Short Instructions for basic operation
                          of nmr500-3 spectrometer.

*   Take out the plastic cap of the top of the sample insertion port.
*   Put your sample into the spinner turbine. Make sure that NMR tube is clean and
     dry. Do not touch the turbine’s shaft by fingers. Use the insert gauge to find out
     the proper sample depth. To achieve a good shimming, the length of a sample
     should be larger than the length of corresponding coil. We are using 5mm coils on
     all spectrometers.
*   Log into your account on spectrometer’s workstation.
     Double click on "Topspin"  icon. You may also open  the Linux  shell window
    “Red Hat->System Tools->Terminal and type in command line topspin”.
    Click the "BSMS" icon on upper “Top Spin” menu or type in command line bsmsdisp.
    The bsms interface will appear. Click the  Lift button. After you
    hear whistling gas coming from the top of the magnet and checked the flow of gas
    with hand place sample on air cushion and push the “Lift"  button again. The
    sample will descend softly into the NMR  magnet.
*  After you seen the green  “sample down” light lit, press “Spin”  button.
    The  light will be read till the sample is at the set speed and will turn green.
*  In the Top Spin under file menu select “New”
    Make sure that under user in this menu is your login name and under “DIR” is
    /opt/topspin. Put the file name, experiment # and processing data # and click “OK”
    button.
    At the prompt at the bottom of the “Tops Spin,  typerpar and choose the
    /opt/topspin/exp/stan/nmr/par/user
    For a proton experiment select “stdh1.QNP”, and choose all option clicking “Read”
    and “OK”  in the next window. Click “Close” as the next. For 13C experiment select
    std13Cdc.QNP.
  Tune the probe by typing atma. Wait until process is completed and

    message atma finished” occurred. Do not type anything while atma is in progress.
    This might hang up spectrometer. For 31P apply the same procedure. For 19F call
    std19Fzg.QNP parameter file and tune the probe by typing atma. 19F tuning can be
    performed using this file, only.  After probe is tuned you can choose different experiment
    e.g. std19Fig.QNP if you need run such. Do not type atmabecause probe is tuned. Experiment will
    work properly.We have following experiments to choose for two channel mode:
    power gated decoupling, gated decoupling and inverse gated decoupling. Power gated
    decoupling applies proton RF before and after pulse giving Nuclear Overhause Effect
    to strength the signal and 13C is decoupled. Gated decupling applies NOE but there is no
    decoupling. Inverse gated decoupling gives decoupled spectrum without NOE.

* At the prompt, type rsh and select the default shims. nmr500-3 is
   equipped with quattro nucleus probe and the default shims files has extension
   “QNP”  default.QNP. If different probe is installed the message will be posted.
   If there is no “lockdisplay” on the screen, at the prompt type lockdisp
   or choose proper icon from the “Top Spin” menu and        resize it according to your needs.
* At the prompt type “lock” and select your solvent from the list provided.
   Perform the magnet shimming.
   Click BSMS icon.
* Select “Z” on the keypad, and change it value to maximize the signal
   Select “Z2”, and repeat maximization. Normally, you do not need to shim higher orders.
   Repeat above steps until the signal is maximized.
   You may also try automatic shimming instead, by typing topshim gui. After shimming showed
   “finished” message close the menu. Come back to bsms menu
* Select lockgain, adjust until the signal is within second line from the top.
* If the lock signal becomes saturated lower the lock power. Most often the good
   working lock power can be found in the range of –25 to –35 DB.
* If the lock fluctuates decrease the lock power until is stable.
   Select “Standby”
* At the prompt, typerga, wait for the messagerga finished” before proceeding to next command.
   You can run experiment using icons or typing commands.
*At the prompt type “ns #, where # is the number of scans. (To see other acquisition
  parameters it is helpful click AcquPars or type eda
*At the prompt, type zg, after spectrum is acquired, choose  "Processing -> Data
   Processing Guide". Click “Window Function and choose proper one to your
   molecule   “Window function type” and "Size of the line broadening”
  Go to the next menu and click “Fourier transform” and choose proper size “SI” for
  your spectrum. Click “OK”
  Click “Phase Correction” Choose “manual” and do it manually (recommended) or “automatic” (not always works).
* Click on “Axis Calibration, select solvent peak or TMS with the left mouse button,
   and type in the solvent chemical shift (reference table is on the bulletin board)
   Click “Baseline Corr.” button and chose proper for your molecule way to get good
    baseline (very important for accurate integration)
   Click “Pick Picking” button and generate the peak list of the spectrum.
* Click the “Integration button” and perform integration.
   When spectrum ready for plotting click the “Plot/Print” button. Choose print with layout and
    start the plotting editor. Click on spectra icon and put your spectrum into the window. Select “1D/2D-Edit”
    and customize spectrum according to your needs. Select the “File->Print” and you will see the preview.
    If you are satisfy click print and spectrum will be plotted.
* After experiment is completed:  Click BSMS icon again.  “Click lock OFF” and
   “spin OFF” buttons
    Quit the lock window.
    Retrieve the sample, Press “LIFT” button.
* Make sure the none of button “lock, “spin” or “lift” lit when you leave.
   Quit BSM menu
   Exit Top Spin
 * Make sure that  Top Spin exited completely, wait another 5-7seconds and from  Linux window choose “Action->logout”
 * Insert the plastic cap on top of the sample insertion port.
 * Record your time in the logbook.
 

                                       Short Instructions for basic operation
                          of nmr500-2 and nmr400-2 spectrometer.

*   Take out the plastic cap of the top of the sample insertion port.
*   Put your sample into the spinner turbine. Make sure that NMR tube is clean and
     dry. Do not touch the turbine shaft by fingers. Use the insert gauge to find out
     the proper sample depth. To achieve a good shimming, the length of a sample
     should be larger than the length of corresponding coil. We are using 5mm coils on
     all spectrometers.
*   Log into your account on spectrometer workstation.
     Choose "Applications->Bruker->Tops Spin 1.3"   to start the Top Spin client.
     On BSMS keyboard Click the “Lift ” button. After you
     hear whistling gas coming from the top of the magnet and checked the flow of gas
     with hand place sample on air cushion and push the “Lift"  button again. The
     sample will descend softly into the NMR  magnet.
*  After you seen the green  “sample down” light lit, press “Spin”  button.
    The  light will be read till the sample is at the set speed and will turn green.
*  In the Top Spin under file menu select “New”
    Make sure that under “user” in this menu is your login name and under “DIR” is
    /opt/topspin. Put the file name, experiment # and processing data # and click “OK”
    button.
    At the prompt at the bottom of the “Tops Spin,  typerpar and choose proper
    parameters.
    For proton experiment select “stdh1.BBO” in case  of nmr400-2 or "stdh1.QNP" in case of
     nmr500-2 instrument
. Choose "All options" click “Read” and “OK”  in the next window.
    Click “Close”.
    For 13C experiment select  "std13Cdc.BBO" (nmr400-2) or "std13Cdc.QNP" (nmr500-2).
    We have following experiments to choose for two channel mode: power gated decoupling,
    gated decoupling and inverse gated decoupling. Power gated decoupling applies proton RF
    before and after pulse giving Nuclear Overhause Effect to strength the signal and 13C is
   decoupled. Gated decupling applies NOE but there is no  decoupling. Inverse gated
   decoupling gives decoupled spectrum without NOE.

* At the prompt, type rsh and select the default shims, "default.BBO" (nmr400-2) and
   "default.QNP" (nmr500-2). If different probe is installed the message will be posted.
   If there is no “lockdisplay” on the screen, at the prompt type lockdisp
   or choose proper icon from the “Top Spin” menu and  resize it according to your needs.
* At the prompt type “lock” and select your solvent from the list provided.
   Perform the magnet shimming.
* Select “Z” on the keypad, and change  value to maximize the signal
   Select “Z2”, and repeat maximization. Normally, you do not need to shim higher orders.
   Repeat above steps until the signal is maximized.
* Select lockgain, adjust until the signal is within second line from the top.
* If the lock signal becomes saturated lower the lock power. Most often the good
   working lock power can be found in the range of –-25 to –-35 DB.
* If the lock fluctuates decrease the lock power until is stable.
   Select “Standby”
   On nmr500-2 at the prompt type atma and wait for the message atma finished” Do not
   type any other command except “stop” while “atma” is in progress. This might results
   in freezing spectrometer. Nmr400-2 does not have automatic probe tuning and this needs
   to be performed manually. Contact facility manager if you wish to learn the tuning procedure.
* At the prompt, typerga, wait for the messagerga finished” before proceeding to next command.
   You can run experiment using icons or typing commands.
*At the prompt type “ns #, where # is the number of scans. (To see other acquisition
  parameters it is helpful click AcquPars or type eda)
*At the prompt, type zg, after spectrum is acquired, choose  "Processing -> Data
   Processing Guide". Click “Window Function and choose proper one to your
   molecule   “Window function type” and "Size of the line broadening”
  Go to the next menu and click “Fourier transform” and choose proper size “SI” for
  your spectrum. Click “OK”
  Click “Phase Correction” Choose “manual” and do it manually (recommended) or “automatic” (not always works).
* Click on “Axis Calibration, select solvent peak or TMS with the left mouse button,
   and type in the solvent chemical shift (reference table is on the bulletin board)
   Click “Baseline Corr.” button and chose proper for your molecule way to get good
    baseline (very important for accurate integration)
   Click “Pick Picking” button and generate the peak list of the spectrum.
* Click the “Integration button” and perform integration.
   When spectrum ready for plotting click the Plot/Print button. Choose print with layout and
    start the plotting editor. Click on spectra icon and put your spectrum into the window. Select “1D/2D-Edit”
    and customize spectrum according to your needs. Select the “File->Print” and you will see the preview.
    If you are satisfy click print and spectrum will be plotted.
* After experiment is completed:  “Click lock OFF” and “spin OFF” buttons.
    Quit the lock window.
    Retrieve the sample, Press “LIFT” button.
* Make sure the none of button “lock, “spin” or “lift” lit when you leave.
   Exit Top Spin
 * Make sure that  Top Spin exited completly, wait another 5-7seconds and from  Linux window choose “Action->logout”
 * Insert the plastic cap on top of the sample insertion port.
 * Record your time in the logbook

 

Short Instructions for basic operation
                          of nmr500-1 spectrometer.

 

 

*   Take out the plastic cap of the top of the sample insertion port.
*   Put your sample into the spinner turbine. Make sure that NMR tube is clean and  
     dry. Do not touch the turbine’s shaft by fingers. Use the insert gauge to find out  
     the proper sample depth. To achieve a good shimming, the length of a sample
     should be larger than the length of corresponding coil. We are using 5mm coils on
     all spectrometers.
*   Log into your account on spectrometer’s workstation.

     Go to Application->Bruker Topspin and double click Topspin3.0 .
     Click the "BSMS" icon on upper “Top Spin” menu or type in command line  bsmsdisp.
     The bsms interface will appear. Click the  Lift ” button. After you
     hear whistling gas coming from the top of the magnet and checked the flow of gas
     with hand place sample on air cushion and push the “Lift"  button again. The
     sample will descend softly into the NMR  magnet.
*   After you seen the green sample down” light lit, press “Spin”  button.
     The  light will be read till the sample is at the set speed and will turn green.
*  In the Top Spin under file menu select “New”
    Put the file name, experiment # (EXPNO)  and processing data # (PROCNO). Under “DIR” type  /opt/topspin/data/username/nmr.

    This is where your data will be stored. Click “OK”    button

    You may chose solvent.

    For Experiment Dirs. select /opt/topspin3.0/exp/stan/nmr/par/user.

    Select experiment.

    The experiment can be also selected by typingrpar choosing   /opt/topspin3.0/exp/stan/nmr/par/user directory.
    For a proton experiment selectstdh1.TXI ”, and  click
     “OK” in the   next window.  For any other nucleus   select appropriate one.
* At the prompt, type rsh and select the default shims. nmr500-1 is
   equipped with triple  nucleus probe and  default shims files has extension
   “TXI”,   default.TXI. If different probe is installed the message will be posted.
   If there is no “lockdisplay” on the screen, at the prompt type lockdisp
   or choose proper icon from the “Top Spin” menu and resize it according to your needs.
* At the prompt type “lock” and select your solvent from the list provided.
   Perform the magnet shimming.
   Click BSMS icon.
* Select “Z” on the keypad, and change it value to maximize the signal
   Select “Z2”, and repeat maximization. Normally, you do not need to shim higher orders.
   Repeat above steps until the signal is maximized.
   You may also try automatic shimming instead, by typing topshim gui. After shimming showed
   “finished” message close the menu. Come back to bsms menu
* Select lockgain, adjust until the signal is within second line from the top.
* If the lock signal becomes saturated lower the lock power. Most often the good
   working lock power can be found in the range of –25 to –35 DB.
* If the lock fluctuates decrease the lock power until is stable.
   Select “Standby”
   At the prompt type atma and wait for the message atma finished” Do not type any other
    command except “stop” while “atma” is in progress. This might results in freezing spectrometer.
* At the prompt, typerga, wait for the messagerga finished” before proceeding to next command.
   You can run experiment using icons or typing commands.
*At the prompt type “ns #”, where # is the number of scans. (To see other acquisition
  parameters it is helpful click AcquPars or type eda
*At the prompt, type zg, after spectrum is acquired, choose  "Processing -> Data
   Processing Guide"
. Click “Window Function and choose proper one to your
   molecule   “Window function type” and "Size of the line broadening”
  Go to the next menu and click “Fourier transform” and choose proper size “SI” for
  your spectrum. Click “OK”
  Click “Phase Correction” Choose “manual” and do it manually (recommended) or “automatic” (not always works).
* Click on “Axis Calibration”, select solvent peak or TMS with the left mouse button,
   and type in the solvent chemical shift (reference table is on the bulletin board)
   Click “Baseline Corr.” button and chose proper for your molecule way to get good
    baseline (very important for accurate integration)
   Click “Pick Picking” button and generate the peak list of the spectrum.
* Click the “Integration button” and perform integration.
   When spectrum ready for plotting click the “Plot/Print” button. Choose print with layout and
    start the plotting editor. Click on spectra icon and put your spectrum into the window. Select “1D/2D-Edit”
    and customize spectrum according to your needs. Select the “File->Print” and you will see the preview.
    If you are satisfy click print and spectrum will be plotted.
* After experiment is completed:  Click BSMS icon again.  “Click lock OFF” and
   “spin OFF” buttons
    Quit the lock window.
    Retrieve the sample, Press “LIFT” button.
* Make sure the none of button “lock”, “spin” or “lift” lit when you leave.
   Quit BSM menu
   Exit Top Spin
 * Make sure that Topspin fully exited wait another 5-7 seconds and from  Linux window choose “System->logout”
 * Insert the plastic cap on top of the sample insertion port.
 * Record your time in the logbook