Juergen Schulte AM360/Tecmag NTNMR Manual 11/19/2021 BASIC OPERATIONS

Juergen Schulte AM360/Tecmag NTNMR Manual 11/19/2021 BASIC OPERATIONS

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Juergen Schulte AM360/Tecmag NTNMR Manual 11/19/2021
BASIC OPERATIONS
================
(Newest manual at:
http://chemiris.chem.binghamton.edu/staff/schulte/AM-Tecmag-Manual.doc
Processing software:
http://chemiris.chem.binghamton.edu/staff/schulte/ntnmr.exe
Alternative:
http://chemiris.chem.binghamton.edu/staff/schulte/MestreC.exe )
A.I Locking and Shimming the Sample (on the console panel)
----------------------------------------------------------
1.
Log on and immediately launch NTNMR.
Click the OK button and switch back to the black Lock Display
window.
2.
Remove the cap from the magnet, press the orange button and then
the “Lift” button.
3.
Remove the standard sample tube and replace it with your own
cleaned sample tube.
Press the “Lift Off” button to lower your sample into the magnet.
Wait until the sample
spins at 10-20 Hz and keep the temperature at 300 K during the
experiment. Cap the magnet.
4.
Set the “LOCK POWER” and the “FIELD” to the proper values for your
solvent:
Solvent
LOCK POWER
FIELD
Solvent
LOCK POWER
FIELD
acetone-d6
25*
550
methanol-d4
30*
640
acetonitrile-d3
30*
560
pyridine-d5
30*
950
benzene-d6
25*
900
TFA-d
45*
1200
CDCl3
40*
900
THF-d8
40*
500
CD2Cl2
35*
750
toluene-d8
30*
900
DMSO-d6
25*
550
water-d2
30*
700
* For concentrated samples only (more than 10 % or more than 100 mg of
sample):
Raise the LOCK POWER setting by 5 to 10 units.
5.
R efine the “FIELD” until you can cleary see the
lock ringing signal.
If you use two solvents, try both FIELD settings and use the
stronger signal.
6.
S et the “LOCK
PHASE” to 250, then press the “AUTO LOCK” button and wait until
its diode and the “LOCK GAIN” diode have stopped flashing.
This may take anywhere from a few seconds to several minutes.
Now the lock signal should look like this:
Choose between automatic or manual shimming (see next page).
A.Ia Manual Shimming of the Sample (using the black lock window and
the wheel)
-------------------------------------------------------------------
1.
Is the lock signal off screen? Decrease “LOCK GAIN” until you can
see it. (Minimum is 22).
Is the lock signal still too high? Decrease the “LOCK POWER” until
you can see it.
Is the lock signal too noisy? Increase the “LOCK POWER” and
decrease the “LOCK GAIN”.
2.
Adjust the “LOCK PHASE” to raise the position of the lock signal
on the screen.
The lock signal may go off the screen. That’s fine, just decrease
the LOCK POWER or LOCK GAIN to let it reappear and then continue
improving the LOCK PHASE.
3.
Adjust the “Z” and “Z2” shims individually to achieve the highest
position for the lock signal.
Again, use LOCK POWER or LOCK GAIN to bring back the signal, if it
disappears off screen.
4.
Continue refining “Z” and “Z2” several times until there is no
further improvement.
5.
Press the “STDBY” button to deactivate the wheel. You can run your
experiments now.
(You may be able to improve the shims by trying automated
shimming.)
A.Ib Automated Shimming
-----------------------
1.
Switch to the NTNMR program and open the file “1 - AdjustShims.tnt”.
2.
Click the Console Toolbar button (button #3) and make sure the
shims section is displayed.
In the Coarse Shims section check only the Z1 and Z2 boxes. All
others must remain unchecked.
You may change the Z1 and Z2 values, if you remember good settings
from previous samples.
In the Shim Parameters section set:
Delay: 2s Step: 10 Target: 0.01
3.
Click on the green ZG button. This will run one single scan (3
seconds).
If the FID is more than 1 cm high, select FID Shim.
If the FID is less than 1 cm high, select Lock Shim.
4.
Click “Read” and then “Start” at the bottom of the window to start
automatic shimming.
This procedure will maximize the signal strength by improving the
Z1 and Z2 shims.
The computer may take several minutes to complete shimming your
sample.
The “Start” button will be off (grey) while shimming. It will come
on (black) when finished.
Don’t do anything else while shimming is in progress! Don’t open
any spectra or programs!
After shimming is finished turn off the console toolbar (button
#3) and run your experiments.
For overnight 13C experiments only: Press “AUTO SHIM”, “Z”, “Z2”, “AUTO
SHIM”.
Do not do this for 1H NMR. It will broaden your peaks and may wipe out
small H,H-couplings.
A.II Routine 1H and 13C Experiments
-----------------------------------
1.
Click File | Open or press Ctrl-O
and select the desired parameter file from the directory
C:\NTNMR\data:
Proton NMR parameters: “1H – solvent.tnt” or “1 – Proton”
Carbon NMR parameters: “13C – solvent.tnt”
2.
Click on “File | Save as “ (not “Save”!!!!), then move to your
research group’s subdirectory.
Type a NEW filename including your lab notebook page number.
This file will later be used to store your spectrum. NEVER OVERWRITE
ANY OLD FILES!
Don’t save your files directly to a flash drive. Copy them later.
3.
Click the first button on the toolbar and type the sample name in
the comment box.
4.
Click the second button on the toolbar or select “View | Dashboard
“ to change parameter settings.
For dilute samples increase the setting for “Scans 1D”
(Acquisition). Use multiples of 8 !!!
For very concentrated samples (>100 mg) set the “Receiver Gain” to
“1” (Hardware tab).
5.
Click on the green ZG button or press Ctrl-Z to start the
data acquisition.
The button will display a real-time view of the spectrum.
This will allow you to see, whether the sample is very dilute
(increase Scans1D)
or too concentrated (If the baseline is distorted, reduce the
Receiver Gain to “1”).
The status bar at the bottom will indicate the progress of the
experiment. Let the scans finish, or:
When the signal-to-noise is sufficient, you can stop the
experiment with the yellow stop button.
If you run an overnight experiment, leave a note with instructions
for stopping and saving the data.
6.
Press Ctrl-S. Only this step will save your data.
7.
Create a new file with ”File | Save as” and add the word
“processed” to the current filename.
Use only this file for processing. You can simply “Save” after
each of the next processing steps.
8.
Press Ctrl-B to correct the baseline.
9.
13C only: press Ctrl-E for an exponential multiplication. (also
for 1H of extremely dilute samples)
10.
1H only: Use “Commands | Zero Fill Commands | Zero Fill” to
improve the resolution.
11.
All data: Press Ctrl-F to Fourier-transform the data and Ctrl-H
for an automatic phase correction.
12.
Perform a manual phase correction (if needed):
Select “Option | Phase Adjustment ”, click on the strongest peak
and click the Set Pivot button.
Use the “Phase 0” slider to adjust the phase of the signal at the
pivot point.
Use “Phase 1” to adjust the other signals in the spectrum.
If you reach the end of the range for either slider, click the
Apply button below the sliders and continue adjusting the phase.
Finally, click the other Apply button at the bottom when finished.
13.
O nly after the phase correction is perfect
try a manual baseline correction:
(only necessary if the baseline isn’t flat)
Display the complete spectrum and use the arrow keys to increase
the baseline to ½ inch.
Select “Option | Baseline Fix ” and click the ”Auto” and “Calculate”
buttons.
Match the curvature of the baseline as closely as possible by
moving the boxes.
Add baseline points with the right mouse button if necessary.
Click “Apply”.
14.
Change the appearance of the ppm scale (This is only a
one-time-adjustment for a PC):
Double-click on the ppm scale below the spectrum to bring up the
Axis Setup window.
My recommended settings in the “Tick Marks” box are: 1, 5 and 1.
Uncheck “Show Grid” and check “Adjust Ticks on Zoom”. Set “Units”
to “ppm”.
15.
Z oom functions:
You can rescale the signal intensities with the “Fit To Window”
button.
Double-click on the mini-spectrum on the top to return to the full
width.
The Up and Down arrow keys on the keyboard adjust the vertical
size of the spectrum.
You can zoom into the spectrum with a click-and-drag operation of
the mouse.
16.
Calibration of the chemical shift reference (use the solvent
signal or TMS, if present):
Expand the reference signal as much as possible and then
left-click on its central peak.
Right-Click anywhere in the spectrum and select Processing | Set
Reference.
Select ppm units and enter the correct reference value. Click OK
when done.
17.
Peak picking
Select Option | Peak Pick.
You can adjust the height of the black horizontal bar that will
appear.
All peaks that exceed the threshold of the black area will be
picked.
Click on Apply when done. The program will only number the peaks
at this point.
Zoom into the spectrum and delete or add peaks. Click Exit when
you are done.
Later, before you print, you can decide what the labels should be
(i.e. ppm).
18.
Integration
Select Option | Integrals.
First, display the complete spectrum and click on Remove to erase
any pre-existing integrals.
Highlight the first signal you wish to integrate. Make sure that
you select a wide enough region
(3-4 times the signal width) to measure accurate integrals. Expand
regions as needed.
Right-click inside the highlighted area and select Add Integral.
Repeat for other peaks.
Click on the Zero All button on the left panel.
Double-click on one of the integrals. (You should know how many
protons it corresponds to.)
You can change the Active Integral to select the integral you wish
to normalize.
Set the Assigned value to the desired value. Click Apply and then
Close.
In the left panel change the labels to Assigned Value and Exit
when done.
19.
Select Option | Amplitude Adjustment to define the width of the
print region (F1 and F2).
Print each 1H spectrum from 10 to -0.5 ppm, 13C from 210 to -10.
Print expansions if necessary.
(Your group may have different requirements for the printing
ranges.)
20.
Use the File | Print Layout dialogue to select and modify the
settings for the printout.
Uncheck Parameters, Line Fit, Print Frame, and Logo. Select an
appropriate Pen Width.
Check Integrals and under Settings check Show Value. Use the same
pen width as above.
Check Peak Picks and under Settings set Precision to 2 or 3 and
select Label by chemical shift.
Grab the ppm scale and drag it to the bottom of the red box.
The print screen key on the keyboard will export the complete
screen to the clipboard. (Reports!)
Click on the printer icon to print out the spectrum. Only exit
after printing!
B. Special 1D experiments:
--------------------------
B.I 13C DEPT-45-90-135 to determine CH multiplicities.
------------------------------------------------------
This experiment will record 3 13C spectra:
#1 (DEPT-45) will have CH3, CH2, and CH peaks positive
#2 (DEPT-90) will have only CH peaks
#3 (DEPT-135) will have CH2 negative and CH3 and CH positive.
Often times the DEPT-135 or the PENDANT experiments are sufficient,
see experiments B.II and B.III on the next page.
-------------------------------------------------------------------
1.
Press Ctrl – O and open the file “DEPT-45-90-135.tnt”.
2.
Open the dashboard and set “Scans1D” to any multiple of 32.
(The experiment cannot be interrupted. Use the exact number of
scans!
32 scans will take approx. 8 minutes, 160 scans = 40 minutes.)
3.
In the frequency section of the dashboard: The F1 Offset Freq. for
your solvent is:
D2O: 6 kHz; Acetone, Acetonitrile, DMSO, Methanol, THF: 7.3 kHz
Chloroform, Benzene, Methylene Chloride, Pyridine: 5.5 kHz
4.
Use “File | Save as” to define the filename in your data
directory.
5.
Start the experiment with Ctrl – Z.
6.
Press Ctrl – S to save the data after the third experiment has
finished.
7.
Processing:
Ctrl – B, Ctrl – E, Ctrl – F, Ctrl – H to process the data on the
screen.
If a manual phase adjustment is needed, use Option – Phase
Adjustment.
Calibrate the spectrum using a known signal from your C-13
spectrum.
Click File – Revert to Saved.
Hold down the shift key and click the NDFT button.
Check the boxes:
Use 1D Settings, Baseline Correction, Fourier Transform,
Use System Phase, Apodization: Exponential, LB: 2
Uncheck every box under the 2D heading.
Click Do It.
8.
Viewing: Your toolbar should show you a few additional fields:
You can select the 2D trace (= the individual DEPT spectrum) you
wish to see.
9.
Printing: Turn off the grid under the View menu.
Zoom into the spectrum to expand the region you want to print.
Adjust the height of the signals.
Go to File | Print Layout and pull down the top edge of the
spectrum to 1/3 its original height.
Use Ctrl – Tab to return to the spectrum and switch to the second
trace.
Go to File | Add to Print Layout and align the two spectra.
Resize, if necessary.
Use Ctrl – Tab to return to the spectrum and switch to the third
trace.
Go to File | Add to Print Layout and align the three spectra.
Resize, if necessary.
Remove the axes and everything else you don’t want for the two top
spectra.
10.
Click the Print button.
B.II 13C DEPT-135 (negative CH2 peaks, CH3 and CH positive, no quat.
C)
--------------------------------------------------------------------
1.
Press Ctrl – O and open the file “DEPT.tnt”.
2.
Open the dashboard and set “Scans1D” to any multiple of 32.
(The experiment cannot be interrupted. Use the exact number of
scans you need!
32 scans will take approx. 2 minutes – approx. 1000 scans per
hour.)
3.
Use “File | Save as” to define the filename in your data
directory.
4.
Start the experiment with Ctrl – Z.
5.
Press Ctrl – S to save the data after the experiment has finished.
6.
Processing just like for normal C-13 spectra.
(Phasing: Remember that CH2 signals are negative, CH and CH3
signals positive.)
B.III 13C Pendant (same as DEPT135, additionally quat. Carbons will be
negative)
----------------------------------------------------------------------
1.
Press Ctrl – O and open the file “Pendant.tnt”.
2.
Open the dashboard and set “Scans1D” to any multiple of 32.
(The experiment cannot be interrupted. Use the exact number of
scans you need!
32 scans will take approx. 2 minutes – approx. 1000 scans per
hour.)
3.
Use “File | Save as” to define the filename in your data
directory.
4.
Start the experiment with Ctrl – Z.
5.
Press Ctrl – S to save the data after the experiment has finished.
6.
Processing just like for normal C-13 spectra.
(Phasing: Remember that Cq and CH2 signals are negative, CH and CH3
signals positive.
The solvent signal will also be negative, TMS - if present - will
be positive.)
B.IVa 13C Gated Decoupling (allows measurement of C,H coupling
constants)
--------------------------------------------------------------
1.
Press Ctrl – O and open the file “Gated Decoupling.tnt”.
2.
Open the dashboard and set “Scans1D” to any multiple of 8.
(The experiment needs at least as many scans as the regular C-13
experiment.)
3.
Use “File | Save as” to define the filename in your data
directory.
4.
Start the experiment with Ctrl – Z.
(If you try to stop the experiment, it may continue to run for
several minutes! Don’t panic!)
5.
Press Ctrl – S to save the data after the experiment has finished.
6.
Processing just like for normal C-13 spectra.
B.IVb 13C Inverse Gated Decoupling (allows integration of 13C signals)
----------------------------------------------------------------------
1.
This is an overnight experiment and requires a very concentrated
sample.
2.
Press Ctrl – O and open the file “InverseGatedDecoupling-C-13.tnt”.
3.
Open the dashboard and set “Scans1D” to any multiple of 8.
Set the “Last Delay” to “30s”.
4.
Use “File | Save as” to define the filename in your data
directory.
5.
Start the experiment with Ctrl – Z.
6.
Press Ctrl – S to save the data after the experiment has finished.
7.
Processing just like for normal C-13 spectra.
Water signal suppression
------------------------
B.V 1H NOE Difference Measurements for one Proton
-------------------------------------------------
Finding the signals for irradiation:
1.
Shim your sample using Z and Z2, then turn off sample spinning!
(VERY IMPORTANT!)
2.
Shim your sample using X and Y. Keep the spin off during the whole
experiment.
3.
Read the 1H parameter file for your solvent.
4.
Open the Dashboard, click on the Frequency tab, and write down the
“F1 Offset Freq.”
Set the “F2 Offset Freq.” to zero. Keep the dashboard open.
5.
Start ZG to get your initial proton spectrum.
6.
Process with: Ctrl-B, Ctrl-F, Ctrl-H. No need for perfect phasing.
7.
First, click the mouse pointer on a point in the spectrum where
there are no signals (~15 ppm).
Select Scripts | Acquisition Scripts | Set Dec. Freq.
If the F2 Offset Freq. is still “0.000… kHz”, restart from step 3.
Write down the value of the new “F2 Offset Freq.” from the
dashboard.
8.
Then, click the mouse pointer on the signal which you want to
irradiate.
There should be no other signals within ½ ppm.
Select Scripts | Acquisition Scripts | Set Dec. Freq.
Write down the value of the new “F2 Offset Freq.” from the dashboard.
Setting up and starting the NOE experiment:
9.
Open the File: “NOE Difference for one proton.tnt”
10.
Enter the “F1 Offset Freq.” that you found in step 2.
11.
O n the
Dashboard, set the “F2 Offset Freq.” to zero.
Set “Scans1D” to the desired number of scans (should be several
hundred).
(800 scans will take approx. two hours.)
12.
C
lick on the Pulse Sequence icon to open the pulse
sequence editor.
In the line O2: right-click on the red icon to open the frequency
table.
Enter both frequency values you wrote down into the table.
13.
Close the pulse sequence editor.
14.
Define a filename (File | Save As).
15.
Start the experiment with: ZG.
Don’t forget to save the data again after the experiment has
finished.
Processing and evaluation:
16.
Ctrl-B, Ctrl-E, Ctrl-F, Ctrl-H
Correct the phase to make the irradiated signal negative and the
NOE signals positive.
Integrate the NOE signals and the negative reference peak, set the
reference integral to “-100”.
The integrals show directly the NOE enhancements in percent.
17.
Print using the Print Layout.
Print using the same ppm range as for the corresponding proton
spectrum.
B.VI 1H NOE Difference Measurements for more than one Proton
This experiment generates one large file which has to be split into 4
or 8 pieces.
Therefore you have to define 4 or 8 frequencies (1 reference + 3 or 7
signals).
---------------------------------------------------------------------
1.
Shim your sample using Z and Z2, then turn off sample spinning!
(VERY IMPORTANT!)
2.
Shim your sample using X and Y. Keep the spin off during the whole
experiment.
3.
Read the 1H parameter file for your solvent.
4.
Open the Dashboard, click on the Frequency tab, and write down the
“F1 Offset Freq.”
5.
Open the file: “NOE Difference (CDCl3).tnt”
Enter the “F1 Offset Freq.” that you found in step 2.
6.
Start the Experiment to get your initial proton spectrum. Stop
after 8 scans.
7.
Process with: Ctrl-B, Ctrl-F, Ctrl-H
8.
First, click the mouse cursor on a point in the spectrum where
there are no signals.
Select Scripts | Acquisition Scripts | Set Dec. Freq.
Write down the value of the new “F2 Offset Freq.” from the
dashboard.
9.
Then, click the mouse cursor on a signal which you want to
irradiate.
Select Scripts | Acquisition Scripts | Set Dec. Freq.
Write down the value of the new “F2 Offset Freq.” from the
dashboard.
10.
Repeat step 7 for all peaks you want to irradiate.
You need either 3 or 7 additional frequencies for this experiment
to work.
11.
O n the
Dashboard, set the “F2 Offset Freq.” to zero.
Set “Points2D” to the number of frequencies that you have
selected.
Set “Scans1D” to the desired number of scans (should be several
hundred).
(800 scans will take approx. one hour per selected frequency.)
12.
C
lick on the Pulse Sequence icon to open the pulse
sequence editor.
In the line O2_2D: right-click on the red icon to open the
frequency table.
Enter all the frequency values you wrote down into the table (4 or
8).
(There have to be exactly as many entries in the table as you
specified in “Points2D”.)
13.
Close the pulse sequence editor, define a filename (File | Save As)
and start ZG.
Don’t forget to save the data again after the experiment has
finished.
14.
Processing: Open the data file.
15.
Select Scripts | Processing Scripts | 2D to 1D and convert the
data.
16.
Extract the single FIDs by using Commands | Data Manipulation |
Read First Half
and/or Commands | Data Manipulation | Read Second Half
combinations.
(i.e. for 4 spectra: #1 is first,first, #2 is first,second, #3 is
second,first, #4 is second,second)
Save each segment separately using unique filenames.
17.
Reference spectrum: Read, process and print the reference spectrum
(#1) first.
Generation of difference spectra: First, close all open spectrum
windows!!!!!
Select Scripts | Processing Scripts | AddSubtract and select the
files that you want to subtract. Make sure the Subtract button is
activated. File2 always has to be the reference FID.
After finishing the subtraction use Ctrl-Tab to find the
difference FID (smallest amplitude)
and process it using Ctrl-B, Ctrl-E, Ctrl-F, Ctrl-J, Ctrl-B.
Integrate the NOE signals and the negative reference peak, set the
reference integral to “-100”.
Print using the same ppm range as for the reference spectrum.
The integrals show directly the NOE enhancements in percent.
B.VII T1 and T2 Relaxation Measurements
---------------------------------------
1.
Read the parameter file for your solvent.
2.
For proton experiments, write down the “F1 Offset Freq.” from the
dashboard.
3.
Open one of these files: T1-1H, T1-13C, T2-1H or T2-13C for the
experiment you want.
4.
For proton experiments, enter the “F1 Offset Freq.” from step 2.
5.
S et “Points2D”
to “10”.
Set “Scans1D” to the desired number of scans (should be very
small).
(1 scan will take approximately 2 (1H) or 4 (13C) minutes per
delay.)
6.
C
lick on the Pulse Sequence icon to open the pulse
sequence editor.
(T1) In the line Delay_2D: right-click on the red icon to open the
list.
(T2) In the line Loop_2D: right-click on the red icon to open the
list.
Enter the following values into the table:
1H-T1: 0.01s 0.1s 0.5s 1s 1.5s 2s 4s 10s 25s 60s
13C-T1: 0.01s 1s 3s 5s 8s 12s 15s 30s 60s 120s
13C and 1H-T2: 2 20 50 100 200 300 400 500 750 1000
(There have to be exactly as many entries in the table as you
specified in “Points2D”.)
7.
Close the pulse sequence editor, define a filename (File | Save
As) and start ZG.
Don’t forget to save the data again after the experiment has
finished.
8.
Processing: Open the data file and process it as usual.
For the T1 experiments correct the phase until all peaks are
negative.
For the T2 experiments correct the phase until all peaks are
positive.
Then click on File | Revert to Saved.
9.
Hold down the Shift key and click on the NDFT button to open the
processing dialogue.
10.
U nder the 1D tab check: Use 1D settings, Baseline
correction, Fourier Transform, and
Use System Phasing. Apodization: Exponential with LB: 0.5 for 1H
and 4 for 13C.
Click on Do It when done.
11.
C lick on the 2D display
button (sixth button from left).
12.
R ight-Click anywhere in the spectrum, select Data
Type | Real
13.
Set Mode to Stack Plot and adjust the levels to see all spectra.
Grab and move the edges and corners of the frame to define the
appearance of the spectra.
Change the amplitude of the spectra as desired.
14.
Select File | Add To Print Layout and define the printout
settings.
B.VIII Pulse Width Determination:
---------------------------------
1.
Read the parameter file for your solvent. (Use a very concentrated
sample.)
2.
Record one scan and process with Ctrl-B, (Ctrl-E for C-13 only),
Ctrl-F, Ctrl-H.
Save the spectrum with File | Save as.
3.
Click the mouse cursor on a signal in the center of the spectrum.
Select Scripts | Acquisition Scripts | Set Obs. Freq.
4.
O pen the
Dashboard
Under Acquisition set Points2D to “25”. Set Scans1D to “1”.Set
Dummy Scans to “0”.
Under Sequence set h90 or p90 to “0u”. Set Last Delay to “60s”.
5.
C
lick on the Pulse Sequence icon to open the pulse
sequence editor.
In the Delay line: click on h90 or p90 and select 2D Table.
A new event line (Delay_2D) will appear at the bottom.
Right-click on the de0:2 item in that line. A delay table box will
open.
Select Auto and enter “2u” as increment value. Click OK.
6.
Close the pulse sequence editor, define a filename (File | Save
As) and start ZG.
Don’t forget to save the data again after the experiment has
finished.
7.
Processing: Open the data file and process it as usual. Manual
phase correction!!!
Then click on File | Revert to Saved.
8.
Hold down the Shift key and click on the NDFT button to open the
processing dialogue.
9.
U nder the 1D tab check: Use 1D settings, Baseline
correction, Fourier Transform, and
Use System Phasing. Apodization: Exponential with LB: 0.5 for 1H
and 4 for 13C.
Click on Do It when done.
10.
C lick on the 2D display
button (sixth button from left).
11.
R ight-Click anywhere in the spectrum, select Data
Type | Real
12.
Set Mode to Stack Plot and adjust the levels to see all spectra.
Grab and move the edges and corners of the frame to define the
appearance of the spectra.
Change the amplitude of the spectra as desired.
Double-Click on the ppm scale and turn it off.
13.
Select File | Add To Print Layout and define the printout
settings.
B. IX Decoupling Experiments (for CHEM 485f/585f only)
------------------------------------------------------
1.
Press Ctrl-O or click File | Open
and select the desired 13C parameter file from the directory
C:\NTNMR\data:
Carbon NMR parameters: “13C – solvent.tnt”
2.
Open the Pulse Sequence Window and the Parameter Dashboard.
Under “Acquisition” set “SCANS_1D” to “8”. Under “Sequence” set
“Last Delay” to “5”.
The following parameters have been optimized for 80% ethylbenzene
in benzene-d6:
a.
High Power CPD Decoupling: Under “Hardware” set “Dec. Attn.”
to “116”.
Insert “DEC_RF” pulses in every column.
Insert and continue “Async Table” phases in the “DEC_PH”
line for all columns, beginning with the second column.
b.
High Power BB Decoupling: Under “Hardware” set “Dec. Attn.” to
“116”.
Remove all phases from the “DEC_PH” line.
Insert “BB_MOD” pulses in every column.
c.
Low Power BB Decoupling: Under “Hardware” set “Dec. Attn.” to
“140”.
Remove all phases from the “DEC_PH” line.
Insert “BB_MOD” pulses in every column.
d.
Off-Resonance CW Decoupling: Under “Hardware” set “Dec. Attn.”
to “116”.
Remove all pulses from the “BB_MOD” line.
Remove all phases from the “DEC_PH” line.
Insert “DEC_RF” pulses in every column.
Run off-resonance experiments for each of the following five “F2
Offset Freq.” values:
4.408 kHz (CH3 on resonance), 4.889 kHz (CH2 on resonance),
6.566 kHz (aromatic H’s on resonance), 10 kHz, 20 kHz.
3.
Press Ctrl-Z or click on the ZG button to start the data
acquisition.
(Wait for the experiment to finish. The counter on the bottom
right will indicate the progress.)
4.
Click on “File | Save as “ (not “Save”!!!!), then move to your
group’s subdirectory,
and select a NEW filename which you want to use to store your
spectrum.
NEVER OVERWRITE ANY OLD FILES!
5.
Repeat from Step 2 to perform the rest of the experiments in a
similar manner.
6.
Processing can be done offline on any computer with processing
software.
Process as any C-13 spectrum.
Print spectra 2a and 2b with a ppm scale and ppm peak picking.
Print all other spectra with a Hz scale and Hz peak picking.
B. X Water Signal Suppression
-----------------------------
1.
Press Ctrl-O or click File | Open
and select “solvent suppression.tnt”
2.
Click on “File | Save as “ (not “Save”!!!!), then move to your
group’s subdirectory,
and select a NEW filename which you want to use to store your
spectrum.
NEVER OVERWRITE ANY OLD FILES!
3.
Open the Parameter Dashboard.
Under “Acquisition” set “SCANS_1D” to any multiple of 8.
4.
Start ZG to get your initial proton spectrum.
5.
Immediately stop the experiment with the yellow stop button and
wait for the scans to finish.
6.
Process with: Ctrl-B, Ctrl-F, Ctrl-H. No need for perfect phasing.
7.
If the water signal is still very strong, click on it.
8.
Select Scripts | Acquisition Scripts | Set Dec. Freq.
9.
Click on the green ZG button or press Ctrl-Z to start the
data acquisition again.
The button will display a real-time view of the spectrum.
This will allow you to see, whether the solvent signal (HDO) has
been suppressed.
If it is still too strong, the “F2 Offset Frequency” needs to be
adjusted again from step 5.
10.
Press Ctrl-S to save your data.
11.
Create a new file with ”File | Save as” and add the word
“processed” to the current filename.
12.
This FID can be processed like any other proton spectrum.
C. Special 2D experiments: (Additional training is needed for your
first sample!)
==================================================================
C.I COSY / NOESY (Durations with default settings: approx. 1 hour / 10
hours)
----------------------------------------------------------------------
1.
Press Ctrl – O and open a Proton NMR file.
2.
Record a proton spectrum, Fourier-transform, calibrate and save it
(Ctrl – S).
3.
Display the complete spectrum on the screen.
Are there any signals above 9 ppm or below -1 ppm? (This is
important for step 5!)
4.
Press Ctrl – O and open the file “COSY.tnt” or “NOESY.tnt”.
Use “File | Save as” to define the filename in your data
directory.
5.
Select: View | Dashboard and select the Acquisition tab.
Make Points1D and Acq.Points both 1024.
Make Points2D = 512 and Scans1D = 8 (for NOESY use 32).
If there were any signals above 9 ppm or below -1 ppm in your
proton spectrum
you will have to increase SW+/- and SW2D by 0.7 kHz for every
additional ppm.
6.
Switch to the Frequency tab.
7.
Make F1 Base Freq. and F2 Base Freq. both 360.13.
Each solvent needs its own values in the F1 Offset Freq. and the
F2 Offset Freq. fields:
(incorrect settings will lead to undesireable folding effects!!)
Acetone: 7.3 kHz Methylene Chloride: 6.1 kHz
Acetonitrile: 7.6 kHz Pyridine: 5.4 kHz
Benzene: 5.5 kHz Trifluoro acetic acid: 4.7 kHz
Chloroform: 5.5 kHz Tetrahydrofuran: 6.7 kHz
DMSO: 7.1 kHz Toluene: 5.4 kHz
Methanol: 7.0 kHz Deuterium oxide: 6.3 kHz
8.
Shut off sample spinning if you want to run a NOESY experiment.
9.
Start the experiment by clicking the ZG button.
Check the duration of the experiment on the status line at the
bottom of the window.
If it takes too long, press the red Stop button and decrease
Points1D, Points2D and Acq.Points. (Try half the previous settings
for each of the three parameters.)
If you have a dilute sample, increase Scans1D (multiples of 8).
RESTART ZG.
Don’t forget to save the experiment again after it has completed.
(Ctrl – S)
10.
Continue with 2D Processing (page 14).
C.II HETCOR (= HSQC, Duration with default settings approx. 1.5 hours)
HETCOR – long range (= HMBC, default settings approx. 10 hours)
----------------------------------------------------------------------
1.
Press Ctrl – O and open a Proton parameter file.
2.
Record a proton spectrum, and process: Ctrl – B, Ctrl – F, Ctrl –
H, calibrate and save it.
3.
Display the complete spectrum on the screen.
Are there any signals above 9 ppm or below -1 ppm? (This is
important for step 8!)
4.
Press Ctrl – O and open a Carbon-13 parameter file.
5.
Record a C-13 spectrum, Ctrl – B, Ctrl – E, Ctrl – F, Ctrl – H,
calibrate and save it.
6.
Press Ctrl – O and open the file “HETCOR.tnt”, if you just want to
see direct connectivities.
Choose “HETCOR-long range.tnt” instead, if you just are interested
in long range couplings.
Use “File | Save as” to define the filename in your data
directory.
7.
Select: View | Dashboard and select the Acquisition tab.
Scans1D should be 32 for a normal HETCOR and 196 for a long range
HETCOR.
By default, Points1D and Acq.Points are both 2048, and Points2D is
128.
These parameters determine the resolution and the duration of the
experiments.
8.
If there were any CH proton signals above 9 ppm or below -1 ppm in
your proton spectrum
you will have to increase SW2D by 0.7 kHz for every additional ppm
to avoid folding effects.
OH and NH proton signals may be ignored!
9.
Switch to the Frequency tab.
Make the F1 Base Freq. = 90.56 and the F2 Base Freq. = 360.13.
Leave F1 Offset Freq. alone.
To avoid folding set the F2 Offset Freq. value according to your
choice of solvent:
Acetone: 7.3 kHz Methylene Chloride: 6.1 kHz
Acetonitrile: 7.6 kHz Pyridine: 5.4 kHz
Benzene: 5.5 kHz Trifluoro acetic acid: 4.7 kHz
Chloroform: 5.5 kHz Tetrahydrofuran: 6.7 kHz
DMSO: 7.1 kHz Toluene: 5.4 kHz
Methanol: 7.0 kHz Deuterium oxide: 6.3 kHz
10.
Start the experiment by clicking the ZG button.
Check the duration of the experiment on the status line at the
bottom of the window.
If it takes too long, press the red Stop button and decrease
Points2D.
(Try half the previous settings.)
If you have reserved more time, increase Scans1D (multiples of
32).
11.
Don’t forget to save the experiment again after it has completed.
(Ctrl – S)
12.
Continue with 2D Processing (page 14).
Processing 2D spectra:
----------------------
1.
First we have to process the reference spectra that you have
recorded earlier:
Open the proton (and in the case of HETCOR also the carbon)
reference spectrum and process them exactly the way you would
usually do (proper phasing and calibration is required).
2.
Find a proton and a carbon signal that you know well and write
down their chemical shifts.
These numbers are needed to calibrate the 2D spectra.
3.
Now you can open the 2-dimensional data file. Only the first trace
will be displayed.
If a ppm axis appears instead of a time axis, advance to the last
2D trace and press Ctrl-F.
4.
Hold down the Shift key and click on the NDFT button to open the
processing dialogue.
5.
Under the 1D tab check only: Use 1D settings and Fourier
Transform.
6.
Under the 2D tab check only: Use 2D settings, Zero Fill, and
Fourier Transform.
7.
Apodization:
For a COSY/NOESY in 1D and 2D choose Sin Bell with 30 for SB Shift
and 1 for SB Skew.
Set SB Width equal to the Points1D and Points2D values (listed
above the spectrum).
For HETCOR use Exponential with LB=5 in dimension 1 and LB=3 in
dimension 2.
8.
Click Do It when all parameters are correct.
9.
S elect File | Save
As and save the processed data with a different filename.
(Suggestion: add a “P” to the filename.) Do not overwrite the
original data file!
Should anything go wrong during processing, you can recover by
rerepeating from step 3.
If you prefer, you can open this file with the ACD-NMR program
now.
It provides much better display and printing options than NTNMR.
Otherwise just proceed from here.
10.
H old down the Shift key and click on the 2D
display button.
Select Magnitude and Contours, and select the appropriate aspect
ratio:
Square for COSY/NOESY or None for HETCOR. Press Apply.
Select the Color: B/W and adjust the intensities by selecting
suitable Start and End levels.
Try to mazimize the signals and to minimize the noise.
11.
If a symmetrization is needed for your COSY or NOESY spectrum (not
for HETCOR!!!):
Select Commands | Symmetrize | Right to left, Low value.
12.
COSY/NOESY only: Right-click on the spectrum and select Reverse
Data | Vertical.
Adjust the Levels again to minimize the noise and to mazimize the
signals.
13.
Double-click the horizontal axis at the bottom to open the 2D Axis
Setup dialogue.
The Tick Marks settings should be: 1, 5, and 1. Check “Adjust
Ticks on Zoom”.
Switch to the vertical section by clicking the tab at the top and
use the same settings.
HETCOR only: Change the vertical spectral width to the same value
as in step 9.
14.
Right-click the diagonal peak or crosspeak that corresponds to the
peaks selected in step 1.
Select Set Reference and click the “Enable Units to Frequency
Domain” button, if present.
Then select ppm as units and enter the correct chemical shifts in
both dimensions.
15.
Right-click in the spectrum and select Reset View.
Select your region of interest and expand it using View | Zoom
Toolbar.
First change the units to “ppm”, then enter the desired limits and
click “Apply”.
Did the signals disappear? Sometimes the proton limits have to be
entered as negative numbers.
Printing 2D spectra:
--------------------
NTNMR’s Print Layout is extremely difficult to use with 2D spectra.
Here is a better way to print:
1.
Stay in the 2D display and select Window | Cascade.
2.
Move the mouse pointer out of the spectrum to remove the
crosshairs.
3.
Press the keyboard’s Print Screen key to copy the full screen to
the clipboard.
4.
Start Microsoft Paint or use your favorite picture editing
software.
5.
Paste the clipboard image into Paint (Ctrl-V).
6.
Activate the Select function and use the mouse to cut out the
spectrum with its axes.
7.
Press Ctrl-C, then Ctrl-N, and then N. Enlarge the white area as
much as possible.
8.
Press Ctrl-V to paste the 2D spectrum into Paint.
9.
Move the 2D spectrum to have 2 inches free space on the top and on
the left side.
10.
Use File | Save As to save the image. (Monochrome Bitmap is
sufficient.)
11.
Switch back to NTNMR and display the proton spectrum or the carbon
spectrum.
Use Option | Amplitude Adjustment to expand exactly the same range
as you did in the 2D.
Adjust the height to maximize the important signals without
cutting them off.
12.
Shrink its window until the spectrum spans the same width as the
2D spectrum.
Remember: In a HETCOR the proton axis is vertical. The C-13 axis
is horizontal.
13.
Repeat from step 2.
14.
If you have a HETCOR you should have 3 bitmap files (the 2D, the 1H
and the 13C)
A COSY and NOESY will only have 2 files (the 2D and the 1H
projection)
15.
Finally, copy and paste the 2D spectrum and its 1D projections
together into one image.
The 1D projections have to fit into the spaces above and at the
left side (rotate) of the 2D.
Here is an example of how a HETCOR spectrum can be imported into a
document:

Emergency Shutdown
==================
1.
On the PC: Terminate any NMR Experiment:
(yellow or red STOP button in the NTNMR window)
2.
Save the data to disk (Ctrl-S)
3.
Press Ctrl – Alt – Del and select Shutdown to shut down the Dell
PC.
4.
Switch off the Tecmag box (behind the console, left)
5.
Pull the red “EMERGENCY” button on the front panel of the
console.
Don’t forget to turn off the other spectrometers in the NMR lab. Now
it it safe to leave.
Restart
=======
1.
Push the red EMERGENCY button back in.
2.
Go behind the console and switch the gray MAIN POWER RESET button
to the left position.
3.
If the console starts beeping continuously, the SCM under the
keyboard has to be reset.
follow the procedure on the printout on the console keyboard.
Set the suggested values for the SWEEP RATE and for the SWEEP
AMPL.
Make sure all the buttons labeled “ON” are really on.
4.
Switch on the Tecmag box (behind the console, left)
(Six red and five green lights should come on.)
5.
Switch on the Dell PC.
6.
After the bootup has finished you should let the spectrometer warm
up for at least 30 minutes before you start any experiments.
Important
When you are done with your session, please:
*
Insert the water/ethanol sample
*
Set the FIELD to 700 and the LOCK POWER to 35
*
Set Z to 1220 and Z2 to 360
*
Press the AUTO LOCK button
*
Shut down the NTNMR Program and log off
*
Sign the log book
*
Remove all your items
*
!!!!!!!!!!!!!!! CAP THE MAGNET !!!!!!!!!!!!!!!!!!
Thank You!
Startup Parameters for the AM360 NMR Spectrometer (old values, do not
use)
---------------------------------------------------------------------
| Only adjust these 3 settings: |
Settings on the Shim Panel
Proton NMR Parameters
Carbon-13 NMR Parameters
Solvent
FIELD
LOCK POWER
LOCK GAIN
F1 Freq. Offset
SR
F1 Freq. Offset
F2 Freq. Offset
SR
acetone-d6
4010
25*
22
7478
5858.0
5217
7478
-3840.5
acetonitrile-d3
4050
30*
22
7875
5900
5217
7475
-3838.4
benzene-d6
4360
25*
22
5624
4003.6
4786
5624
-4269.1
chloroform-d
4360
40*
22
5750
3986.6
5217
5750
-4239.0
DMSO-d6
4010
25*
22
7313
5692.7
5228
7313
-3827.3
methanol-d4
4100
30*
22
7200
5692.0
5200
7200
CD2Cl2
4250
30*
22
5600
3800
5300
5600
pyridine-d5
4500
30*
22
5624
4003.6
4786
5624
-4431.6
TFA -d
4800
45*
22
4663
2504
4223
4663
-4831.5
THF-d8
4020
40*
22
6927
5305
5228
6927
-3989
toluene-d8
4500
30*
22
5625
4004.4
4786
5625
water-d2
4170
30*
22
6529
4908.5
4975
6529
-4029.8
* For concentrated samples only (more than 10 % or more than 100 mg of
sample.):
Raise the LOCK POWER setting by 5 to 10 units
Sample Preparation:
1.    Choose an NMR solvent appropriate to your compound.
• Chloroform is the standard solvent to try first. Be aware that it
can be acidic.
• If your compound is not soluble in chloroform, try benzene (nonpolar
or average polarity compounds), acetone (dissolves almost anything),
DMSO or methanol (polar compounds).
2.    Find a clean, dry NMR tube.
• If your proton spectra consistently show a peak near 2.05 ppm, the
tube wasn’t dry enough.
(Traces of acetone may be present, even is the tube appears to be
dry!)
• After washing NMR tubes with acetone, lay the tubes flat on a layer
of paper towels in the oven for at least two hours at max. 50 °C
before using them again. A vacuum oven is preferred.
• Standing the tubes upright in a flask or beaker in an oven is not
recommended, as the tubes might warp or paramagnetic rust particles
might fall into the tubes.
• Compressed air contains mineral oils and is not recommended to dry
NMR tubes.
• Store clean NMR tubes uncapped, preferably laying down.
3.     Dissolve your sample.
• Make sure your sample is free of solvent; if your compound is not
volatile,
placing the flask on a high vacuum line for 5-30 minutes is a good
idea.  
• Measure the correct amount of sample into a vial.
• For a solid, use 10-20 mg for a routine 1H and 50-100 mg for a
routine 13C NMR.
You can use less, but your experiments will take longer.
• For an oil or liquid, dip a glass pipette into the liquid (one drop
is enough for 1H NMR).
• Dissolve the sample in 0.75 ml of the NMR solvent.
4.     De-gas your samples (for NOE or NOESY experiments).
• Use several “Freeze – Pump – Thaw” cycles to remove dissolved
oxygen.
• Easy alternative: bubble some N2 or Ar gas through your solution.
5. Put the solution into the NMR tube.
If any solid remains, filter the sample into the tube through a
pipette with a cotton plug.
6. Acquire your spectrum.
18