VnmrJ - Mercury 300 Handout August 2009 1

VnmrJ - General Information for Hg_1, Hg_2, Hg_BI

NMR Facility Director: David VanderVelde, x3004,

NMR Facility Spectroscopist: Scott Ross, x6069,

NMR Facility Website: You can get copies of this and our other handouts there.

GLAs:Hg_1: Jessica

Hg_2: Paul

Hg_3: Sean Kedrowskix6009

Hg_BI: Ted

Daytona500: Chris

Indy500: Pam

FID-600: Chris

To get started, contact one of the Hg GLA’s to find out the date and time of the next training session.

Hg_1, Hg_2 and Hg_BI are 300 MHz Spectrometers with auto-switchable probes (1H, 19F, 13C, 31P). Hg_1 and Hg_2are located in the sub-basement of Crellin while Hg_BI is located in room 250 at the Beckman Institute.

Hg_1 and Hg_BI are both capable of variable temperature (VT) NMR in the range of (-80 - + 130oC)

Sign up rules:

Hg_1: M-F8:00 am – 10:00 pm30 minutes Sign up no more than 24h in advance.

10:00 pm – 8:00 amunlimitedSign up for nighttime hours no earlier than

Sa-Su8:00 am – 8:00 pmmax 2 hrs4 pm the previous day

8:00 pm – 8:00 amunlimited

Hg_2: M-Su8:00 am – midnight10 minutes

12:00 am – 8:00 amunlimitedSign up no more than 24h in advance.

Hg_BI: M-F8:00 am – 10:00 pm30 minutes

10:00 pm – 8:00 amunlimited

Sa-Suanytimeunlimited

****** Separate training is required for Hg_3, Indy, Daytona and FID-600. ******

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Preparing for your experiment

Here are a couple of things to do before setting up your NMR experiment:

  1. You are REQUIRED to subscribe to the NMR users mailing list. You can do so at this website:
  2. You must sign up for time on WebCal. Thewebsite is:
  3. When you first sign into your account, you must set up an account password. To set or change it, open a terminal window and typepasswd and hit enter. You’ll be prompted for your new password twice.Close the terminal window, logout and log back in.
  4. Before using the spectrometer, you must ALWAYS sign the log book. Enter the date, your initials and group initials, your lab extension (or a number at which you can be reached if you are an off campus user), sign up time, nuclei and solvent
  5. For best results, sample volume should be ~600µLwhich corresponds to about a 5 cm solvent height. Make sure the solvent height covers the depth guage window. PLEASE DO NOT ADJUST THE DEPTH GAUGE. Reduction of sample height below 4 cm canlead to longer shimming times and degrade peak shape.

VnmrJ - Mercury 300 Handout August 2009 1

VnmrJ Experimental Interface

  • The VnmrJ experimental interface consists of multiple sections which can be dragged to expand or contract in size, be hidden, or be closed independent of each other. Closed sections can be redisplayed using the View menu on the Menu Bar.
  • The Menu Bar provides access to operations such as choosing experiments, acquire, process, display, and plot a spectrum. It also provides access to settings and preferences.
  • The Tool Bar contains buttons that provide quick access to common functions, such as open a saved spectrum or save the current one.
  • The tabs for vertical panels allows you to choose what is displayed on the left side of the panel, including fast access to the commonest 1D and 2D processing functions, and a “holding pen” for commonly accessed items.
  • The Hardware Barcontains the trash can, Temp/Spin/Lock monitors, acquisition details and a history of all messages and a message display.
  • The Folder Tabs and Pages contain folders and pages which can be accessed by clicking on the respective tabs on the action controls bar. Use the Start panel to setup new samples and prepare for experimental runs. The Acquirepanel can be used to set acquisition parameters while the Process panel can be used to adjust processing parameters and process data.
  • The Action Controls are buttons that change depending on the currently displayed panel.
  • The Graphics Canvas displays current spectra and graphics
  • The Advanced Function Bar opens a command line entry field and text output field. In principle, you can run VnmrJ without ever accessing this feature, but most people use a mix of mouse and text driven operations in their daily work.
  • The Graphics Control Buttonsare used to control the interactive display in the graphics canvas. When a spectrum is displayed, these buttons enable you to perform interactive actions on the spectrum or FID. A few buttons are common to all display modes, with more that are specific to FID, 1D spectrum, 2D spectrum, or integral displays. The graphics and their functions are given below:

Experimental Setup

  • Login
  • Start VnmrJ

Click on the VnmrJ icon OR

type vnmrj in a Terminal window.

  • Eject D2O standard and Insert your Sample

Click the Starttab.Under the Standard page, click EJECT OR in the command line, type e to eject.

Wipe the sample and spinner. To insert your sample, click INSERTOR in the command line type i to insert.

  • Select experiment and solvent

Click on EXPERIMENTSin the menu bar, and then select a 1D or 2D experiment from the list.

Using the Start Tab, enter your sample information and chooseyour solvent from the drop down list. Alternatively, you can type in solvent = ‘solvent molecular formula’. The molecular formula of the solvent must be in lower case.

  • Spin and Temperature

The spin rate and the temperature can be adjusted from Spin/Temp page under the Start tab. The typical spin rate is 20Hz. For VT NMR instructions, see GLA.

  • Find z0

To do this, click on the Lock page in the Start tab. Turn the lock off and click on Find z0. This often establishes lock by itself. If not, it should be very close to resonance, and clickingLock Scan may be all that is needed. If that doesn’t happen, follow the manual lock procedure below. To autoshim, click onGradient Shim. This should take about 3 minutes. The GLA will explain the current performance of gradient shimming on the instrument you are being trained on.

  • Manual Lock

Click on the Lock page in the Start tab. Turn lock off to ensure that you find the best signal, click on Lock Scan, and increase power and gain.

Adjust Z0 to maximize lock signal (look at the #) so that there are fewer periods in the wave. The increment can be changed from 1 to 10 to 100 by clicking the middle mouse button. To change the DAC value, move the slider with the mouse, enter a value directly or click the button with the left (decrease) and right (increase) mouse buttons.

The line that crosses the spectral window represents how close the deuterium resonance is to the lock frequency. When the two are matched, the line should be flat.

Turn the lock on. Power and gain should be adjusted so that the signal is not saturated and they are close to the same value. Do not adjust the lock phase. Click on Lock Scanto close the lock display.

  • Reload standard shim file (optional)

The standard shim file provides a consistent starting point for shimming, and should give reasonable shims. In case of difficulty with finding lock, or if the lock level seems very low, try this first. To load the current shim file, type rts on the command line, then enter standard. Then type suto load the shim values into hardware.

  • Shim

When shimming, the current in shim coils is adjusted to make the magnetic field as homogeneous as possible.

Click the Shim page in the Start tab. A lock meter appears and controls for Z1 and Z2 appear next to the top right of the meter. Make surethe Lock Scanbutton is not depressed.

Click the left mouse button on the button to decrease the value by the amount of the “increment” displayed on the right side of the button. Click the right mouse button to increase the value.

Maximize signal by changing Z1 and Z2 in either direction. Start with Z1, go to Z2, and then back to Z1 iteratively until the lock signal is maximized. Adjust the lock gain if necessary (if lock signal > 100). After shimming, return to lock window and adjust power and gain so lock signal ~ 70.

Data Acquisition and Processing

  • Set up experiment parameters

To view standard parameters, click on the Acquire tab. To change the spectral width, relaxation delay and number of scans, click on the Acquisition page to make changesOR typed1 = ##or nt = ##. Set the block size by typing bs = ##. This will allow you to Fourier transform the data after the number of scans indicated in the block size.

  • Acquire spectrum

Type ga or go to acquire spectrum. ga allows you to stop by typing saand resume acquisition by typing ga again. You can also click the Acquire button to start an acquisition. Click on Stop to pause the acquisition. Clicking on Acquire again after stopping will resume the acquisition (You can also do this by click on acquisition from the menu bar and select resume acquisition). During or after acquisition, type wft to transform the data and view spectrum OR after data is transformed, click the “display FID graphics” to display FID or click the “1D Spectrum graphics” to display a 1D spectrum.

Type aph to autophase. To terminate the acquisition, type aa or click Stop.

  • Data Processing and Display Tools

Click on the Process tab and then the Display page. Several parameters such as the display mode, axis, amplitude scaling, screen position, reference, find peaks, baseline correction and others can be accessed and manipulated from this page. The baseline correction can only be performed after integration.

  • 1D Spectrum Display Buttons

To the left of the display is the spectral display graphics control buttons.

Click on the Cursor or Box to change from a single cursor to a box (vertical red lines). To expand the area between the cursor, click on the Expand button. Type fullorfto display the full spectral area. The Grab and move button opens the interactive spectral window mode. Use the left mouse button to adjust the starting time of the display. Use the right mouse button to adjust the width of the display. Then use the left button again to move the display left or right.

Previous commands work just the same and can be typed into the command line. A list of useful commands is provided on page 6.

  • Phase

Click the Phase button. Place the mouse arrow on the region of interest and click the left mouse button. A horizontal line appears and two vertical cursors are place on either side of the mouse arrow. Within the two vertical lines, move the mouse above or below the horizontal cursor.Click and drag the left or right button to adjust the phase. The left button can be considered the “coarse” adjust while the right button the “fine” adjust.

Move to another region outside the vertical lines and repeat until the spectrum is phased. To exit the interactive phasing mode, select Cursor or Box.

  • Integration

Click on the Set integrals button then click on Integral resets. To select integrals, left click on either side of peak to be integrated going from left to right. To undo integrals (while in RESETS mode), right click. Integrals are undone from right to left. When done, click on full integral three times (i.e. full integral, no integral then set integral). To clear all integrals, type cz in command line. To exit integral resets mode, click the return button.

Integral values can be set and/or normalized in the cursors/integration page.

To print or display integral values, vp≥12. Type vp=12. dpir displays integral values below the scale. pirplots integral reset values. Integral lines must be displayed on screen to print.

  • Baseline correction (optional)

The dc (drift correction) command turns on a linear baseline correction, using the beginning and end of the displayed spectrum. The cdc (clear drift correction) command turns off this correction.

The bc command turns on 1D and 2D baseline correction. This will only work if all peaks are integrated.

  • Peak frequency

Peak frequencies above a selected height can be displayed and plotted. Click the Threshold button; a horizontal line will appear. Hold down the left mouse button while dragging the mouse to select the height.

dpf displays peak frequencies on screen. ppf plots peak frequencies above threshold. To exit this mode, type ds to display spectrum.

  • Plot spectrum

To set up printing for the first time, go to the File menu, choose Printers … and make a selection from the drop down menus (usually it will be ljplot and ljprint).

The region displayed on the screen will be plotted. Type pl followed by any of the following commands:

pscale prints scale

pir prints integral reset values

ppf prints plots frequencies

pltext prints text line

ppa prints minimal parameters

pap prints ALL parameters (incl. text).

Then type page to print.

For example: pl pscale pir pap page will print the spectrum, horizontal scale, integral values, all parameters, and text.

pll page will print a list of the plot frequencies and intensities on a separate page.

Alternatively, you can click the Plot page under the Process tab. In this page, you can select all the items you’d like to see printed, then click Auto Plot, or Manual Plot. You can plot directly to a PDF file, or choose Preview to open the spectrum in Adobe Acrobat. If you like it, you can also save the PDF file from there after previewing it. Remember to select Printer as the destination again to get paper plots!

  • Save spectrum

Click File and choose Save As … The default directory will be vnmrsys/data in your home directory. You can create additional folders there to organize your data, or save spectra up to your home directory. To save a spectrum, enter a file name (it should not contain spaces or nonstandard characters). The program will automatically add the extension .fid to your name and create a folder containing your raw data in binary form, and some text parameter files. Don’t store personal data in system level folders above /home/your-name. All data in or below your home directory is backed up nightly to the server.

  • Retrieve old spectra

To pull up saved data, use the file browser on the left to open up your data folder. Double click on the fidfile you wish to open (or drag it onto the graphics canvas) and the spectrum will be displayed on the graphics canvas.

You canaccess your data remotely using Novell-style network drives from each spectrometer, reflecting all data currently on the spectrometer, or from the server, which holds data older than what is retained on the spectrometer. You can also use any secure ftp client that supports the SSH2 protocol to retrieve data from the spectrometers. (FileZilla is a popular Windows-based secure ftp program.) Either of these can be useful for making your own backup copies of spectra, which we highly recommend you do, or for using our site licensed MestReNova software for processing and analysis on your own computer.

  • Finish

Eject sample and re-insert standard. Return to the Lock page under the Start tab and lock on the D20 standard.Adjust the power and gain so that the lock level sits at ~ 50. Exit VnmrJ by typing in exit in the command line or by go to Utilities on the menu bar and click Exit. To logout, clickActions on the menu bar on the desktop, then Logout.

  • Problems

All problems with the spectrometer should be reported to David Vander Velde, Scott Ross, or a GLA AND noted in the log book.

If your sample breaks in the probe, report the solvent and identity of the compound in your sample to lab staff so the probe can be promptly and safely cleaned. THIS QUALIFIES AS AN EMERGENCY.

If the D2O standard is broken or missing, please notify NMR personnel.

If the printouts have big black streaks on them, then the printer needs new toner. Notify NMR personnel.

If you are having problems locking and/or shimming, try reloading the standard shim set if you have not done so. Verify the lock phase is correct for the system. Then try a standard sample to see if the problem is with your sample. If none of these things work, contact NMR personnel.

VnmrJ - Mercury 300 Handout July 2009 1

Useful Commands

nt=###set number of transients

bs=##set block size

sw=####change spectral width

d1=##change relaxation delay

rts(‘standard’) sureload standard shim file

acqidisplays ACQI window, try this command if ACQI button does not appear.