|
Instrument |
Nuclei
Observed |
Tuning
Needed? |
2H
Gradient Autoshimming |
VT
Operation |
MERCURY-300 |
1H, 19F,
13C, X |
19F, X ONLY |
YES |
-20 to
+80 ºC |
|
INOVA-400 |
1H, 13C,
19F, 31P*, X |
X ONLY |
YES |
-20 to
+80 ºC |
|
INOVA-500
- DBG |
1H, 19F,
13C, X |
19F, X ONLY |
YES |
-80 to
+150 ºC |
INOVA-500 - HCN |
1H, {13C},
{15N} |
YES |
YES |
-20 to +
80 ºC |
INOVA-600 |
1H, {13C}, {15N}
|
YES |
YES |
-20 to +
80 ºC |
***NOTE***: You must
perform the following (A, B, and C) only ONCE PER HOST COMPUTER and each
WORK STATION!!!!!
·
Log into the host computer by using your assigned username
and password.
·
In the workspace area, right-click and select “Tools”
followed by “Terminal”.
·
At the prompt, type vnmr to launch the
software.
After launching VNMR, you can
define the home session, which will launch VNMR automatically when you log
in. This is “host computer specific” –
setting the home session on one computer does not define it on
another. You must do this for
each host computer that you work on.
However, it only needs to be done once to work properly.
·
After launching VNMR as described above, be sure to close
the terminal window and any other applications that you don’t want running when
you log into Solaris.
·
Right-click on the workspace (blue area) and select “Tools”
followed by “Desktop Controls”.
·
Open the “Screen Style Manager” by double left-clicking on
the icon.
·
Disable the screen saver and the screen lock by clicking the
“Off” radio buttons. Hit Apply and OK.
·
Close the Application Manager.
·
Open the “Startup” menu.
·
Select the radio button for “Return to Home Session” under
the At Login: prompt.
·
Disable the Logout Confirmation if you would like by
selecting “Off”.
·
Click “Set Home Session” to define the session for your
subsequent login attempts.
C. The “Newuser” Macro
This macro will define the printer/plotter for you, define the gradient amplifier configuration, and also create 9 experiments in your home directory. You should only have to use this macro ONCE per host computer you log into (presumably the first time you use the computer).
· Type newuser in the VNMR command window.
·
Type e to eject the sample spinner from the
probe.
·
***ONLY HOLD THE SPINNER AROUND THE BLACK PART NEAR THE
TOP!!!***
·
Remove the standard (the tube with the yellow and black
tape). Please place the standard in the
sample holder, do not lay it flat on the console!!! If you break the standard you are required to purchase a
replacement!
·
Insert your sample tube into the spinner and measure the
depth of your sample with the spinner using the depth gauge.
·
Place your sample into the magnet.
·
Type i to insert the spinner back into the
probe.
·
Click {Main Menu}, {Setup}, {Nucleus, Solvent}.
·
Select the appropriate nucleus and solvent.
·
Type su to initialize the console for the
experiment you just selected.
·
Open the {Acqi} window.
·
Click {Lock}
·
Turn the spinner {On} and the Lock {Off}.
·
Turn the lock power and the lock gain up until you can see a
signal (I usually max them out … you’re going to lower them again later).
·
Adjust Z0 to the appropriate setting such that you see a
single “step” and the line is approximately flat. Note that the line might be flat and downward, this is OK, you
can adjust this in a minute using the lock phase.
·
Lower the lock power and the lock gain and continue tweaking
Z0 until you cannot increase the lock level any higher.
·
Turn the lock ON.
·
Maximize the lock level using the lock phase parameter. Lower the lock power and the lock gain as
necessary to maintain a lock level of ~ 40 – 70.
·
If the lock signal fluctuates up and down rapidly,
your lock power is too HIGH!!! This is
the result of saturating the lock signal with too much power. Turn the power down until the signal
stabilizes, and be sure that you optimize the lock phase setting.
Shimming manually (or “by hand”) is an art form, but can be mastered with practice. To access the shim control panel, go to the {Acqi} window and click {Shim}. You will see three readings: two level bars and a “lock level” indicator (a number). The idea here is to maximize the lock level reading, producing a higher “current lock level” with each change in the shim values.
To load the default shim file, which is called “LOAD_ME” in most cases (it should be posted near the spectrometer), use the command: rts(‘LOAD_ME’) su. If you notice that your lock signal is very weak (typical for CDCl3), or you are having trouble getting “on resonance”, be sure that you’ve loaded the default shim file. You can try touching the shims up manually (described below) as well.
· Start by making sure the spinner is on and regulated at 20 Hz.
· Load the default shim file (filename posted near the spectrometer) – rts(‘filename’) su
· Adjust Z1 to maximize the lock level
· Adjust Z2 to maximize the lock level
· Re-adjust Z1 and see if the lock level goes any higher. If it does, check Z2 again.
· Repeat the process until you cannot maximize the lock level any further.
· Check the lock phase to be sure the lock level is at a maximum. Adjust the lock power and the lock gain to bring the lock level down if necessary.
· In some cases you may need to adjust Z3 and Z4. If you adjust these, be sure to go through and re-optimize the lower Z shims. Any time you make an adjustment to a higher shim you must re-optimize the lock level with the lower shims.
· If the lock level approaches 100%, be sure to lower the lock power and the lock gain to maintain a lock level of between 40 and 70.
· Once you are finished shimming, re-optimize the lock phase (again lowering the lock power and lock gain if necessary).
Disclaimer:
Gradient autoshimming is a modern convenience to NMR
spectroscopists. It is not, however,
always a substitute for manually shimming an NMR magnet. In the event there is a problem with the
gradient shimming capability of a system, you can still shim the magnet by hand
and obtain quality spectra, and you will be expected to do so.
Be sure that the proper shim map
file and parameter set are loaded. If
you are in doubt, perform the following (though this should only need to be
done ONCE!). If you are sure your
account is set up correctly for gradient autoshimming, skip to Step 2.
Step 1
(ONLY NEEDS TO BE DONE ONCE per host computer or if probe
is changed!!!!, check posted signs and log book if necessary.)
·
Type gmapsys
·
Click {Shim Maps}, {Shim Map Files}, {Cd to Systemdir} (if
you do not see the {Cd to Systemdir} button, click {Cd to Userdir} and it
should show up).
·
Highlight LOAD_ME.fid (or the appropriate shim map for the
instrument and probe combination you are using).
·
Click {Load Shimmap & Params}
·
Click {Return}
·
Click {Quit}
Step 2
·
Click {Main Menu}, {Setup}, {Shim}, {Gradient Autoshim on
Z}.
·
When the rms error is less than 1.00, it should stop
gradient autoshimming and your sample should start spinning. Be sure this is so, and if it is not, turn
the spinner on manually in the Lock window {Acqi}.
·
Set the number of transients (scans) by typing nt=##
(multiples of 4 are best). Set the
block size (bs) in the same manner: bs=##
(must be a multiple of 4!!)
·
Click {Main Menu}, {Acquire}, {Go, Periodic WFT}
·
Alternatively, type go and when the data is
finished being collected, type wft to weight and transform the
FID. Or, type ga and the
data will automatically be processed when it is finished being collected.
·
Click {Main Menu}, followed by {Data}. This will move you to the directory
/data/your username. An alternative is
to type cd(‘/data/your username’) in the vnmr command
window. *** ALL OF YOUR DATA MUST
BE SAVED IN THIS DIRECTORY IN ORDER TO RETRIEVE, PROCESS, AND PLOT IT FROM
OTHER TERMINALS ON THE NETWORK.
·
Type svf(‘filename’) to save the file. You should then check the contents of your
data directory (type ls in the command window) to be sure that
the file has in fact been saved. It
will be a directory having a .fid extension and will contain four files: fid, log, procpar, and text. If you see any of these files missing, you
should resave your data and check again.
If you encounter any further problems, seek assistance from the facility
staff.
Note: Work from this point on should be carried
out on the Sun workstations located in S. T. Olin B69. Time on these workstations is not regulated,
nor billed on a “per hour” basis like the spectrometers. In an effort to maximize spectrometer
throughput, please do not tie up the workstations with data processing,
plotting, and analyses.
·
Click {Main Menu}, then {Data}. You should see a message saying “Directory is now /data/your
username” and your list of files should appear on the screen. Highlight the file you wish to load by
left-clicking once so that the filename is rendered in inverse-video
coloring. In the menu bar, click
{Load}, {Process}, and select from {Transform} (for no weighting), or {Weight,
Transform} to apply weighting to your FID before FT’ing.
·
View the entire spectrum by clicking {Full}
·
Autophase your data by typing aph.
·
Manually adjust phasing if necessary by clicking {PHASE} and
adjust the phase of the upfield (right side) region of your spectrum (left
mouse button is “coarse”, right mouse button is “fine”); this will adjust the zero-order
phasing paramter (frequency independent; so all peaks will move during this
operation. Left click on the downfield
side (left side) of your spectrum and adjust the phasing of only the peaks
between the cursors. This is the first-order
phase correction and is frequency dependent.
You’ll notice the peaks on the other side of the spectrum tend not to
move much (if at all) during first-order phasing.
·
Should you find that you are having a difficult time
phasing, try resetting lp=0 and rp=0 and starting
over.
·
In some cases, using aph may introduce a phase
error by attempting to autophase a noise spike near the edge of your
spectrum. You may then see a “rolling
baseline”. This is particularly true in
19F spectroscopy. In this
case, use aph0 instead.
This adjusts only zero-order phasing.
You may need to touch up the phasing by hand as well.
·
In all cases, make sure you blow up the vertical scale of
the spectrum and inspect the baseline, as often times what appears to be decent
phase adjustment is actually not very good at all.
·
Set your internal reference standard by putting the cursor
as close to the peak maximum that you can, and typing nl rl(##p),
where ## is the value of the reference peak in ppm.
· To display the peak frequencies in ppm above the peaks, you must set the threshold by clicking {Th} and adjusting the yellow threshold line such that it touches all of the peaks you want picked on your plot. Type dpf in order to display the peak frequencies on the screen. When plotting your spectrum, the command ppf sends the output to the plotter instead of the screen.
· If you would like the frequencies displayed in hertz, type axis=’h’ and then plot the peak frequencies as usual. In this case, they would be displayed in hertz, such that you do not need to take into account the spectrometer frequency when analyzing J couplings. A good way of doing this is to use axis=’h’ (dpf or ppf) axis=’p’. This will display only the peak frequencies in hertz, keeping the scale in the more familiar d format (ppm).
·
Integrate peaks by clicking {Partial Integral}. If your integral line is slanted, you can
perform a drift correction by typing dc. Adjusting the integral line can also be
doing using {Lvl/Tlt}, followed by the left mouse button.
·
Define integral resets by clicking {Resets} and then left
clicking on either side of the desired integral. If you change window size (expand, full, etc.) then you must
click {Resets} before you attempt to integrate a region.
·
If your spectrum has a relatively flat baseline, it is not
necessary to integrate peaks not of interest to you. However, if you should need to apply
baseline correction because of a bumpy or unattractive baseline, then you must
integrate every peak in your spectrum, even if you don’t intend to use them in
your analyses, in order for the correction to function properly.
·
After defining all of the integral resets, type bc
if you desire to use baseline correction.
·
Set a reference integral value by putting the cursor on the
integral you wish to define, and click {Set Int}. Enter an appropriate value for the integral.
·
To display the integral values on the screen, move the
vertical position of your spectrum to at least 12 (type vp=12)
and type dpir.
·
Clear integral resets by typing cz. You can undo
·
To put a title on your spectrum, type text(‘title’). You can make a multiply lined title by using
double backslashes: \\. For
example: text(‘Ethylbenzene in
CDCl3\\July 07, 2003\\Anthony M. Condo’) would produce the following as
your title in the upper left-hand corner of your spectrum:
Ethylbenzene
in CDCl3
July 07,
2003
Anthony M.
Condo
·
The two parameters sp (start of plot) and wp (width of plot)
allow for you to define the chemical shift scale plotted on your spectrum. This allows you to use the exact same scale every
time you run a spectrum. For
example, if you want your plot to display -0.2 ppm to 11.0 ppm, you would type sp=-0.2p
wp=11.2p. Note that sometimes
the region does not display itself correctly, if this is the case, try typing sp=##p
again.
·
If you want to automatically scale the vertical size of your
spectrum, issue the command vsadj. This will scale the spectrum so that the tallest peak (whether it
be solvent, TMS, or sample) is near the top of your page. Two variants of this command are vsadjh
(for 1H spectra) and vsadjc (for 13C
spectra), whereby the solvent and TMS peaks are suppressed from the vertical
adjustment. You can set the scale
manually by typing vs=##.
·
Adjust the vertical threshold used to determine which peaks
will be “peak picked” by clicking {Th} and moving the yellow line such that it
touches the lowest peaks you want picked on the spectrum. Toggle the threshold off by clicking {Th}
again. Display the peak frequencies on
the screen by typing dpf.
·
Be sure the data on the screen looks like you want it to on
paper. You can issue the plotting
commands by using the menu buttons or by typing the commands in bold. If you are going to use the menu, start by
clicking {Main Menu}, {Display}, {Plot} and selecting the plotting choices as
follows:
·
{Plot} pl:
Plots the spectrum (blue portion of what is on the screen).
·
{Scale} pscale: Plots the scale.
·
{Integral Labels} pir: Plots the
integral values below your spectrum.
Note that if you have the integral resets defined on the screen (green
lines), these will be plotted as well.
Toggle them off by selecting {No/Part/Full Integral} in the menu bar
until they disappear. The values will
be saved, all that you are doing is eliminating the green lines from your
spectrum.
·
{Peaks} ppf:
Plots the peak frequencies above your peaks according to your threshold
setting.
·
{All Params} pap: Plots a complete list of acquisition parameters, including your
title (text file).
·
{Params} ppa:
An abbreviated list of acquisition parameters.
·
{Page} page:
Sends your selected plotting commands to the printer. Only use this when you’ve selected all of
the options you wish to plot.
·
To plot your peak frequencies on a separate page in a
tabular format, use {Line List} pll, {Page} page.
·
This must be done on a Sun workstation located in S.
T. Olin B69, as the printer here is set up as a postscript printer.
·
Render your data to look exactly how you would like it to
appear in the file. This includes the
vertical scale, chemical shift scale, etc.
·
Plot the data using the command line (pl pscale ppf pap
… ), and issue the command page(‘filename’)
·
The data will be output to the file you specify above. It can be imported to a number of
applications in this manner. GhostView
(available online) can be used to view and manipulate the data and save it in
an appropriate format (.jpg, .pdf, etc.) for import into scientific documents,
papers, presentations, etc. See the
facility staff if you need assistance.
·
At this point, you must re-save your data if you want all of
your processing parameters to be saved.
It is advisable to resave using the same file name so as not to create
duplicate files of the same compounds.
To simplify this process, type svf(file) (the word file
NOT the filename) … this assumes you’ve saved the file correctly before. Type y when asked if you wish
to overwrite the file.