sequence as follows 1 Selecta sample with known diffusion coefficient NMR Spectroscopy User Guide 01 999343 00 B 1207 10 5 2D DOSY Spectroscopy A doped water sample is a good choice for this calibration at 25 C temperature The diffusion coefficients of HDO are 10 34 107 9 m sec at 5 C 19 02 10719 m sec at 35 C and 30 271019 m sec at 40 C Equilibrate the sample temperature at 5 C 25 or 40 C before starting the gradient calibration Diffusion coefficients are strongly temperature dependent Run a proton detected 2D DOSY sequence with a diffusion delay of 50 70 msec and 12 15 gzlvll values The signal attenuation between the weakest and strongest gradients ideally is a factor of 6 7 Process the data using proper window functions and baseline correction Calculate the D value of the sample Enter dosy grad calib and the correct diffusion coefficient for the temperature of the sample during the experiment i e 19 02 at 25 C on the command line The current DAC to G value is recalculated and if requested the gcal value of the probe file is also updated The proper g
67. 1207 7 2 Display Tools Display page The Display page on the Process tab provides appropriate display parameters including display mode axis and amplitude scaling Display menu The Display menu provides tools for displaying multiple spectra plotting and creating insets A typical use of these tools might be to expand a region on a spectrum 1 Display the spectrum click the spectrum icon on the graphics control bar 2 Select the region to expand left click on the spectrum to place the cursor on the left boundary of the region of interest and right click to designate the right boundary Use the left mouse button to drag the left cursor and right button to drag the right cursor until the desired region is between the cursors 3 Expand the region click the magnifying glass icon on the graphics control bar Display Parameters FID and spectral display is governed by parameters on the Display page Start Acquire Process Transfor Full Clear Scree 32 c J Display Mode Axis Amplitude Scaling Reference Baseline Correct Phased O Hertz O Normalized By Solvent DC Correct Absval PPM Absolute By TMS Autofind Integrals Power O kHz Cancel BC Correct P A By Cursor Screen Position Scale Adjust Find Peaks Full Center Autascale Reference cursor to Peak Threshhold Left Rignt z 6 62 ppm v E Display Arrays Display offsets Nearest Line Horizontal Label horizon
68. 1207 NMR Spectroscopy User Guide 243 Chapter 11 Multidimensional NMR 244 3D Display Display the data as two dimensional planes of the 3D data set in any of the three orthogonal directions Skew planes are not supported nor are full 3 dimensional displays One command getplane extracts the 2D planes from the 3D data set in one or more of the three orientations After the planes are extracted in this manner they are displayed with the dplane macro The parameter index2 keeps track of which plane is on display The macro next p1 displays the next plane from the plane currently on view Another macro prevpl shows the previous plane from the current plane The dsplanes start plane stop plane macro produces a graphical 2D color or contour map for a subset of 3D planes specified by the arguments The dconi program is used to display the planes The plplanes macro is available to plot a series of 3D planes The new concept of time domain frequency shifting can be employed to good use in 3D NMR where spectra in the indirectly detected directions are often folded by accident or by choice The parameters 1sfrq 1sfrq1 and 1sfrq2 cause the frequency of the spectrum to be shifted as part of the Fourier transformation process 3D Pulse Sequences Simply write a sequence that includes a d2 and d3 delay these delays may also be d2 2 or d3 2 when are writing sequences Use the parameters phase and phase2 to select between th
69. 183 Chapter 10 DOSY Experiments 10 9 Processing 2D DOSY Experiments Processing Steps page 184 Correcting Systematic Gradient Errors page 184 Extracting Spectra page 184 Displaying Integral Projection page 185 DOSY Processing Buttons page 185 Do not process the data with the dosy macro until the acquisition is complete Processing Steps The buttons for processing DOSY data are described in DOSY Processing Buttons page 185 Process the acquired DOSY data to give a 2D DOSY spectrum as follows 1 Click on the Calculate Full DOSY Spectrum button to extract the diffusion data from the spectra and synthesis of a 2D DOSY spectrum with the macro dosy Refer to Calculate Full DOSY Spectrum page 186 for a description and limitations of data processing The two dimensional DOSY display and plot is constructed by taking the band shape of a given signal from the first lowest gradient area spectrum The shape is then convoluted in a second dimension with a Gaussian line centred at the calculated diffusion coefficient The linewidth is determined by the estimated error of the diffusion coefficient as obtained from the fitting process The following steps although not required are recommended a Click on either the Fiddle TMS and Fiddle no TMS button if there is a suitable reference line that slowly diffuses b Clickon the Basline Correct All Spectra button to apply baseline correction using the macro fbc
70. 186 FDM Filter Diagonalization Method 152 156 FID display 104 phase rotation 103 shimming on the 432 vertical scale adjustment 106 viewing a particular FID 103 fid display toolbar 380 Fid moving 367 fiddc3d parameter 243 fiddle 165 fiddle command 323 324 Fiddle program 322 fiddle program 185 fiddle2D command 325 fiddle2d command 325 fiddle2Dd command 325 fiddle2dd command 325 fiddled command 325 fiddleu command 325 FIDs acquisition time too short 99 convert multiple FID into single FID 100 distortion from hardware 99 extend direction 99 440 NMR Spectroscopy User Guide intensity 95 left shifting 98 phase rotation 98 varying one or more parameters 146 weighting function 93 Fields 115 393 fields 393 File Browser buttons 413 open a file 414 save a file 414 file browser open navigation window 365 414 system tool bar icon 379 File button 240 file formats Plot Designer 140 portable gray map 141 PostScript 141 file menu 365 Filter Diagonalization Method FDM 152 156 filter part numbers 250 filters for indirect detection 250 final simulated spectrum frequency limits 315 finding z0 47 fine power control 36 first evolution time 243 first point distortion 221 first order baseline correction 122 125 FITS file format 140 fitspec command 321 fitspec indata file 321 322 fitspec inpar file 321 322 fitspec outpar file 321 322 fixed Gaussian frac
71. 1p1 and rp1 Most of the setup macro set 1p1 and rp1 to zero so that the first display will indicate the need if any for phase correction in fy The same techniques as used in 1D phasing are employed here with a minor difference 232 l 2 Enter u11 to display the full data matrix in a full chart display To phase the 2D spectrum use the horizontal cursor present in the interactive display to identify a peak toward the right hand edge of the spectrum Note the trace number indicated at the top of the display memorize this by setting r1 equal to its value Select one or more other traces at f4 values more toward the center and left parts of the spectrum These will be the most sensitive to work with if there is a diagonal in the spectrum with large peaks Use r2 r3 etc to memorize these trace values A minimum of two is needed one at the far right and one at the far left Enter ds r1 Phase this spectrum like a 1D spectrum using the Phase button in the displayed menu Click the mouse on the peak displayed near the right edge of the spectrum Phase up this spectrum thus setting rp1 Do not click in the left part of the spectrum at this time Enter ds r2 The second trace appears Click the mouse near the right edge of the spectrum to fix rp1 at the previously determined value and do not rephase Move the mouse to the peak at the left click and phase it thus setting 1p1 Enter ds r1 to recheck rp1 Repea
72. 2 Preparing for an Experiment 2 1 Sections in this chapter 2 1 Starting VnmrJ on page 27 22 Preparing the Sample this page 2 3 Ejecting and Inserting the Sample on page 29 24 Loading a Probe File on page 30 2 5 Tuning Probes on Systems with ProTune on page 31 2 6 Tuning Probes on Standard Systems on page 34 Starting VnmrJ 1 Log on to the workstation 2 Double click on the VnmrJ icon 2 2 Preparing the Sample Sample preparation and positioning in the turbine affect the efficiency of auto shimming methods Variations in bulk magnetic susceptibility at air to glass glass to solvent and solvent to air contact points can contribute a dominant portion of the variation of field homogeneity from sample to sample The time spent shimming or even the need to shim is largely dependent on the care in controlling the effects of these contact points Selecting a Solvent page 27 Setting the Sample Height page 27 Sample Position Using the Depth Gauge page 28 Sample Tubes page 29 Selecting a Solvent Most samples are dissolved in a deuterated solvent that does not react or degrade the sample The instrument can be run unlocked if the sample must be run using a solvent that is not deuterated Setting the Sample Height Experimentation and calculation show that the liquid column length must be at least three times the length of the observe coil window to minimize end effects
73. 3 Homospoil Control Shim Supply Homospoil Time Limit Varian 14 20 ms 200 ms Varian 18 to 40 20 ms 200 ms The behavior of homospoil gradients is quite different from that of a pulsed field gradient The gradient strength is much weaker than the traditional PFG and the recovery time is much longer because of eddy currents The strength and recovery of the gradient depends on the shim coils and system hardware Typically these gradients are suitable only for profile type experiments and unsuitable for gradient coherence selection experiments such as GCOSY and GNOESY For most gradient experiments pulsed field gradients are preferred if available Homospoil gradients are suitable for H and H gradient shimming on some systems see Table 3 for system configurations Homospoil Gradient Shimming for H or H First configure the homospoil gradients to use homospoil gradient shimming Follow the procedure in Mapping Shims and Gradient Shimming page 64 Use Find z0 before gradient shimming to use homospoil deuterium gradient shimming with different solvents 4 4 Configuring Gradients and Hardware Control 1 Confirm that PFG or homospoil gradients are installed on your system See the previous sections in this chapter A PFG probe is required 2 Confirm that the gradients are active by checking that gradt ype and pfgon are set appropriately for your system Use config to change gradtype if necessary Use System Settings to set p
74. 367 pulse tuning through the directional couplers 307 pulse width calibration 149 Pulsed Field Gradient Double Stimulated Echo 179 pulsed field gradient shape creation 341 pulsed gradient experiments 158 pulses with interleaved acquisition 308 pulses with interleaved acquisition and alternating phase 308 pulsetool command 355 356 Pulsetool program 355 pure absorption 2D data 225 pure absorption spectra 225 putwave macro 352 pw parameter 351 pw90 parameter 84 pwr command 97 pxbss 232 Pxfid command UNIX 354 pxrep 232 pxshape macro 344 352 Pxsim command UNIX 354 Pxspy command UNIX 354 Q Quadrature BR24 multiple pulse acquisition 306 Quadrature MREV8 multiple pulse acquisition 306 quadrupole echo 305 quarter wavelength cable 34 quitting Plot Designer 141 R r macro 232 radial shims 56 rate of VT gas flow 416 rd 279 rd rof3 minimum value 279 Read button 242 Read Text button 242 reading binary peak file 242 text peak file 242 real channel 95 real time 2D 215 receiver gating 37 receiver overload 84 Redorlonepul 303 372 01 999343 00 B 1207 Redorltancp 304 372 Redor2onepul 304 372 Redor2tancp 304 372 redosy 165 Redraw display 107 385 ref pw90 parameter 351 ref pwr and ref pw90 calibration data 343 ref pwr parameter 351 reference deconvolution 185 322 fiddle program 322 reference frequency 112 reference line 112 reference literature DOSY related
75. 3D transformation process needs to be followed by the process of extracting the 2D planes from the full 3D data set This can be done separately with the getplane command but most often is combined with the t 3d command In general and especially for heteronuclear experiments the f f4 and ff planes are the most interesting The ff plane is not only generally less useful but also is considerably slower to extract from the data The recommended command to use for 3D transformation therefore is ft3d 1 3 2 3 which performs the 3D transform and extracts the two interesting planes in one step Solvent suppression works on t4 FIDs of 3D spectra just like in the 1D and 2D cases Following the transform set plane 1 3 or 2 3 and then use the dproj macro to display the projection of the data on that plane or dplane n to display the nth plane The reset 3 macro will reset parameters after a partial 3D Fourier transform 11 13 4D NMR Acquisition 246 The addpar 4d macro creates the parameters ni3 sw3 d4 and phase3 that can be used to acquire a 4D data set the macro par4d functions the same as addpar 4d The parameter ni3 is the number of t increments sw3 is the spectral width along the third indirectly detected dimension d4 is the incremented delay and phase3 is the phase selection for 4D acquisition Processing and display in 4D are currently not available in VnmiJ NMR Spectroscopy User Guide
76. 999343 00 B 1207 13 3 Setting up for Solids Experiments i Select any probe from probes shown in the drop down menu j Select the name of the solids probe from the dropdown menu The probe name must be explicitly selected after the probe file has been created k Click Close to load the probe file and exit the pop up window Starting the Rotor 1l Set the MAS automated speed controller to AUTO mode 2 Verify that the correct module name is shown on the Spin Temp page Load or reload the correct probe file for the installed probe if the module name is not correct Select Thin or Std to select the correct Max Speed Set the Target Hz for spinning Press Start on the Spin Temp page De dms 09 Wait for the speed to regulate The LOCKED light on the controller is on when spinning is in regulation The current speed is displayed on the Spin Temp page and on the controller Changing the Rotor Speed 1 Enter a new Target Hz value 2 Press return 3 Wait for the speed to regulate Stopping the Rotor Press Stop to stop the rotor Setting the Bearing Pressure The bearing pressure is set automatically based on the value of Bearing Max psi as roughly a linear function of the Target Hz spin rate Make a fine adjustment for the bearing as follows 1 Set Bearing Span 0 2 Set the Bearing Adjust psi to the change in pressure positive or negative 3 Reset Span 100 to lock the new bearing pressure in place
77. AT of the TMS line even if they are higher than the refer ence line tmsref tries avoiding those signals by taking Reference cursor to 0 00 the line furthest to the right in that area as long as it is at least 10 of the main Si CH signal Large signals within 0 6 ppm for IH or 6 ppm for 5C to the right of TMS might lead to misreferencing Clears the reference line by removing any spectral referencing present and turns off referencing References the spectrum based on the current cursor position To reference the spectrum based on a line position in the spectrum first use the Find nearest line button on the Process page then click By Cursor Parameters used in spectral referencing Reference line frl The distance in Hz of the reference line from the right edge of the spectral window This line is the spectral position used to set the referencing It can be the signal of a frequency standard such as TMS or any line such as a solvent signal with a known chemical shift in ppm or a position in the spectrum where such a line is expected to appear Reference position rfp The difference between the reference line and the reference frequency zero position of the scale in Hz Referencing a spectrum using the signal of a frequency standard such as TMS use reference position is 0 The distance of the reference frequency from the right edge of the spectrum is reference line reference position Spectr
78. B 1207 Chapter 15 Pulse Analysis Sections in this chapter 15 1 Pandora s Box on page 341 15 2 Pulse Shape Analysis on page 354 15 1 Pandora s Box Pandora s Box Pbox software creates shape pattern files for experiments involving shaped rf pulses composite pulses decoupling and mixing patterns adiabatic rf sweep waveforms and pulsed field gradient shapes The goal of Pbox is to simplify generation and use of different waveforms in NMR experiments so that the user does not need to be an expert in selective excitation Pbox makes the use of complex waveforms as simple as using ordinary rectangular pulses Not only does Pbox provide all the necessary parameters pulse width power dm dres etc when the shape files are created but this information can be extracted at any time from Pbox shape files by macros or directly within pulse sequences More than 160 different shapes are available from the Pbox library Create a New Waveform page 341 Calibrating the RF Field page 343 Creating Waveforms by Macros page 344 Creating Waveforms in an Operating System Terminal Window page 345 Pbox File System page 345 Pbox Parameters page 349 Wave String Variables page 351 Pbox Macro Reference page 352 Pbox Commands Using a Terminal page 353 Create a New Waveform 1 Open the Pbox window to access the tools for creating waveforms a Click Edit on the menu bar b Select Ne
79. Default C13 The example window below shows the Default H1 page which is used for setting the proton frequency Other Default pages available are Default C13 Default F19 and Default qX S Acquire Process Acqui re Acquire amp Transform Sto Show Time Sequence Arrays 3 stdih Display Sequence Acquisition Pulse Sequence Spectral Width ppm ee ea TE Transform size Not used z Channels Downfield 11 0 Upfield 1 0 Line Broadening Hz None Ww Flags Pulse Width degrees 90 ws i Plot when done Future Actions Enter pulse angle o0 m 5 Spectrum As Displayed Relaxation Delay sec i T Parameters Full Top Left Number of Scans 16 bd Peak Values On Spectrum Spin 20 Hz Integrals Tune method lohi Y 82 NMR Spectroscopy User Guide 01 999343 00 B 1207 5 2 Acquisition Settings Transmitter and Decoupler Positioning Set transmitter and decoupler values in the Channels page fari Acquire Process Show Sequel An ae Default H1 stdih Display Sequenti Acquisition Channels Observe 2 Decouple 1 Decouple Decouple a SR Nucleus Freq 100 075MHz A1 100 075 MHz 0 000 MHz 0 000 MHz Flags Offset 0 0 Future Actions Dec On off Dec Modulation 90 Degree at Par us at dmf Waveform at resolution degrees degrees The Observe Offset field pe
80. ERRE 168 Table 13 DgcsteSL dpfgse Parameters eee tentent ete t rete entere 169 Table 14 Dbppste we Paratetets ene emer preme PE AE TEE aS 170 Table I5 Dbppsteinept Parameters scosceso etones seriero iesire serieen eie eesi 171 Table 16 Dbppste CG Parameters ree eR OTHER PHP ERES 175 Table T7 DesteSL CC Parameters e erret eet roe Y R ER YD ERE Fer ento 177 Table 1S DecsteS LCC Paramelets eet o Peeters neret 178 Table 19 Dpfedste Parameters eoe eU Mi aes 180 Table 20 Dgcstecosy Parameters eere reete tenete eed doe dee Pee dedu desc 188 Table 21 Decstehmqc Parameters nire e tO RHET DUO OTI ERR SEES 189 Table 22 Dgcstehmqc ps Parameters etre stet test reet rtu ee noe dro foit buo deeds 193 Table 23 Dbppste ghsqcse Parameters cisien eet eter retener rien ener 194 Table 24 Dcosyidosy Parameters 2 2 Ae cero ERR eene tha e Uer sees sles EIE Eee p eet 197 Table 25 Dhom2djidosy Parameters eese nennen enn em nennen 199 Table 26 Dghimqcidosy Parameters erect eret REPRE 200 Table 27 Parameters for HMQC Pulse Sequences esee ne 261 Table 28 Basic Solids Calibration Parameters eeeeeeeeneemen nenne 271 Table 29 Spin Simulation Related Commands and Parameters sess 314 Table 30 Deconvolution Commands and Parameters eee 320 Table 31 Fiddle Command and Variants eese enne 322 Table 32 Add
81. FID HOM seo predicted pts divide by F 7 Left Shift Frequency starting at F coefs on BEN offset FT 1D 1st Increment FTDataSize Acq Pts rn END FT 1D All JF 1k x 256 lal i pen lex pts Transform F2 mr Bk v 1024 Left shift FID Coi Full 2D Transform Weighting involves backward extension of the time domain data with linear prediction the default value is then 0 5 and the first point of each interferogram by the F1 value default fpmult1 value is 0 5 for the indirectly detected dimension 1st Pt Multiplier compensates for first point distortion see Otting Widmer Wagner and W thrich J Magn Reson 1986 66 187 jx 01 999343 00 B 1207 NMR Spectroscopy User Guide 221 Chapter 11 Multidimensional NUR 222 The effect of using the F2 value in 1st Pt Multiplieris to perform a linear baseline correction on all f data reducing negative going ridges along f in phase sensitive 2D data This correction is not needed in experiments such as COSY where the FID starts at zero and grows or in absolute value mode presentation if pseudo echo or sinebell processing is used because the processing function goes to zero at t5 0 forcing all FIDs to start at zero amplitude Determine the best value of 1st Pt Multiplier empirically It can be determined manually before during or after the 2D experiment by using FT 1D 1st Increment button on the Process page Enter dc or u
82. Find Peaks Display Arrays Display offsets Nearest Line Horizontal Label horizontal Mark at Cursor Vertical vertical Clear Marks Buttons used to control the display of arrayed data Click on the Process tab 2 Select the Display page 3 Click on a Display Arrays button Horizontal Display arrayed spectra horizontally and divide available display width into equal portions Vertical Display arrayed spectra stacked vertically with each spectrum displayed using the full width of the screen Label add a label to the spectra Custom Use a custom Label 4 Enter values for the Display offsets horizontal enter a value in mm for the separation between spectra vertical enter a value in mm for the separation between spectra Stacked Spectra Display Using the Graphics Tools Icon Function Display the first arrayed spectrum and display 1D graphics toolbar with the following icons at the top or left side if the bar is horizontal Display next spectrum Display previous spectrum Display arrayed spectra stacked vertically with each spectrum displayed using the full width of the screen Display arrayed spectra horizontally and divide available display width into equal portions Hide or show axis under the spectra Label the spectra Return to previous graphics display tool OBL EB 118 NMR Spectroscopy User Guide 01 999343 00 B 1207 7 9 Aligning and Stack
83. Frame page 399 01 999343 00 B 1207 NMR Spectroscopy User Guide 397 Chapter 16 VnmrJ Experimental Interface 398 Inset Frame Buttons and Tools The buttons delete one or all inset frames and restore the default frame to full size Buttons and tools Function Delete Inset Delete the selected inset insat Ba Delete all Delete all inset frames N a Full size Restore default frame size Delete inset A ow reds s Delete allay v Show frame border Select the inset mode tool Reset frame EE xl Default mode tool Creating the Inset Frame An inset frame has the full capability of the default frame The only difference is the default always exists and an inset frame can be created or removed Create an inset frame within the default viewport frame as follows Figure 114 Creating an Inset Frame Select the Frame vertical panel Select the inset mode tool Place the cursor at the low field left side of the region to be expanded as shown in Figure 114 frame 1a Hold the left mouse button down and drag the inset window to the high field right side of the region Drag the cursor down to set the height of the inset frame see Figure 114 frame 1b Release the mouse button to create the inset frame see Figure 114 frame 2 Zooming in on a Region Within an Inset Frame 1 2 Select the default mode tool EI Click inside the frame to make the frame active A frame has a yellow border when it is act
84. Gradient Compensated Stimulated Echo AV COSY Table 20 Dgcstecosy Parameters Parameter Description delflag y runs the Dbppste sequence n runs the normal s2pul sequence del the actual diffusion delay gti total diffusion encoding pulse width gzlvl1 diffusion encoding pulse strength gstab gradient stabilization time 0 0002 0 0003 sec tweek tuning factor to limit eddy currents can be set from 0 to 1 usually set to 0 0 gzlv12 gradient power for pathway selection gt2 gradient duration for pathway selection sspul flag for a GRD 90 GRD homospoil block gzlvlhs gradient level for sspul satmode yn turns on presaturation during satdly yy turns on presaturation during satdly and del the presaturation happens at the transmitter position set tof right if presat option is used satdly presaturation delay part of d1 Satpwr presaturation power hsgt gradient duration for sspul alt grd flag to invert gradient sign on alternating scans default n lkgate_flg flag to gate the lock sampling off during the diffusion sequence qivl quantum filter level 1 single quantum 2 double quantum DAC to G parameter to store the gradient calibration value set by setup dosy The diffusion gradients gt 1 must be synchronized with sample spinning when using a nano probe gt1 1 0 srate trunc gt1l srate 0 5 where srate is the sample spinning speed Process N type data with w t2d 1 0 0 1 optional add the t2dc arg
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