UVU401
DLO - 5Mar2013
U400 Checkout
This handout contains instructions on some of the most basic operations on the Unity 400 spectrometer
system. The purpose of this training/checkout is two-fold. 1) To provide you with the minimum, yet
sufficient, information and skills so that you are able to operate the spectrometer independently, safely, and with
acceptable efficiency, and 2) provide you with enough information to collect meaningful data. There is much
more to be learned, however, if one is to make full use of any NMR spectrometer.
During your training on the U400,
1. Your trainer (NMR Liaison) must be present at all times.
2. Ask as many questions as possible; think about what you are doing.
3. No practice on research samples is allowed.
4. Complete at least two separate training sessions where each session includes basic procedures and
especially: use of ResLog, sample entry, locking, and shimming.
During the checkout, you are expected to
1. Observe operational procedures, such as changing samples, locking and shimming, login and logoff, etc.;
2. Understand what you are doing and why you are doing it, such as the use of load, gain, su, etc.;
3. Understand the setting and consequences of key parameters, such as np/fn, at, sw, nt, d1, pw, lb, etc.;
4. Generate a complete set of spectra in two hours.
After training by the NMR Liaison, the staff will discuss:
1. Procedures for dealing with broken glass, in general, and broken NMR tubes, in particular.
2. Any questions that you may still have and/or show you any techniques that you might need in the immediate
future which are not covered in the training/checkout, such as data backup, locking on an unusual solvent,
shimming on the FID, and so on.
The following handouts deal with individual topics covered in this checkout in much more detail:
1. UVU405 — Sample Preparation, Positioning, and Insertion
2. UVU407 — Locking
3. UVU409 — Shimming
4. UVU430 — Abbreviated Command and Parameter List
FINALLY, PLEASE FOLLOW A FEW SIMPLE HOUSE RULES:
1. OBSERVE ALL OPERATIONAL PROCEDURES CAREFULLY.
2. IF THERE IS SOMETHING THAT YOU DON'T KNOW OR ARE NOT SURE ABOUT, PLEASE ASK.
3. USE COMMON SENSE AND DON'T RUSH -- THIS WILL GO A LONG WAY IN AVOIDING COSTLY MISTAKES.
4. REPORT ANY PROBLEM TO LAB STAFF AND/OR WRITE IT DOWN IN THE LOGBOOK.
2
Explanation of Types of Commands Found in this Handout:
1. The vnmr software and the UNIX operating system are both case sensitive. This means that the computer
distinguishes whether the letters are entered in upper case (i.e. CAPITALS) or lower case. The user must be
careful to type the correct case for each letter in a command.
Example: jexp1 is not the same as JEXP1
2. Some commands are line commands and are typed in by the user followed by a return (signified by <rtn>).
Example: su <rtn>
3. Some commands are executed by clicking a mouse button with its pointer on a "button" found on the screen.
The execution of these commands are indicated by a two letter designation (LC {left click}, RC {right
click}, or CC {center click}) followed by a word or words in shadow or bold that would appear in the
button.
Example: LC Main Menu
This means to click the left mouse button with its pointer on the button that says "Main Menu".
4. Some commands are executed by the mouse itself. These commands are indicated by a two letter
designation (LC, RC, or CC) and a description of what the user should do in parentheses.
Example: LC (at 6 ppm)
This means to click the left mouse button with the mouse cursor positioned at 6ppm.
5. Parameters are entered by typing the parameter name followed by a equal sign, the value, and a return.
Example: nt=16 <rtn>
*
*
*
*
*
3
CHECKLIST
You should have taken the BASICS test and have completed the Practice Plotting handout before starting
training on the U400 spectrometer. If you haven't done so, I suggest you do it now.
My purpose in writing this handout is two-fold. First, it is a detailed roadmap of how to operate the
U400 to acquire the specific data required. Along the way, however, you are meant to acquire the skills for the
second goal - to acquire your own data. In order to accomplish the second goal, you have to be thinking while
doing the first. It is possible to succeed in the checkout with little thought on your side - if you can be satisfied
with not understanding how a significant proportion of your thesis data is acquired.
The purpose of this handout is to teach you how to acquire data. The main steps in that
process are:
1.
Ejecting the current sample.
2.
Inserting the new sample.
3.
Locking.
4.
Shimming.
5.
Setting up acquisition parameters.
6.
Acquiring data.
7.
Processing and evaluating data (Is it shimmed well-enough? Is the spectral width and digital
resolution correct? Is the sensitivity sufficient for integration? Do you need to re-acquire the data?)
8.
Saving the data.
9.
Logging off the instrument properly when finished.
NOTE: ALL PLOTTING IS TO BE DONE ON THE DATA STATION OR SOME OTHER
COMPUTER – NOT ON THE SPECTROMETER
The checkout is divided into the following parts:
Part I. Taking a "Routine" or "Normal 1H Spectrum: 0.1% Ethylbenzene in CDCl3
Part II. 1H Sensitivity, 0.1% Ethylbenzene in CDCl3
Part III. 13C{1H} Spectrum of 20 mg Menthol in 0.5 mL Acetone-d6
Part IV. Logoff
Part V. Plotting
If you have any problems or if you find any errors as you go through this handout, please let me know.
Vera V. Mainz, Director
NMR Lab
4
To start, log onto Reslog for the U400 and then log onto the spectrometer.
NOTE: If the keyboard doesn’t work, you probably have not logged onto Reslog properly!
1. SIGN UP IN THE LOG BOOK
2. CHANGE WORKING DIRECTORY
When you sit down at the spectrometer you should see the following message if the previous user logged off
properly:
This Is U400
*************
Next User:
Enter logon to start
If you do NOT see this message, type:
logoff <rtn>
runs the logoff macro to reset default settings
You now want to change the current working directory (should be "/export/home/data/tmp") to your fid
directory (i.e., "/export/home/data/username") as follows:
logon <rtn>
Input your directory name:
your_username (e.g., johnsont)<rtn>
enter your directory name at the prompt
(IMPORTANT: You should stay in this directory for the duration of the practice.)
Part I. Taking a "Routine" or "Normal 1H Spectrum: 0.1% Ethylbenzene in CDCl3
THE MOST COMMON COMMENT ON THE CHECKOUT PROCEDURE I HAVE RECEIVED OVER
THE YEARS IS: "I'VE COMPLETED THE CHECKOUT. NOW, HOW DO I TAKE A REAL
SPECTRUM." MY SOLUTION IS TO TRY TO TEACH YOU TO PAY ATTENTION TO WHAT YOU
ARE DOING.
LOOK AT THE CHECKLIST FOR THIS HANDOUT AND NOTE THE STEPS COMMON TO
OBTAINING ANY SPECTRUM. OF THESE STEPS, THIS HANDOUT GUIDES YOU THROUGH
STEPS 1-6, WITH ENDLESS DETAIL. STEPS 7-9 SHOULD HAVE BEEN TAKEN CARE OF
DURING THE PRACTICE PLOTTING PART OF YOUR TRAINING.
RECOGNIZE THAT UNTIL YOU ARE TAKING YOUR OWN DATA, YOU MAY WANT TO RELY ON
A HANDOUT TO REMIND YOU OF THE VARIOUS COMMANDS. YOUR MOST IMPORTANT JOB
IS TO LEARN HOW TO ACQUIRE MEANINGFUL DATA AND HOW TO ANALYZE IT. I CAN
HELP YOU ACHIEVE THE FIRST GOAL. YOU MAY SPEND THE REST OF YOUR SCIENTIFIC
CAREER LEARNING HOW TO ACHIEVE THE SECOND.
5
Insert the Sample
LC Acqi (top menu bar, right-hand side)
LC eject
connect to VNMR ACQUISITION window
eject sample
1) Remove the sample: Carefully climb the ladder and remove the sample from the top of the upper barrel of
the magnet. Avoid touching the narrow part of the spinner to keep it clean and prevent spinning problems.
2) Position your sample in the spinner: The correct drawing to position your sample in the spinner is located
on the ladder beside the magnet as well as on the wooden block between the magnet and the two-bay console.
Using the drawing on the left, place the spinner edge on the wood and match the bottom of the NMR tube to the
bottom of the tube in the drawing (133mm). When positioning the sample, make sure that your eyes are at the
same level as the bottom of the tube in the drawing. Otherwise, the sample could be mis-positioned by as much
as 5 mm. Ask the LAB staff or your trainer for a demonstration of this the first time you train on this
instrument. If you do not position the NMR tube to within 1 mm of the position on the drawing, the standard
shim libraries may not be very close and a substantial amount of shimming may be required. If you position the
NMR tube lower than shown, the sample will not spin.
3) Place the sample: Place your sample back on the top of the upper barrel of the magnet (with the eject air
still on) and make sure that the spinner does not get caught on the lip of the spin stack. (If this happens, the
sample will hang momentarily when the eject air goes off, then fall suddenly and usually break in the probe
when it hits the bottom.) Then,
LC insert
insert sample (listen for two clicking sounds as the
eject air goes off and the sample slowly drops in)
Lock on the Sample
Still in the VNMR Acquisition Window,
LC LOCK
connect to interactive lock window
NOTE: Next to the LOCK button at the top of this window is a button labeled SPIN: with off/on
buttons next to it. The current spin rate is displayed at the bottom of the lock window. Check if the
sample is spinning. If it is NOT spinning, check that the SPIN: on button is highlighted. The spin rate
is set at the bottom of this window with the Spin button. The rate should be set to 20 - if it isn't,
please set it to 20 at this time.
If the lock is in the ON condition, go to the Shim window.
LC SHIM (see procedures on following page)
======================================================================
If the Lock is in the OFF condition, THIS IMPLIES YOU ARE SWITCHING TO A SAMPLE WHICH
DOES NOT HAVE THE SAME LOCK SOLVENT. GO THROUGH THE PROCEDURE BELOW.
REMEMBER, IF YOU ARE CHANGING SOLVENTS, YOU MUST EVENTUALLY RESET Z0,
lockpower, lockgain, AND PERHAPS THE lockphase.
LC LOCK:off
turn lock off
NOTE: If you click on LOCK:off before the lock signal appears, the lock status may be incorrect, i.e.,
the lock could be off while the indicator is at the "LOCK:on" position, and vice versa. If this happens, Close
and reconnect to VNMR ACQUISITION window.
6
Adjustment of Parameters in the Interactive VNMR ACQUISITION Window
Place the mouse pointer in a button (such as -1+) for the appropriate function (such as lockpower) and left click
to decrease its value by the number of units selected, or right click to increase its value by the same amount.
Remember, the lock must be in the off condition to change Z0:
LC LOCK:off
turn lock off
RC lockpower and lockgain buttons
increase lock power (~30) and lock gain (55 - 60).
NOTE: In general, a lock power of 10 units greater than the normal setting is used for locking (see
handout UVU407 for some guidelines on the setting of lock power for various solvents). With the increased
lock power and gain, a sine wave should be seen if the lock is off resonance. If the lock is on or near resonance,
a flat or near flat line will be seen which may rise up under these conditions.
LC or RC Z0 buttons
"zero beat" the sine wave to bring the lock to
resonance condition; handout UVU407 onLocking
has a reference chart for Z0 for different solvents
To “zerobeat” means that Z0 is adjusted until the sine wave becomes a flat line and rises up, which is
an indication that the lock is on resonance. The change in Z0 from the Z0 for CDCl3 is proportional to
the change in ppm between CDCl3 and the other solvent. See the tables below for guidance.
U400 – Finding the Lock Z0
CDCl3
D2O
d4-thf
d4-methanol
DMSO
d8-toluene
d6-acetone
d3-acetonitrile
Chemical Shift (ppm)
7.26
4.65
3.58
3.30
2.48
2.09
2.04
1.93
Δ Z0
0
150
211
228
275
297
300
306
Δ ppm
0
2.61
3.68
3.96
4.78
5.17
5.22
5.33
U500, VXR500, UI500NB – Finding the Lock Z0
CDCl3
D2O
d4-thf
d4-methanol
DMSO
d8-toluene
d6-acetone
d3-acetonitrile
Chemical Shift (ppm)
7.26
4.65
3.58
3.30
2.48
2.09
2.04
1.93
Δ Z0
0
-3150
-4441
-4779
-5769
-6240
-6300
-6433
Δ ppm
0
2.61
3.68
3.96
4.78
5.17
5.22
5.33
7
Then
LC LOCK:on
LC lockpower buttons
turn the lock on
reduce lock power. For the QUAD probe, this is set
to around 20-25 for most CDCl3 samples, 10 - 15
for C6D6, and 5 - 10 for acetone-d6. See handout
UVU407 for more details.
LC lockgain buttons
adjust lock gain to maintain a lock level of 40-90%.
ALWAYS MINIMIZE LOCKPOWER, MAXIMIZE LOCKGAIN.
LC or RC lockphase buttons
adjust lock phase to maximize the lock level
NOTE: Lock phase is dependent on the shims. After its initial optimization, one should readjust the
lock phase after shimming on Z1C and Z2C, especially when large changes of the shim gradients have been
made. Shimming on the lock level requires that the lock phase is adjusted correctly. This will usually only
have to be adjusted when switching to a solvent other than CDCl3.
Shim on the Sample
LC SHIM
LC or RC Z1C -4+ button
LC or RC Z2C -4+ button
LC or RC Z1C -1+ button
LC or RC Z2C -1+ button
LC or RC Z1 -16+ button
LC or RC Z2 -64+ button
LC or RC Z1 -4+ button
connect to interactive shim window
adjust Z1C to maximize the lock level
adjust Z2C to maximize the lock level.
adjust Z1C to maximize the lock level
adjust Z2C to maximize the lock level.
adjust Z1 to maximize the lock level
adjust Z2 to maximize the lock level.
adjust Z1 to maximize the lock level
a) Repeat Z1C and Z2C shimming interactively (i.e., if one is changed, the other should be readjusted) until
maximum lock level is achieved. You may want to re-optimize the lock phase now if large changes of these
shim gradients have been made.
b) Then, Z1 and Z2 are adjusted interactively until maximum lock level is reached (usually starting with -16+,
then -4+).
c) Normally, Z3 is not changed. If Z3 is changed, Z1 and Z2 will need to be re-optimized.
NOTE: No shimming on Z4 should be needed for routine experiments, unless you are observing a
sample with very different physical properties from those of the standard or a sample of unusually short length.
When you finish shimming check that the lock level is between 40 - 90, then
LC Close
Close Acqi window
NOTE: You can insert the sample, lock and shim, then setup acquisition parameters, or insert
the sample, setup acquisition parameters, then lock and shim. Both methods are correct,
neither is better than the other; however, you must load a shim library before shimming or you
will be wasting your time. You will have to decide which way you want to proceed with your
own samples. However, pick a method and stick with it or you will forget to do something
critical for your measurement.
8
Select Standard Parameters
jexp1 <rtn> (if you are not in exp1)
LC Main Menu
LC 2:Setup
LC 1:H1,CDCl3
Acquire a Preliminary Spectrum with Autogain
nt=1 <rtn>
gain? <rtn> (should say gain = Not Used)
ga <rtn>
join experiment 1
select main menu
select setup menu
select standard parameters for H1 nucleus in CDCl3
set number of transients
gain='n' enables autogain, in which the gain is
adjusted automatically at the start of the acquisition
start acquisition (will wft when complete)
When acquisition is complete, the console will beep and the message "Acquisition complete" will
appear.
f full aph <rtn>
display full spectrum to a full screen and autophase
dscale <rtn>
display a scale
Reference the Spectrum (setting the CHCl3 to 7.26 ppm)
LC (at the left side of the phenyl region, ~7.5 ppm)
RC (at the right side of the phenyl region, ~7 ppm)
LC 3:Expand
vsadj <rtn> (or CC on top of peak at the desired height)
LC (at the center of the highest peak)
nl <rtn>
rl(7.26p) <rtn>
expand region inside cursors
adjust vertical scale
place cursor on the CHCl3 signal
select nearest line
reference the selected line to 7.26 ppm
ft <rtn>
Fourier transform without line broadening
Expand very closely around the CHCl3 peak – enough to isolate this peak from the rest of the
resonances. Place the cursor on the CHCl3 peak.
dres <rtn>
measure linewidth at half-height for CHCl3 signal
fn=4*np ft <rtn>
increase digital resolution via zerofill, ft
dres <rtn>
measure linewidth at half-height for CHCl3 signal
If the lineshape is correct (no assymetric features) and acceptable (see below), note the LW 1/2 in the
logbook, e.g., 0.1% ETB LW 1/2 =0.42 Hz.
IN ORDER TO EVALUATE THE LINESHAPE YOU SHOULD EXPAND CLOSELY AROUND THE
CHCl3 PEAK, i.e., ISOLATE THE CHCl3 PEAK ON THE MONITOR. EVALUATE THE LINESHAPE
(MAKE SURE IT IS LORENTZIAN, SYMMETRIC, AND WELL-SHIMMED). RE-SHIM IF
NECESSARY, AND IF THE LINESHAPE IS ACCEPTABLE, THEN CHECK THE LINEWIDTH AT
HALF-HEIGHT. IF THE LINEWIDTH IS BETWEEN 0.3 - 0.5 Hz, PROCEED TO THE NEXT STEP.
Start Experiment and Enter Text
nt=32 <rtn>
ga <rtn>
Enter text while waiting for acquisition to complete:
set number of transients
start acquisition (will wft when complete)
9
text('month/day/year, your name, your advisor's initials, STANDARD 1H SPECTRUM') <rtn>
When acquisition is complete, check and make sure that the current working directory is your fid
directory before saving the data:
pwd <rtn> (should say "/export/home/data/your_username" and not "/export/home/data/Temp" or anything
else)
If you are not in your own fid directory, change it now with the logon command as described
previously. Once you are in the correct directory, save the data by using either the menus or the svf
command, as shown below: NOTE: You should only use one of these methods to save data.
Note what number the bs parameter is set to. bs? <rtn> This parameter controls how often the data
is written to memory while data collection is going on. For example, if bs=16, then data will be written
to memory only when ct=16 OR when the data collection is finished if nt < bs.
If bs=16, and ct>16, you will find 16 scans in the memory. You can transform with wft or ft, and
evaluate whether the data is good enough for your purpose. If it is, you can stop the acquisition in
two ways.
sa – stop acquisition, stops on the next acquisition, update the memory with all data collected.
aa – abort acquisition, stops immediately, will NOT update the memory from the last update via bs.
Save the fid Using the Menus
LC Main Menu
LC 7:File Menu
LC 5:Save
INTH1 <rtn>
select main menu
select file storage/retrieval menu
save fid in current working directory
enter filename for the fid
OR Save the fid Using the svf Command
svf('INTH1') <rtn>
save fid in current working directory
NOTE: You will plot this spectrum later on either the SunDS or via NUTS. See Part V of this handout.
Part II. 1H Sensitivity, 0.1% Ethylbenzene in CDCl3
THIS SPECTRUM IS NOT ACQUIRED USING DEFAULT PARAMETERS, BUT WITH THE
SPECIFIC PARAMETERS REQUIRED FOR THIS MANUFACTURER'S SPECIFICATION. YOU
ARE REQUIRED TO DO THIS DURING THE CHECKOUT TO PROVIDE A TEST OF YOUR
SHIMMING SKILLS, AND SO THAT YOU CAN CHECK THE INSTRUMENT PERFORMANCE
YOURSELF IF YOU BELIEVE SOMETHING IS WRONG WITH THE SYSTEM SENSITIVITY.
NOTE: NINE TIMES OUT OF TEN WHEN SOMEONE COMPLAINS THAT "this sample should
have much better sensitivity than I'm getting", THERE IS SOMETHING WRONG WITH THE
SAMPLE, NOT WITH THE SPECTROMETER.
Display, and Phase Spectrum
ds <rtn> (if spectrum is not displayed on the screen)
f full aph <rtn>
enter interactive spectrum display
display full spectrum to a full screen and
10
autophase
Reference the Spectrum (setting the solvent peak to 7.26 ppm)
NOTE: This is exactly the same type of procedure used in the U400 Plotting Practice handout.
The critical issue is that you should not type return after an rl command, e.g., rl(7.27p), UNLESS the
left cursor is on the peak of interest.
LC (at the left side of the phenyl region)
RC (at the right side of the phenyl region)
LC 3:Expand
LC (at the center of the CHCl3 solvent peak)
nl <rtn>
rl(7.26p) <rtn>
Reset Spectral Window
dg <rtn>
f <rtn>
setsw(10,-0.5) <rtn>
expand region inside cursors
select nearest line
reference the solvent peak to 7.26 ppm
display group parameters
display full spectrum
resets sw to 10.5ppm and resets the center
frequency (tof) as appropriate for the sweep width.
Enter Standard Parameters for the S/N Experiment
pw=pw90 <rtn>
set the observe pulse width
gain='y' <rtn>
turn off autogain
gain? <rtn> (should say gain = 32, or some other number)
show gain value selected by autogain above
gain=gain-5 <rtn>
set gain to 5 below that selected by autogain to
offset the larger pulse angle used in the S/N
experiment
nt=1 <rtn>
set number of transients
d1=60 <rtn>
longer pre-acquisition delay to ensure full
relaxation
lb=1 <rtn>
set line broadening weighting function
Start the S/N Experiment
ga <rtn>
start acquisition (will wft when complete)
Enter text while waiting for acquisition to complete:
text('month/day/year, your last name, your advisor's initials, S/N MEASUREMENT') <rtn>
Save the Data Using Menus
LC Main Menu
LC 7:File Menu
LC 5:Save
SNH1 <rtn>
select main menu
select file storage/retrieval menu
save fid in this working directory
enter filename of fid to save
OR:
Save the Data Using the svf Command
svf('SNH1')
save fid in current working directory
Phase and Reference the Spectrum
11
ds <rtn> (if spectrum is not displayed on the screen)
f full aph <rtn>
dscale <rtn>
nl rl(7.26p) <rtn>
enter interactive spectrum display
display full spectrum to a full screen and autophase
display scale
reference the CHCl3 line to 7.26 ppm
Measure S/N and Store Value in Register
LC 3:Full
display full spectrum (same as typing f <rtn>)
LC (at 6 ppm, or type cr=6p <rtn>)
RC (at 2.5 ppm, or RC to bring up a second cursor and type delta=3.5p <rtn>)
LC 3:Expand
expand region inside cursors
vsadj <rtn> (or CC on top of peak at the desired height) adjust vertical scale
LC (at 5 ppm, or type cr=5.0p <rtn>)
RC (at 3.5 ppm, or RC to bring up a second cursor and type delta=1.5p <rtn>)
dsn <rtn> (The value should be >120.)
measure signal-to-noise, with the quartet as the
signal and 5.0 - 3.5 ppm as the noise region
Record your S/N ratio in the logbook {e.g., 0.1% ETB, S/N=130}. This value should be >120:1 for the
current standard sample with the QUAD probe. Make sure pw=pw90 and lb=1. If these parameters
are set correctly and dsn<120,, reshim and reacquire the spectrum ONCE MORE. If you fail to meet
this standard, continue on with your practice and let Vera know you had trouble meeting this standard
during the checkout.
NOTE: You will plot this spectrum later on either the SunDS or via NUTS. See Part V of this handout.
Part III. 13C{1H} Spectrum of 20 mg Menthol in 0.5 mL Acetone-d6
Insert the Sample
See instructions in Part I of this handout
Lock and Shim
LC Acqi
connect to VNMR ACQUISITION window
LC LOCK
connect to interactive lock display
Check Spin rate; see instructions in Part I.
Follow locking instructions in Part I.
NOTE: This sample is in Acetone-d6, and therefore has a very different Z0 value than
CDCl3. To lock:
1) Leave the lockpower and lockgain at the default values for CDCl3.
2) Turn the LOCK: off.
3) Zero beat the lock display with Z0. See Table in Part I.
4) When this has been accomplished, turn the LOCK: on.
5) Decrease the lockpower by 16, and adjust the lockgain to achieve an acceptable lock
level.
If the lockpower has not been set to a low enough value, you will notice that the lock
level will be unstable, i.e., fluctuating with a time constant based on how much "too
much" lockpower you are using.
LC SHIM
connect to interactive shimming display
12
Follow shimming instructions in Part I.
NOTE: Acetone-d6 usually has a slower response rate, so you should check to see how
long you need to wait after you change a shim value before the lock level stabilizes.
LC Close
disconnect from Acqi window
Set up the Experiment for 1H
NOTE: THE NORMAL WAY TO CHECK HOW WELL YOU HAVE SHIMMED ANY SAMPLE, EVEN
IF YOU ARE ONLY ACQUIRING A 13C SPECTRUM, IS TO CHECK THE 1H SPECTRUM.
LC Main Menu
LC 2:Setup
LC 3:H1
LC Acetone
nt=1 <rtn>
ga <rtn>
select main menu
select setup menu
select H1 nucleus
select acetone solvent
set number of transients
start acquisition (will wft when complete)
When acquisition is complete,
ft <rtn>
f full aph <rtn>
dscale <rtn>
Fourier transform without line broadening
display full spectrum to a full screen and autophase
Expand around and examine the acetone pentet at around 2ppm. Check the LW½ for the middle line
of the pentet. If the LW½ > 1 Hz, Z1 and Z2 have not been optimized properly. In other words, you
have not been patient enough while shimming this sample. Go back to the Shimming window and
make sure the lock level is maximized. If the sample is well-shimmed, you should be able to split this
multiplet almost to the baseline, with LW½ < 1 Hz.
Note LW1/2 (use dres command) of middle peak of acetone pentet (LW1/2=___________ ) in the
logbook.
YOU HAVE NOW EVALUATED THE SHIMMING IN THIS SAMPLE. BE PREPARED TO
DEFEND YOUR CRITERIA. WHEN YOU DECIDE THE SAMPLE IS WELL-SHIMMED,
PROCEED TO THE NEXT SECTION.
Set up the Experiment for 13C
LC Main Menu
LC 2:Setup
LC 5:C13
LC Acetone
nt=1 <rtn>
lb? <rtn> (What is the default lb?)
select main menu
select setup menu
select C13 nucleus
select acetone solvent
set number of transients
current value of the line broadening.
Start the Experiment
ga <rtn>
start acquisition (will wft when complete)
Enter text while waiting for acquisition to complete:
text('month/day/year, your name, your advisor's initials, \\MENTHOL SAMPLE') <rtn>
13
Process the Data
f full aph <rtn> (You may need to manually phase.)
vsadj <rtn>
dscale <rtn>
nl rl(29.8p) <rtn> (Make sure the cursor is on the
middle line of the septet!)
display full spectrum to full screen and autophase
adjust vertical scale
display scale
reference the methyl septet of the solvent to
29.8ppm
YOU ARE NOW GOING TO SET NT TO A LARGE NUMBER AND ACQUIRE THE 13C
SPECTRUM UNTIL YOU ACHIEVE A SENSITIVITY OF 20-25, MEASURED USING THE
PARAMETERS GIVEN BELOW. NOTE THAT bs=16 IN THE dg PARAMETER GROUP. THIS
INDICATES THAT EVERY 16 SCANS, THE RESULTANT FID WILL BE WRITTEN TO MEMORY.
IF YOU NOW DO A wft, YOU CAN SEE THE CURRENT 13C SPECTRUM, AND MAKE
DECISIONS ABOUT IT.
nt=1000 <rtn>
time <rtn>
(should say: Total acquisition time is 38.6 minutes.)
ga <rtn>
set number of transients
computes the time required for an experiment
start acquisition (will wft when complete)
AFTER THE MESSAGE "exp1: BS1 completed" APPEARS, TYPE
wft <rtn>
weighted Fourier transformation
f full aph <rtn>
display full spectrum to a full screen and autophase
vsadj <rtn>
adjust vertical scale
dscale <rtn>
display scale
wp=100p <rtn>
set width of plot
sp=60p <rtn>
set start of plot
LC (at 120 ppm, or type cr=120p <rtn>)
RC (at 80 ppm, or RC to bring up a second cursor and type delta=40p <rtn>)
dsn <rtn>
measure S/N ratio using the largest peak in display
as the signal and 120 - 80 ppm as the noise region
Keep checking the dsn value with this procedure, until the dsn value is approximately 10:1.
WHEN THE DSN VALUE IS ~10:1, SAVE THE DATA AS MEN USING EITHER THE MENUS OR
THE svf COMMAND DESCRIBED ABOVE.
Record your S/N and the number of scans in the logbook {e.g., menthol, S/N (NT=132)=10.4}.
svf('MEN')
sa <rtn>
save fid in current working directory
stop the acquisition at the current transient
NOTE: You can either stop the acquisition and then save the data or save the data and then stop the
acquisition. Experience indicates that the second option is safer, and it is shown above.
NOTE: You will plot this spectrum later on either the SunDS or via NUTS. See Part V of this handout.
14
Part IV. Logoff
This instrument should always be left in a standard configuration, which can be accomplished by
following the procedure below:
1. Log off the Instrument
logoff <rtn>
macro to reset the spectrometer to default
conditions
This macro does the following: a) load standard shim library 'QUAD', b) change working directory to
‘/export/home/user1d/data/Temp’, c) set plotter to 'PS_AR', d) joint exp1, e) select standard 1H/CDCl3
parameters, f) set all lock parameters to those for CDCl3, and f) perform experiment setup.
2. Insert the 1% CHCl3/CDCl3 Standard Sample
3. Lock onto the Standard
The Lock should be ON when you walk away from the instrument and the proper message should be
on the monitor. If not, logoff again.
4. Sign off in the Log Book and Log off on the Reslog
terminal
Part V. Plotting
You will plot the following spectra on either the SunDS or via NUTS on your own computer. These spectra
need to be emailed or hand-delivered to Tracie or Vera within one working day of your checkout. Same day
workup is preferred.
If plotting on the SunDS, logon the SunDS
logon <rtn> or LC Log On
Select a spectrometer from the list below [1-6]:
1 <rtn>
select the u400 spectrometer
Input your directory name:
your_username <rtn>
enter your directory name, or the directory you
saved your spectra in if not under your username.
NOTE: If you don’t have a user directory by the
time you practice on the u400, see Tracie Hubert as
soon as possible.
Load the SNH1.fid Directory
LC Main Menu
LC File Menu
LC SNH1.fid
LC 3:Load
select main menu
select file storage/retrieval menu
select the SNH1.fid directory
load the selected data to current experiment
15
Transform, Display, and Phase the Spectrum
wft <rtn>
f full aph <rtn>
dscale <rtn>
weighted Fourier transformation
display full spectrum to a full screen and autophase
Reference the Spectrum (setting the CHCl3 to 7.26 ppm)
NOTE: You are referencing this spectrum using the residual CHCl3 peak. You should always expand
around the peak to be referenced and make sure that the cursor is on the proper peak before typing
the reference command, rl(##p).
nl rl(7.26p) <rtn>
select nearest line and reference the selected line to
7.26 ppm
Measure S/N and Store Value in Register
LC 3:Full
display full spectrum (same as typing f <rtn>)
LC (at 6 ppm, or type cr=6p <rtn>)
RC (at 2.5 ppm, or RC to bring up a second cursor and type delta=3.5p <rtn>)
LC 3:Expand
expand region inside cursors
vsadj <rtn> (or CC on top of peak at the desired height) adjust vertical scale
LC (at 5 ppm, or type cr=5.0p <rtn>)
RC (at 3.5 ppm, or RC to bring up a second cursor and type delta=1.5p <rtn>)
dsn <rtn> (The value should be >120.)
measure signal-to-noise, with the quartet as the
signal and 5.0 - 3.5 ppm as the noise region
dsn:r1 <rtn>
store signal-to-noise value in register 1 in the dgs
parameter group
Plot Spectrum and Print Parameters
pl pscale pap page <rtn>
printon dg dg1 dgs printoff <rtn>
plot spectrum with scale and the dg parameter
group
print all parameter groups
Load the INTH1.fid Directory
LC Main Menu
LC File Menu
LC INTH1.fid
LC 3:Load
select main menu
select file storage/retrieval menu
select the SNH1.fid directory
load the selected data to current experiment
Transform, Display, and Phase the Spectrum
wft <rtn>
f <rtn>
full <rtn>
aph <rtn>
dscale <rtn> or LC Dscale
weighted Fourier transformation
display full spectrum
display spectrum to a full screen
autophase
display scale (it's in ppm because axis='p')
Reference the Spectrum (setting the CHCl3 to 7.26 ppm)
16
NOTE: You are referencing this spectrum using the residual CHCl3 peak. You should always expand
around the peak to be referenced and make sure that the cursor is on the proper peak before typing
the reference command, rl(##p).
nl rl(7.26p) <rtn>
Integration
f <rtn> or LC 3:Full
LC 2:Integral
LC 4:Part Integral
cz <rtn>
cdc <rtn>
dc <rtn>
select nearest line and reference the selected line to
7.26 ppm
display full spectrum
enter integration routine
enter integration routine with integral blanking
clear previous integral reset points, if any
cancel previous drift correction, if any
apply drift correction
Expand around the region of interest (place the two cursors near each region to be integrated, then LC
3:Expand), e.g., the phenyl region.
Select the areas to be cut by using
LC 6:Resets
LC on the left and right sides of the signal(s) to set integral zero points
Repeat this process for the rest of the signals you want to integrate in this area; then
f <rtn> or LC 2:Full
display full spectrum
Continue expanding and making your integral cuts in this way until the cuts for all areas of interest (the phenyl
region at ~7 ppm, the quartet at ~3 ppm and the triplet at ~1 ppm) are set.
NOTE: Every time you switch to another expansion, you will need to LC 6:Resets
ds <rtn>
display spectrum
Place the cursor on the integral line for the QUARTET.
LC 2:Integral
enter integration submenu
When you do the next step the cursor will disappear. It is still in position.
LC 7:Normalize
Current integral is 100.00. New value?
2 <rtn>
set integral normalization scale to 2 protons for the
quartet and displays normalized integral values
(should give values ~ 7, 2, and 3). NOTE: If you
are in an expanded window only the integral values
for the peaks displayed will appear. You can use
the f full dli command sequence to display all
integrations
wp=10.5p <rtn>
sp= - 0.5p <rtn>
vsadj <rtn>
set width of plot
set start of plot
adjust vertical scale
isadj <rtn> (or CC on top of an integral at desired height) adjust integral vertical scale
Plot Spectrum with Integrals and Integral values
vp=12 <rtn>
set vertical position of spectrum to 12 mm so that
integral values can be plotted under the spectrum
17
pl pir pscale pap page <rtn>
printon dli dg dg1 dgs printoff <rtn>
plot with integrals on the spectrum and integral
values under the spectrum
print integral table and parameter groups
Turn off Integral Display
ds <rtn> (if 2:Full Integral is not visible on the menu)
LC 2:Integration
LC 3:No Int
vp=0 <rtn>
display spectrum
turn off partial integral display
turn off integral display
set vertical position of spectrum back to zero
Load the MEN.fid Directory
LC Main Menu
LC File Menu
LC MEN.fid
LC 3:Load
select main menu
select file storage/retrieval menu
select the SNH1.fid directory
load the selected data to current experiment
Transform, Display, and Phase the Spectrum
wft <rtn>
f full aph <rtn>
vsadj <rtn>
dscale <rtn>
nl rl(29.8p) <rtn> (Make sure the cursor is on the
middle line of the septet!)
weighted Fourier transformation
display full spectrum to a full screen and autophase
adjust vertical scale
display scale
reference the methyl septet of the solvent to
29.8ppm
wp=100p <rtn>
set width of plot
sp=60p <rtn>
set start of plot
LC (at 120 ppm, or type cr=120p <rtn>)
RC (at 80 ppm, or RC to bring up a second cursor and type delta=40p <rtn>)
dsn <rtn>
measure S/N ratio using the largest peak in display
as the signal and 120 - 80 ppm as the noise region
dsn:r1 <rtn>
store S/N value in register 1
Set Plot Limits
wp=100p <rtn>
sp=0p <rtn>
vsadj <rtn>
set width of plot
set start of plot
adjust vertical scale
Peak Picking
LC 6:Set Th
select threshold menu
LC (drag the horizontal cursor up or down to set the threshold level, including the solvent signal)
dpf <rtn> or LC 7:Peak Pick
display peak frequencies above the spectrum
Plot Spectrum with Parameters and Peak Frequencies
pl ppf pscale pap page <rtn>
printon dll dg dg1 dgs printoff <rtn>
logoff <rtn>
plot spectrum with peak picking in ppm
print parameter lists with peak frequencies in ppm
18
SOME UIUC VARIAN NMR MACROS OF INTEREST are below.
=========================================================================================
SOME UIUC VARIAN NMR MACROS OF INTEREST:
ffa
disp
proc
f full aph cdc dc
f full aph cdc dc vsadj dscale
wft f full aph cdc dc ds vsadj dscale
ppmh
diff
doi
ipart
plot
plotT
plotI
plotA
plotAs
wp=10p sp=-0.5p
r1=delta r1? [displays the difference in Hertz between two cursors]
f full intmod=’partial’ cz cdc dc isadj
intmod=’partial’
pl pscale pap page
pl pscale pltext page
vp=12 pl pscale pir pap page
pl(‘all’) pap page
pl(‘all’) pscale pap page