Automation Training on the V400

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Automation Training on the V400 October 2008
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• V400 will be used with in automation mode with
  the autosampler only.
• There are 100 positions available on the
  autosampler.
• Do not manually tune the probe
• Do not manually lock your sample

1-50
51-100
Important rules to follow
Doing any of these will mess of the automation
for subsequent users
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What needs to happen on a daily basis?

• The autosampler needs to be cleaned of any
  samples from the previous day each morning .
  Remove the NMR tube from turbine and put both the
  tube and turbine on the shelf near the tray.
• The automation queue needs to be restarted once
  per day in the morning. The first person of the
  day needs to restart it (most of the time that
  will be Stephen). It will not harm anything to
  restart it more than once during the day but it
  will make data retrieval more confusing.
• How do I tell if it has been restarted yet?

Shelf
Tube Rack
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Current automation directory if the previous day
then you need to make a new file for today
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• To make a new days automation directory
• Go to File
• and select New automation run

• Remember only the first user of the day needs to
  do this.
• Once you do create a new automation directory the
  autosampler will table will be wiped clean and
  the study queue will be blank.

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Looking at just right autosampler table
Study queue blank
NO PARAMETERS HERE FOR FIRST USER NEED TO ADD AND
DOUBLECLICK AN EXPERIMENTAL PROTOCOL
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Autosampler Zones
Zone set to 2
Zone set to All
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• General procedure for submission of a sample
• 0. login will be shown later
• 1. Put sample in next available position on the
  autosampler beside the magnetic
• 2. Switch to autosampler table view in VNMRj if
  it is not available (click x and o to go back and
  fourth)

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Click x to go to spectrum view
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Click O to go to autosampler view
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General procedure for submission of a sample
3. Click on the position in the autosampler table
(software) where you put the same on the physical
autosampler
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• 4. Select desired experiments you want to run on
  the sample
• 5. Modify the desired experiments (for 2D
  experiments it will modify your proton experiment
  by setting the radio button MinSW turn MinSW
  off)
• Modify the experiments through the acquisition
  tab

General procedure for submission of a sample
(Continue)
MinSW Located under Aquire ? Prescan (will try
to minimize the spectral width for 2D experiments
by you may lose some peaks of interest)
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General procedure for submission of a sample
(Continue)
6. Uncheck Plot all data, make sure Auto Lock and
Gradient Shim are checked, make sure spinner is
on.
You never want to deselect these
If the first person does this all subsequent
experiments for the day will inherit it
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General procedure for submission of a sample
(Continue)
Enter name here (used for file
name) Alphanumeric, dashes, spaces, and
underscores
Copy name here (used for runlog)
Use unix style cut and paste, highlight first
with mouse then go to where you want to paste and
click the middle mouse button
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7. Submit the experiments to the day or night
queue for starters, day queue will be limited to
15 minutes per sample, the night queue to 4
hours/sample, and no restrictions on weekends Day
queue starts at 800 am and night queue starts at
700 pm. This may change in the future if
needed and it will be announced in a
sil_users_at_unr.edu mailing list email. If more
time is needed come talk to me or Paige and will
adjust the settings in the software (time
allotments are setup in the administration
software) 8. Switching users Click on the
Switch operators button after you have submitted
your samples for analysis. This will present a
login screen for the next user. You do not log
in and out of the computer only switch operators
within the vnmrj software.
General procedure for submission of a sample
(Continue)
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General procedure for submission of a sample
(Continue)
Change user here
Current logged in operator
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General procedure for submission of a sample
(Continue)
Use SIL username and password
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Miscellaneous

• Retrieving a sample after you submit your sample
  to the automation queue, the sample is not
  retrieved from the bore of the magnet unless
  there is another sample to analysis. If you want
  your sample back immediately, add the deuterated
  chloroform in a standard 8 inch tube to the queue
  and run a 1D 1H spectrum on it.
• Data retrieval Each day an automation folder is
  made with the name auto_year.month.day under that
  folder will be a folder with you name and your
  data in it. Periodically (???) this will be moved
  to the correct folder on argenta.
• Tube breakage
• if a tube is broken during a autosampler run.
  Notify Stephen, Ben, Paige
• clean up your broken glassware and dispose of it
  in the proper broken glass bin, not the general
  garbage
• Picked the wrong solvent
• this may cause the system not to lock on your
  sample and the system will abort running your
  sample and go on to the next sample in the queue.
  If it does abort your sample your sample will
  appear red in the autosampler table, indicating
  an error
• Make sure you use standard 8 inch NMR tubes, NO
  SHORT TUBES
• Offline processing Learn MestReNova, it will
  make your life easier

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TUBES

• NO SHORT (vertically challenged) NMR TUBES
• The autosampler will most likely grab them wrong
  and break them.
• If it does manage to pick it up right the short
  tube will generally fail autolock or autoshim.
• Use standard 8 inch tubes only for V400

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Green successfully run sample Red error Yellow
submitted to day queue Light blue
running Purple submitted to night queue
Autosampler table colors
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Miscellaneous (This slide applies to all Varian
Spectrometers)
Light blue means its turned on and regulated
good Red means turned on but not regulated ok,
but wait for regulation before analysis Yellow
means turned off bad, everything should be turn
on and regulated
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IUPAC method for referencing heteronuclei dissol
ve your sample in a deuterated solvent with
TMS acquire a one-dimensional 1H spectrum off
your sample acquire a one-dimensional
herteronuclear spectrum, for example
31P jexp1 load and process 1H
spectrum jexp2 load and process 31P
spectrum type mref(1,2) this references your
31P (or any other nuclei) off the TMS frequency
Ann. Magn. Reson., Vol. 1, Nº 1, 43-64, 2002
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• If instruments status changes to inactive
• Open a terminal and type su acqproc then press
  Enter
• Press the reset button in the console
• Wait 1 minute until all lights are blinking
• Type su acqproc again in terminal window and
  press Enter
• ON V400 ONLY press reload button to reset
  autosampler
• Launch vnmrj software
• Press proton and double click (or drag) green
  proton in study queue to load experiment into
  memory
• Load in the latest shims by going to tools ?
  locator ? double click latest shims
• Close locator window and type su
• go to the acquire tab and make sure spin is
  checked (this is a bug to me)
• Go the start tab and turn on temp regulation and
  spin regulation
• Document that you did this in the log

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Applying weighting/Apodization functions to you
FID

• A way to increase signal-to-noise (most commonly
  to 13C spectra) or resolution
• Weigh in 1D
• Apodize a 2D getting rid of feet around peaks
  that you did not collect enough data

SINC wiggles or feet
Sinc(x)sin(x)/x
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Type wti in command line to go into interactive
weighing
Observed spectrum Fourier transform (FID
weighing function)
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Applying a line-broadening function to increase
signal-to-noise
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Applying a shifted gaussian function to increase
resolution
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2D Spectrum

• Load fid
• Type wti(1) and apply a weighing function
• Type wft1da(dc)
• Find a pick of large intensity
• Record its index value

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Apodization
Index value
Pick intensity light blue line
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Apodization

• Type wti(index value) -in this case type
  wti(698)
• Apply an apodization funtion
• Type wft2da(dc)

SINC wiggles
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Apodization
Apply Gaussian to get rid of sinc wiggles