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Bruker Avance 300 NMR Spectrometer Operating Instructions for Topspin 2.1 – August 2009

WARNING: Strong magnetic and radiofrequency fields are present in the vicinityof the NMR instrument. Computer diskettes and other magnetic media (e.g.,ATM cards, credit cards, and Metrocards), as well as some watches, can bedamaged if brought too close to the magnet. An extreme hazard exists for thosewith pacemakers or metal prosthetics. Keep all tools and other magnetic materials away from the magnet.

Inserting your sample:

1. Turn off SPIN and LOCK on the control panel. Make sure the black dust cap is off the

magnet bore.

2. Eject the sample using the LIFT ON/OFF button on the control panel.

3. Remove the marking tag from your sample tube, and wipe the tube with an ethanol-

moistened Kimwipe. Remove the spinner turbine from the top of the magnet bore, holding

the assembly by the glass NMR tube. Avoid handling the plastic part of the spinner turbine,

especially the black-and-white tape.

4. Place the spinner turbine assembly into the sample depth gauge and gently remove the NMR

tube, holding the top of the spinner turbine in place with your index finger. Set that tube

aside, and replace it with your sample tube, gently adjusting your tube in the spinner turbine

to the appropriate depth. Make sure that the bottom of the depth gauge is on the “2” setting.

5. Holding the spinner turbine/tube assembly by the top of the glass NMR tube, remove it from

the depth gauge and wipe the lower part of the glass tube with the ethanol-moistened

Kimwipe. Replace the depth gauge in the large glass beaker where it is kept.

6. Place the spinner turbine into the top of the magnet bore. It will float there on a cushion of

compressed air.

7. Insert the sample using the LIFT ON/OFF button on the control panel.

8. Once the green SAMPLE DOWN light goes on, press the SPIN ON/OFF button on the

control panel to start the spinner air. The green light on the SPIN ON/OFF button will blink

until the set spin rate (20 revolutions per second) is reached at which point the green light

remains on steadily.

Things that can go TERRIBLY WRONG during the sample insertion process:

1. The plastic sample depth gauge is narrow enough that it will actually fit into the top of

the magnet bore. Do NOT put the depth gauge into the magnet. What goes into the

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magnet is the spinner turbine with the NMR tube in it. Make sure you understand

which the spinner turbine is and which the depth gauge is.

2. If the eject air is not on when you place the spinner turbine with your sample in it back

in the top of the magnet bore, the whole assembly will go crashing down into the

magnet. This can result in a broken tube and a very laborious process of removing and

cleaning the probe. Make sure the eject air is ON before setting the spinner turbine

with your sample in it at the top of the magnet bore.

3. Never put an empty spinner turbine into the magnet bore. There must always be an

NMR tube in the spinner turbine when it is placed at the top of the magnet bore,

otherwise the assembly cannot be ejected with compressed air.

Setting up a new experiment:

1. A new experiment can be set up by starting from an old experiment and creating a new place

to acquire and store NMR data. If the student who used the instrument just before you ran a 1H (proton) spectrum and you also wanted to run a 1H experiment, you could start from her

experiment and use it as a template. There may be occasions, however, when you need a

fresh start.

2. In the browser at the left of the main Topspin window in the folder D:\ open the folder

“orgolab”.

3. If you are setting up a 1H experiment, open the folder “1HTemplate_9_02” and double click

on the folder “3”. The message “No raw data available. No processed data available”

appears. This is OK; you are interested in the experiment parameters, which you will copy to

your new experiment, not the data.

4. If you are setting up a 13C (carbon) experiment, open the folder “13CTemplate” under

“orgolab” and double click on the folder “1”.

5. If you are setting up a DEPT135 experiment, proceed as you would for a 13C spectrum, with

steps 6-13 below. Then follow step 14.

6. Type edc in the main window command line. Name the current data set. Always name your

NMR data sets as follows: (a Roman numeral representing your notebook number: i.e., I or

II)-(your initials)-(the page number of your notebook on which the experiment started). For

example, an experiment name might be I-CMR-11. Avoid spaces in the data set name.

When you prepare your NMR sample in the lab, be sure to label your NMR tube with a

marking tag that includes the sample name in the above format. That way you will have the

information available in the NMR room when you set up the NMR experiment.

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7. Set the experiment number (EXPNO). You can have more than one NMR experiment under

the same data set name. This is very useful when you are running more than one NMR

experiment on the same sample, a proton and a carbon experiment, for example. Start with

experiment number 1.

8. The process number (PROCNO) will almost always be 1.

9. Be sure you are saving data in directory (DIR) “D:” and that the User is “orgolab”.

10. Specify the solvent from the pull-down list.

11. For the Experiment entry, make sure “Use current params” is selected.

12. Provide a title to be plotted with your spectrum. Start with the experiment name (e.g., I-

CMR-11). On a separate line or lines you can add other information (e.g., Diacid from Diels-

Alder reaction).

13. Click OK.

14. For DEPT135 spectra, click on the AcquPars tab, and change the PULPROG parameter to

dept135.

Establishing the deuterium lock:

1. Type rsh (recall shims) in the command line of the main window. Select the shim file

“today” with a left mouse click. Click “Read” at the bottom of the current window. The

status bar at the bottom of the main window will show “rsh: finished.” If you are running

consecutive experiments, where you do not remove your sample from the magnet, you only

need to recall the shims for the first spectrum; do NOT re-recall them.

2. Open the lock window by typing lockdisp.

3. If necessary, re-enter the main window by left clicking anywhere on the main window. Type

lock in the command line of the main window. Left click to select the appropriate solvent in

the solvents table window, and then click OK. You can watch the autolock in the lock

window. It may be necessary to click on the lock window or on the lock display tab at the

bottom of the screen in order to bring the lock window to the front. The lock level line

should climb until it reaches a steady height on the grid of the lock window. When locked,

the status bar at the bottom of the main window will show “lock: finished.” If you are

running consecutive experiments, where you do not remove your sample from the magnet,

you only need to lock the sample for the first spectrum; do NOT re-lock.

Shimming:

1. Press the Z1 button on the control panel. Turn the round knob on the control in regular

increments so as to maximize the lock level as shown in the lock window. There is a delay

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between the turning of the knob and the change in the lock level indicator. So turn the knob

a half of full turn, then wait a second or two to see the effect.

2. You can move the lock level line without changing the shims by pressing the LOCK GAIN

button near the top of the control panel and adjusting the lock level line with the knob. This

kind of adjustment is useful if you find it easier to shim with the lock level line on one of the

grid lines or if the lock level line goes off the top of the lock window scale as you shim.

3. Once you have optimized Z1, press the Z2 button on the control panel and optimize that shim.

4. Return to Z1 and re-optimize that shim.

5. Press the STD BY button on the control panel to disable the control panel knob.

6. If you are running consecutive experiments, where you do not remove your sample from the

magnet, you only need to shim the sample for the first spectrum; there’s no need to re-shim.

Tuning the probe:

1. Next you will need to make sure that the instrument is tuned to the right frequency for the

experiment you have set up. For example, a proton experiment requires our NMR

spectrometer to be tuned to around 300 MHz (300 million cycles per second); a carbon

experiment requires our spectrometer to be tuned to around 75 MHz. To start the tuning

process, type wobb in the main window command line.

2. Wait for the message “wobb: 50 Ohm measured, displaying wobble curve…” to appear in the

bar at the bottom of the main window.

3. The curve dipping to a minimum near the center of the screen is the wobble curve. When the

instrument is properly tuned, the dip of the curve will be lined up with the vertical line and

will be as close as possible to touching the small triangle at the bottom of the vertical line. If

the instrument is out of tune continue to step 4, if it is already tuned properly skip to step 8.

4. Tuning is adjusted on the underside of the magnet at the so-called “probe.” For 1H

adjustments you will use the two sticks toward the back of the probe. For 13C adjustments

you will use the bronze-colored sliders on the front of the probe. You can monitor the tuning

either on the screen or by looking at the lights on the upside-down-T-shaped part of the pre-

amplifier that is just to the left of the magnet. The object in tuning is to center the wobble

curve on the screen as described in part 3, or, if you are looking at the pre-amplifier, to get all

the lights into the green region of the upside-down T.

5. For either 1H or 13C, adjustments can be made to two different parameters: the “tune” and the

“match.” For 1H these are adjusted with the sticks described in part 4. The tune stick is

labeled with a “T” and the match stick is labeled with an “M.” For 13C the adjustments are

made with the brass-colored sliders on the front of the probe. You will only need to make

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adjustments to the finest control slider, which is the one furthest to the right for either tuning

or matching. To move the sliders for 13C adjustments, use the tool that is hanging by a

beaded chain from the bottom of the probe. Make sure you know whether you are tuning

for 1H or for 13C and use the correct adjustment controls on the probe. If you try to

tune for 1H using the brass sliders or for 13C using the sticks, not only will the wobble

curve not respond, you will also completely detune the other channel!

6. The tuning controls move the wobble curve left and right on the screen and affect the left-to-

right lights on the pre-amplifier. The matching controls move the wobble curve and pre-

amplifier lights up and down.

7. Carefully adjust the tuning and matching until you have achieved proper tuning as shown by

the position of the wobble curve on the screen or all-green lights on the pre-amplifier. Note

that only very slight changes in the tuning and matching settings are required. Also,

there is a delay between the adjustment and the response of the wobble curve on the screen or

on the pre-amplifier lights. So make a small adjustment, then wait a few seconds to discern

the effect. You will note that the tune and match adjustments are to some extent

interdependent, so it may be necessary to go back and forth in adjusting the two.

8. Once you have tuned the instrument, left click on the stop sign icon ( ) in the toolbar of the

WOBB window (just above the wobble curve). The WOBB window will then close, and

“wobb: finished” will appear in the bar at the bottom of the main window.

Acquiring and transforming the data:

1. Type getprosol in the main window command line. This loads the settings necessary to run

your experiment. The message “getprosol: finished” is displayed in the bar at the bottom of

the main window.

2. Set the number of scans by typing ns in the main window command line. A pop-up window

will appear with the current setting for NS. You will usually use NS = 16 for 1H spectra and

NS = 64 for 13C and DEPT135 spectra. If the NS value is already correct, just click OK.

Otherwise, type the desired NS value and click OK.

3. Set the receiver gain by typing rga in the main window command line. Wait until the

message “rga: finished” appears in the bar at the bottom of the main window. Do NOT type

rga for carbon of DEPT135 spectra.

4. Type zg to start the data acquisition. Once the message “zg: acquisition running” appears in

the bar at the bottom of the main window, you can watch the data acquisition in the FID

window, which opens automatically.

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5. Data acquisition for the 1H experiment takes only a few minutes, while the 13C data

acquisition takes about 15 minutes. If you need to run both 1H and 13C experiments on the

same sample, do the 1H acquisition first. Then set up the 13C experiment, and while the 13C

data is being acquired you can go back to the 1H experiment and do the data processing and

plotting (see below).

6. If you are doing a long 13C acquisition and want to go to a 1H data set that you acquired

earlier under the same data set name, just type re experiment number in the command line

of the main window. For example, if you ran the 1H spectrum as experiment number 1 under

I-CMR-11 and then set up your carbon experiment as experiment number 2, also under I-

CMR-11, you could start the 13C acquisition in experiment 2 and then type re 1 to recall the 1H data.

7. When the acquisition is complete, the message “checklockshift: finished” will appear in the

bar at the bottom of the main window. For 13C spectra, the message “zg: finished” may

appear in the bar at the bottom of the main window instead.

8. Type ef in the command line of the main menu to multiply your data by an exponential

function and to transform the data from the time domain into the frequency domain. The

multiplication emphasizes the data acquired at the beginning of each scan, leading to better-

looking spectra. The transformation is a mathematical operation called a Fourier transform.

9. Type apk in the command line of the main window to phase correct the spectrum.

10. Type abs in the command line of the main window to smooth and level the baseline.

11. Process your spectrum (see p. 83)

Ejecting your sample and replacing the standard sample:

1. Be sure data acquisition is complete before you eject your sample. Acquisition is still going

on if lights are flashing at the very top of the locking/shimming control panel.

2. If there is another student waiting to use the spectrometer after you, your sample will be

replaced by her sample. Follow the instructions starting from the beginning of this handout.

If you are the last person to use the spectrometer for the day, follow the instructions below.

3. Turn off the SPIN and LOCK on the control panel. Make sure the black dust cap is off the

magnet bore.

4. Eject the sample using the LIFT ON/OFF button on the control panel.

5. Wipe off the standard sample tube with an ethanol-moistened Kimwipe. The standard

sample tube is flame-sealed and has a small label near the top that says “1H APP TEST/ 1%

3-HEPTANONE/ 99% CDCl3/ 968120-93(C)”. Remove the spinner turbine from the top of

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the magnet bore, holding the assembly by the glass NMR tube. Avoid handling the plastic

part of the spinner turbine, especially the black-and-white tape.

6. Place the spinner turbine assembly into the sample depth gauge and gently remove your

NMR tube, holding the spinner turbine in place with your index finger. Set your sample tube

aside and replace it with the standard sample tube, gently adjusting the tube in the spinner

turbine to the appropriate depth. Make sure that the bottom of the depth gauge is on the “2”

setting.

7. Holding the spinner turbine/tube assembly by the top of the glass NMR tube, remove it from

the depth gauge. Place the depth gauge in the large beaker designated for that purpose.

Wipe the lower part of the NMR standard glass tube with the ethanol-moistened Kimwipe.

8. Place the spinner turbine into the top of the magnet bore. It will float there on a cushion of

compressed air.

9. Insert the sample using the LIFT ON/OFF button on the control panel.

10. Put the marking tag back on your NMR sample tube.

11. Replace the black dust cap on the top of the magnet bore.

12. Wait for the green SAMPLE DOWN light to go on. Do not press the SPIN ON/OFF button

on the control panel to start the spinner air; the spectrometer is left with the spinner air off.

A friendly reminder of things that can go TERRIBLY WRONG during the sample

insertion process:

1. The sample depth gauge is narrow enough that it will actually fit into the top of the

magnet bore. Do NOT put the depth gauge into the magnet. What goes into the

magnet is the spinner turbine with the NMR tube in it. Make sure you understand

which the spinner turbine is and which the depth gauge is.

2. If the eject air is not on when you place the spinner turbine with your sample in it back

in the top of the magnet bore, the whole assembly will go crashing down into the

magnet. This can result in a broken tube and a very laborious process of disassembling

and cleaning the probe. Make sure the eject air is ON before setting the spinner

turbine with your sample in it at the top of the magnet bore.

3. Never put an empty spinner turbine into the magnet bore. There must always be an

NMR tube in the spinner turbine when it is placed at the top of the magnet bore,

otherwise the assembly cannot be ejected with compressed air.

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13. Type rsh in the command line of the main window. Select the shim file “today” with a left

mouse click. Click Read at the bottom of the window. The status bar at the bottom of the

main window will show “rsh: finished.’

14. Type lock in the command line of the main window. Left click on CDCl3 on the solvent list.

You can watch the autolock in the lock window. It may be necessary to click on the lock

window or on the lock icon at the bottom of the screen in order to bring the lock window to

the front. The lock level line should climb until it reaches a steady height on the grid of the

lock window. Do NOT shim.

15. In the main window, type exit in the command line. Click OK on the pop-up window to

verify that you really do want to leave the program.

16. Under the Start tab at the bottom of the desktop, choose Log Off from the Windows session.

Verify that you indeed wish to Log Off Windows.

17. When you leave the NMR room, take your sample tube, printouts, and any other

belongings with you.

**Instructions for processing your spectrum start on p. 83.**

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Processing and Plotting Your NMR Spectrum Display summary – helpful tips:

The above shows the buttons for changing the display. Useful buttons include:

• This resets the horizontal display which is useful when the spectrum is outside the normal window or to return to the full spectrum after an expansion.

• Expansions: The easiest way to do horizontal expansions on the screen is to click the left mouse button and drag.

Calibrating the spectrum:

1. The spectrum that you see on the screen can be manipulated by left clicking on some of the

icons in the toolbar in the upper part of the main window. The icons give an indication of

what their functions are, and if you place the cursor on a particular icon, without clicking, a

brief description of that icon’s function is given.

2. The spectrum can also be manipulated by placing the cursor on the spectrum itself, causing a

vertical line cursor to appear. This is illustrated in the procedure for calibrating the spectrum

to a particular spectral line, described in this section.

3. Identify the peak or peak pattern to which the spectrum will be calibrated. For example, in

the 1H NMR spectrum of the Diels-Alder reaction diacid product, you will calibrate the

spectrum to the center line of the quintet from incompletely deuterated dimethyl sulfoxide

(DMSO-d6) that appears at 2.50 ppm.

4. Expand the reference peak. Move the mouse to place the cursor to the left of the reference

peak. Left click and drag to the right. A second vertical line cursor appears. Position it to

the right of the reference peak and release the mouse button. The area between the cursors is

displayed.

5. Left click on the “Spectrum calibration” icon on the top toolbar or type the command .cal

in the command line. This takes you into the calibration routine and generates a red vertical

cursor in the data window.

6. Move the cursor to the reference peak (the center line of the DMSO pentet, for example).

Left click. A pop-up window appears, showing the current frequency of the chosen spectral

line, in ppm. Type the appropriate value from the solvent reference table (2.50 for the

DMSO example) and click OK. This sets the reference.

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Integrating:

1. To integrate 1H NMR spectra (13C spectra are not integrated) start from the main window and

expand an appropriately sized region of the spectrum. Choose the size of the expansion so

that you will be able to integrate the various peak regions accurately. Left click on the

“Interactive integration” icon in the top toolbar or type .int in the command line. You

will now use the toolbar in the data window during the integration procedure.

2. To get rid of the automatically chosen integrals, click the “Select/Deselect all regions” icon

( ) then click the “Delete selected regions” icon ( ). Confirm that you really want to

delete the selected integrals.

3. Click the “Define new regions using cursor” icon . Left click and drag the cursor to

define each integral region.

4. Calibrate the integrals by setting one of the integral regions equal to the corresponding

number of protons. Place the cursor in the desired integral region. Right click and choose

Calibrate from the list. Enter the appropriate calibration value and click OK.

5. To leave the integration routine, click the “Terminate integration mode, save regions”

(save+return) icon or type .sret in the command line.

6. To display the integral regions on the spectrum in the data window, right click on the

spectrum and choose “Display Properties”. Select the “Integrals” and “Integral labels” check

boxes. Click OK. It is not necessary to display the integrals or integral labels on the

spectrum in order for them to print.

Peak picking:

1. Peak picking refers to creating a list of peak shifts to be printed. Display the full spectrum or

an expanded region, as appropriate.

2. Click the “Manual peak picking” icon in the top toolbar or type .pp in the command line.

You will now use the toolbar in the data window during the peak picking procedure.

3. In the toolbar in the data window, make sure define region is selected (it should be

shaded green). Left-click and drag to draw a green-shaded box in the spectral window

around the tops of the peaks you want to pick. Go to step #4 to modify this box.

4. Right click in the data window. Choose “Pick Peaks on Ranges” to pick the peaks within the

green shaded area.

5. To add a peak manually to the already listed ones, click and select peak with cursor and

left click.

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6. Click the “Terminate peak mode, save added peaks” icon (save+return) or type .sret in

the command line.

7. To display the integral regions on the spectrum in the data window, right click on the

spectrum and choose “Display Properties”. Select the “Peak labels” and “Integral labels”

check box. It is not necessary to display the peak labels on the spectrum in order for them to

print.

Title:

Click on the Title tab in the data window and edit as appropriate.

Plotting your spectrum:

1. Type cy in the command line. For a 1H full plot, set CY = 15. For 1H expansions try CY =

10. For 13C plots you may have to experiment a bit with the CY setting, but try starting with

CY = 10. CY is the size in centimeters of the biggest peak on the printed page. Sometimes,

particularly in 13C NMR, the largest peak will be due to the solvent, so you may need to adjust

the CY value in order to get the peaks for your compound to be appropriately sized.

2. Set the left and right plot limits. It is a very good idea to always plot a standard spectral

window for the full plot of your spectrum. For 1H, the region 10 to –0.5 ppm is a typical

choice. For 13C, use 220 to –20 ppm. In most cases, all peaks will be within these regions,

and using a standard plotting window will allow you to compare spectra easily. For some

spectra, (the 1H NMR of the Diels-Alder diacid product is an example), there will be a peak or

peaks outside this window, and you will have to plot a wider spectral window. To set the plot

limits, click on the “Exact zoom” icon (magnifying glass with “E”) in the top toolbar or type

.zx in the command line. A pop-up window will appear, allowing you to enter the display

range.

3. Click on the “Print active window” icon (printer) in the top toolbar or use Ctrl P from the

keyboard.

4. In the resulting window, select “Print with layout - start Plot Editor” and select a LAYOUT

from the drop down menu. For 1H full views use “+/NewHfull.xwp”. For 1H expansions use

“+/NewHexp.xwp”. For plotting 13C data use “+/NewCfullexp.xwp”. The 1H full view layout

is set up to show parameters, integrals, and peak frequencies (in ppm). The 1H expansion

layout is set up to show peak frequencies (in Hz) but not parameters or integrals. The 13C

layout shows parameters and peak frequencies. Select the “Use plot limits from screen/CY”

option. Click OK.

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5. The Topspin Plot Editor opens, showing the spectrum in its layout as it will be printed. It may

be necessary to click on the Topspin Plot Editor tab at the bottom of the screen to bring the

window to the front. For more about the Topspin Plot Editor including helpful tips, see #10

below.

6. In the Topspin Plot Editor window, click on the “Print” icon (printer) in the top toolbar or use

Ctrl P from the keyboard to send the layout to the printer.

7. Under the File menu at the top of the Topspin Plot Editor window, choose Exit to return to

your spectrum in the Topspin program.

8. To plot 1H expansions set CY = 10 as described in step 1 above. Next, expand the appropriate

region in the data window, then go to the print window as described in step 3 above and

continue as described in the subsequent steps.

9. To plot 13C expansions, you may find it useful to expand the appropriate region in the data

window, leaving CY set to the current value (i.e., CY = 10), then type plotexp in the

command line. This takes you to the Topspin Plot Editor, showing the expansion for printing

but leaving the peaks sized as they were in the full plot. The advantage to plotting the 13C data

in this way is that the relative sizes of the peaks are maintained in the expansions.

10. Topspin Plot Editor tips: To print using the plot editor, select File, Print. Select “Print with layout – start Plot Editor (plot)”. Choose LAYOUT +/1D_H.xwp. Click OK.

The Plot Editor is a very versatile graphic object editor. It allows several different spectra to be plotted on the same page, expansions to be plotted on the same page, and many other features. An important idea to remember about this editor is that it is only a display editor. All objects, i.e., integrals, peak lists, etc, must be defined from within the main Topspin program before you enter the Plot Editor. A picture of the left side of the interface is shown. The current “mode” is in the lower left corner. The mode controls the type of actions performed by the mouse. The mode is set by clicking on its icon. The most useful modes are:

• Spectrum mode – used to draw spectra and is always the first mode used,

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• Object Selector mode – used to edit already drawn spectra. Objects can be moved and resized and the spectra within them can be moved and expanded.

• Expand mode. This is just one way of making an expansion. By scrolling down with the left button you draw out a rectangle which defines the region to fill the object.

• Multi-spectra mode. This is one way to bring in several spectra and allows control of their alignment.

• Other useful modes include Title and Annotate (ABC), which is found by clicking on the Basic button.

Object selection and editing Each spectrum brought into the editor is considered an object. The object as well as the spectrum within it can be moved, resized, deleted, and edited. Set the mode to object selector. Then click within the drawn spectrum to edit it. Green dots should now surround this object. Using the left mouse button, the object can be resized. Using the middle mouse button, the object can be moved. These tasks are accomplished by placing the pointer on a green dot “handle”, depressing the mouse and dragging. Selected objects can be deleted by clicking on delete. To edit the spectrum within the object, while the green dots surround a spectrum, click on 1D-Edit. From here you can expand, or move the spectrum within the object. Expansions can be made in this way. This is also where integrals and pick peaking are turned on. Integrals and peak picking Integrals and peak peaking may automatically be displayed on start-up but if they are not, follow this procedure: To display integrals or peak peaks for a given spectrum, they are turned on within the 1D-EDIT editor. For peak peaking, however, an additional step is required before this step. Click on Topspin, then Topspin interface, and then create peak list. Integrals and peak peaking must be defined from within the main Topspin program prior to displaying them here. If you have forgotten to do these steps you do not need to exit from Plot Editor. You simply need to go back to the Topspin window to change them. Then within Plot Editor, under the Topspin tab at the top, select update data.