After installation and configuration of vnmrJ follow the following steps to obtain NMR data.
Procedural Steps to Acquire NMR Data with Varian 300 MHz NMR
A Linux workstation is used to process NMR data.
Preparing for an experiment
Before beginning an experiment, the following must be done: • Start VnmrJ • Prepare the sample and position the sample tube in a turbine • Load the probe file • Install the probe, tune, and calibrate if necessary.
Starting VnmrJ
A generic procedure using the same typed commands used for VNRM 6.3C can also be used. The following menu allows users to open VNMRJ via an icon as well as open a browser or terminal window.
A user name must first be assigned by the system administrator before login. Start VnmrJ from a command line in a Terminal window or by clicking the VnmrJ icon in the CDE window. To Start VnmrJ from a Terminal Window. First open a Terminal window:
a. Right-click in an open area of the workspace. b. In the Workspace Menu, go to Tools->Terminal. At the command line, enter vnmrj. host:username> vnmrj Press the Return key after typing vnmrj. To Start VnmrJ from the CDE Toolbar click on the vnmrJ icon. Read about the Sample Position Using the Depth Gauge and Probe tuning. It is not required for normal proton and carbon analyses. Details for various probe tuning protocol are described.
Selecting an Experiment VnmrJ provides several ways to choose and load an experiment. First from the menu bar or from the Locator. After an experiment is selected, VnmrJ reads and loads the standard parameters and then reads the probe file and loads the probe calibrations. Menu Click on Experiments in the menu bar, then click on a 1D experiment in the list. The list of experiments contains some submenus.
Locator Click on an experiment in the Locator and drag it into the graphics canvas (or double-click on the experiment).
Ejecting and Inserting the Sample The spectrometer is equipped with hardware and software to provide computer control of sample ejection, insertion, spinning, locking, and shimming. This section covers computer controlled sample ejection and insertion.
To Eject a Sample Always eject first (even if no sample is in the magnet) to start airflow to carry the sample. The eject air is turned on and, under computer control, the sample, if present, rises back to the top of the upper barrel. Remove the sample and replace it with another sample. Using the Start Tab The Insert and Eject buttons are on the Start tab. 1. Click the Start tab to open the setup tab. 2. Click the Eject button.
To Insert a Sample When inserting a sample, the sample tube gradually lowers down the upper barrel under computer control. After a five-second delay, the bearing air is turned off momentarily, allowing the turbine to seat properly. The two-stage sample insertion operation is provided for safety reasons. Because the tube itself is used as the bearing surface in this barrel, the tube must drop down the barrel slowly enough to avoid breaking when contact is made with the conical guide. The second stage drop then permits the tube to slide into the bearing cylinder. Using the Start Tab 1. Perform a sample ejection (even if no sample is in the magnet) to start airflow to carry the sample. 2. Insert the sample by placing it in the top of the upper barrel. The sample must be supported on a column of air before it is released. 1. Click the Start tab to open the setup tab. 2. Click on the Standard page. 3. Click Insert. 3. Spinning the Sample
Spinning the Sample The liquids Spinner panel appears after selecting Spin/Temp page under the Start tab, for the Liquids Spinner.
Liquids Spinner The spin rate is adjusted from the input window or the Acquisition window. Typical spin rates are 15 for 10-mm tubes and 20–26 for 5-mm tubes. When a sample is inserted, the last entered spin rate is used to regulate sample spinning. The actual spin rate is indicated three ways: • The Spin chart displays button on the hardware bar displays a history of the sample spin rate.
• In the Acquisition Status window, the actual rate is given as well as a spin regulation indication. • In the remote status unit, the spin rate is shown by the spin light: If light is off, the sample is not spinning. If light is blinking, the sample is spinning but not at the last requested rate. If light is steady, the spin rate is being regulated at the last requested rate.
1. Click the Start tab. Select the Spin/Temp page. The controls for changing spinning speed consist of an entry field, a slider bar, and a button for disabling or enabling spinning. 2. Adjust the spinning speed with either of these methods: • Enter a spin rate in the text entry field. • Drag the slide control. The value changes proportionally as the mouse moves. • Click in the slider bar to move the slider by one increment. Sample Temperature Set the temperature for VT control in the Standard page and regulate the temperature by clicking on Spin/Temp page. The following steps describe a typical operation sequence: 1. Open the Spin/Temp page under the Start folder. 2. Set the desired temperature by entering a value or using the slider, and click Regulate Temp. 3. Set up the acquisition for the experiment as usual, using the Acquire folder. 4. Click the Temp button on the hardware bar to display the temperature display chart. 5. Start temperature control with the Setup Hardware button on the Start folder, or with the Acquire button on the Acquire folder.
To Change the DAC Value 1. Shift-left-click on the button. 2. Enter a new value and press Return. Lock Buttons and Controls The Lock and Shim buttons (Z0, Lock Power, Lock Gain, Lock Phase, and Z, X, and Y shims) provide on-the-fly adjustment. The slider values can be moved with the mouse or entered directly.
Lock Control Methods A number of methods are available for controlling lock on the Standard page in the Start tab: • Leave lock in the current state. • Run an experiment unlocked. • Use simple autolock. • Use optimizing autolock. • Perform full optimization of lock.
Protocol for Adjusting the Shims
Adjusting Shims -- Shim coils produce small magnetic fields used to cancel out inhomogeneity in the static field. In shimming, the current in shim coils is adjusted to make the magnetic field as homogeneous as possible. Computer-controlled digital-to-analog converters (DACs) regulate the room-temperature shim coil currents. Every time a new sample is introduced into the magnet or probe is changed, it is necessary to readjust the shims. Various protocols for adjusting shims are described.
• Loading Shim Values • Loading a Shim File • Saving a Shim File • Shim Gradients • Automated Shimming on the Lock • Which Shims to Use on a Routine Basis • Shimming Different Sample Geometries
Data Acquisition • Acquiring a Spectrum • Acquisition Settings • Pulse Sequences • Parameter Arrays • Stopping and Resuming Acquisition
• Automatic Processing • Acquisition Status Window
With a spectrometer configured to perform the proper experiment, with a sample spinning, locked, and shimmed, select parameters to acquire data. There are two aspects to selecting parameters. The first is the frequency-related aspect—setting the position and size of the spectral window. The second is the pulse sequence-related aspect. Processing Data • Weighting Function • Interactive Weighting
• Fourier Transformation • Phasing • Advanced Data Processing Displaying FIDs and Spectra • Displaying a FID or 1D Spectrum • Display Tools • Graphics Control Buttons • Phasing • Line Tools • Spectral Referencing • Stacked FID Display • Inset Display • Integration •Molecular Display and Editing (JChemPaint and Jmol)
Plotting and Printing • Plotting • Plot Designer • Color Printing Plotting and printing of data are highly individualized activities. Each user has specific ideas about proper formats, necessary expansions, etc.
Plotting Plotting is based around the concept of a plot file. Items selected on the Plot page are added to a temporary plot file and the Plot Page button submits the plot file to the plotter. The Clear Plot button removes the plot file After the spectrum or FID is displayed, you can set up and submit a plot using the selectionson the Plot page under the Process tab.
Working with Experiments In the Locator, NMR experiments are contained in Workspaces (also called experiments). • To view the Experiments in the Locator, click the Locator Statements icon ( ) and select Sort Workspaces. • To open (connect to or join) an Experiment, drag it to the graphics window. • To create a new Experiment, click File -> New Workspace. • To delete an Experiment, drag the Experiment from the Locator to the trash can icon. To view the Experiments on a system in the Process tab Text Output page, enter explib. The monitor displays the Experiment library of the currently available Experiment files (exp1, exp2, ..., exp9999). When multiple experiments are created, an issue arises concerning how to individually work with each experiment. To handle this matter, only one experiment is allowed at a time to be currently active (i.e., in the foreground for manipulation), although background processing can be occurring in other experiments at the same time. The mp, mf, and md commands move (copy) FIDs and parameters between Experiments: 1. Click on Edit 2. Select one of the following options: • Move Parameters… • Move FID… • Move Text… • Move Display parameters… 3. Fill in the information requested in the popup window.
Multi-FID (Arrayed) Spectra Many NMR experiments require obtaining a series of FIDs, related to each other through the variation of one or more parameters. For example, suppose it is necessary to run a series of spectra at four different temperatures: 30°C, 50°C, 70°C, and 90°C. Instead of acquiring four separate sets of data, it is possible to create an array in which the temp parameter is given four successively different values. These four subexperiments are now all treated as a single experiment. Entering go begins successive acquisition of all four experiments. One command can be used to transform all the spectra, one command to display all the spectra on the screen simultaneously, one command to plot all the spectra, and one command to save all the spectra. • Arrayed Parameters • Multiple Arrays
• Setting Array Order and Precedence • Interactively Arraying Parameters • Resetting an Array • Array Limitations • Acquiring Data • Processing • Display and Plotting • Pulse Width Calibration Step-by-Step
