PNMR for Liquid Samples

PNMR is a Windows95 program that provides an analog-to-digital interface between the data acquisition computer and the NMR. It is used to set data acquisition parameters such as receiver gain, sweep width, relaxation delay, etc., starts and stops acquisitions, digitizes the incoming signals and writes the resulting file to the hard disk. Basically, the PNMR program handles everything except data processing, which is performed exclusively by the NUTS program.

The following describes the basic PNMR commands needed to generate 1D spectra and to save data to disk.

The PNMR program runs in a window, usually with a blue background. It always displays a listing of instrument configuration settings, which can be changed depending upon the sample under analysis or the type of experiment being run.

The top of the window is used to display the FID as data are acquired. Listed at the bottom of the window are the data acquisition parameters, a brief description of what the parameter does, and the current parameter setting.

Note the PNMR program issues messages during data acquisition that appear in the top right corner of this main window. Read these messages before proceeding with data processing. Wait until the PNMR message window disappears after data acquisition before switching to the NUTS window for data processing.

Basic Explanations of PNMR commands:

Command Prompt for PNMR are typed in at the prompt and issued by pressing the 'Enter' key. The command prompt appears at the bottom left of the main PNMR window and looks like this: H1>. The 'H1>' prompt means that the instrument is ready for a proton analysis. There are other prompts to indicate instrumental readiness for other types of analyses. If the prompt is anything other than 'H1>' type: NU H1 and then press the Enter key. This should result in an 'H1>' prompt. Then re-initialize the instrument settings by typing: RE H1.INI and then press the Enter key. The instrument should now be ready for operation. The command prompt is like the DOS prompt C:\>

A summary of the most common commands is given below. The commands arranged in the order of use.

Start Data Acquisition -- At the command prompt, type: ZG and press 'Enter'. This starts data acquisition mode and the FID appears on screen as the analysis progresses.

Start Data Acquisition and Set Receiver Gain Automatically -- At the command prompt, type: ZGA and press 'Enter'. This starts GS mode and automatically selects a suitable Receiver Gain (RG) setting before switching to data acquisition mode. In data acquisition mode the FID is on screen as the analysis progresses. While the total sample run time is a little longer than using ZG, it is excellent when analyzing multiple samples of unknown concentrations. Remember ZGA may have difficulty determining which of two gain settings is the optimum and oscillate back and forth between them. The gain value can be seen at the top of the screen while ZGA is running. If oscillation occurs, press Ctrl-K to quit and manually set the Receiver Gain parameter to the lower of the two values, then start the acquisition using ZG.

Changing Data Acquisition Parameter Values -- To change any of the data acquisition parameters listed above; type the two letter abbreviation, a space, the new value, and then press the 'Enter' key. For example, typing, RG 10 and then pressing 'Enter' changes the Receiver Gain to 10. Note that when a parameter is changed, it is updated in the list immediately.

Quitting the Program -- To quit the program, type: QUIT and then press 'Enter'. To quit GS mode or an active data acquisition, press Ctrl-Q to return to the command prompt, then quit.

Write the Current FID to a Data File -- Newly acquired (raw) data is stored in a temporary file named pnmr.fid which is overwritten with each successive acquisition. To save raw data with a different file name and/or to a different directory; acquire the data, wait for the command prompt, and then type:
WR <pathname><filename.fid> and press 'Enter'

Note that there must be a space between WR and <pathname>. An example is: WR A:\MYDATA.FID which would write the file MYDATA.FID to a floppy disk in the A: drive. Always save data to an external floppy.

Run the Basic Shimming Routine -- Load the sample tube labeled 'water' which should be in the sample rack on the bench behind the magnet. Set RG to 5. At the 'H1>' command prompt, type: SHIM and press 'Enter'. PNMR enters GS mode and displays a continuous FID and waits for an imput to set RG. Press Ctrl-Q to quit GS mode and start the shimming routine. As the shimming routine runs it asks questions about the settings of the shim controls, and also tell how to change the settings as it runs. Follow the instructions on screen. When the optimization is finished, the shimming routine will stop. Record the new shim settings in the Logbook, along with the date, time, user name, professor, and write "Basic Shim Procedure".

Reinitialize Spectrometer Hardware -- At the command prompt, type: INI and press 'Enter'. The spectrometer is reset and the default PNMR settings loaded.

GS Mode -- GS mode is used in manual mode only during the basic shimming routine. Remember, to quit GS mode, press Ctrl-Q or Ctrl-K.

Basic Explanations of PNMR data acquisition parameters:

SI -- SIze of the file which will hold the collected data. Increasing the size parameter increases the number of data points collected per second, which can increase the resolution of fine structure in the final spectrum. SI can be set to a maximum of 32k (32768) but will not affect chemical shift or integration of the final peaks. SI is linked with SW (see below). Note that more is not necessarily better, and generally this parameter is left at the default value of 8k (8192).

NS -- Number of Scans collected during data acquisition. Generally, acceptable data can be collected using only one scan, but increasing the number of scans will improve the signal-to-noise ratio for the final spectrum. Note that the NS parameter is displayed as 'X/Y' where X is the number of Dummy Scans (DS, see below) and Y is the number of data acquisition scans (NS).

DS -- The number of Dummy Scans performed before the data acquisition scan sequence. Dummy scans pulse the sample in exactly the same manner as the data acquisition scans (NS), except that the receiver is switched off. This allows the sample to respond to the pulse program and relax before data is acquired. Generally, dummy scans slightly reduce the magnitude of the signal from the initial data acquisition pulse, but usually improves (narrows) the peak width in the final spectrum.

RG -- Receiver Gain parameter, sets the gain of the receiver coil preamplifier. Setting a higher number improves sensitivity, but there are limits. RG is dependent upon the concentration of the sample and thus may require adjustment for each and every different sample preparation. What is most important in setting RG is to avoid excessive amplification of the signal, which overloads the preamplifier and distorts the data. When overloading occurs, the FID is displayed in red:

It's usually best to set DS 0 and NS 1 until the correct RG setting is found for the sample, then set DS and NS to higher values. If there is an error message, reduce RG by 5 and run the sample again. Continue reducing RG in increments of 5 until the error message no longer appears after data acquisition. However, for very fine adjustments increase RG in increments of 2 until the error message appears again, then back off by two units.

The normal exit message displayed if RG does not overload the preamplifier will not show when the RG is set too low. If RG is too low, the signal-to-noise ratio of the spectrum will be adversely affected. This can be seen in the NUTS window as a very noisy baseline and relatively small sample peaks in the processed data.

In general, start data acquisition using ZGA instead of ZG. Note that RG 20 is the optimum value for the ethylbenzene test sample, and that RG 5 is optimum for the water sample. See GS Mode for realtime RG optimization. See ZGA for automatic RG adjustment before data acquisition.

PW -- Pulse Width timing parameter. PW sets the length of time that the RF pulse is on, and is adjusted so that the sample protons respond by aligning their magnetic 'spin' vectors at a specific angle to the initial magnetic field of the large NMR magnet. Different pulse durations result in different angles of alignment. A pulse duration resulting in an angle of 90 degrees is called a '90 degree pulse', and results in the strongest signal from the sample. We will only use a 90 degree pulse program for proton analysis, but other timings are also named for their characteristic alignment angles; '45 degree pulse', etc., and have specific uses. These alternate pulse programs will be described in more detail in other experiment.

RD -- Relaxation Delay timing parameter. RD sets the length of time that the data acquisition software waits between successive RF pulsing of the sample. When the sample is RF pulsed it's energy increases as the protons magnetic 'spin' vectors are forced out of alignment with the initial magnetic field of the large NMR magnet. When the pulse stops, the sample begins to 'relax' as the protons magnetic 'spin' vectors return to alignment with the initial magnetic field, but this relaxation does not occur instantaneously. Depending upon the sample, a short period of time is required to ensure that all protons in the sample have returned to alignment, and this period of time is called the Relaxation Delay. If all of the sample protons are not allowed to relax completely between pulses, phasing of the spectrum and peak integrations will be adversely effected.

See T1 and T2 Experiment for more detail on optimization of RD. While the default time of 1 second is adequate for most small molecule samples, if RD is set to 3 seconds it ensure that almost all sample types will run OK. Note that if NS=1 then RD has no effect other than increasing run time.

SW-- Sweep Width of the spectrum in Hertz. SW defines the range of frequencies that are swept during data acquisition. The default setting of 1000 Hz is adequate for almost any sample, corresponding to a maximum PPM value of 16.67 in the final spectrum. Note that SI and SW are linked. For a given SI, the wider the sweep width the lower the apparent resolution of the spectrum. This occurs because a fixed number of data points must be spread across larger and larger intervals. In almost all cases, however, the default values of SI=8192 and SW=1000 are quite acceptable.

SF -- Spectrometer Frequency. The operating frequency of the local oscillator and the resonance frequency of protons in the applied 14.092 Gauss magnetic field. The default value is 60.01 MHz. Never change these values.

DF -- Decoupler Frequency. The operating frequency of the decoupler oscillator. Not used for proton NMR. The default value is 1 MHz. Do not adjust this value.

DP -- Decoupler Power. Not used for proton NMR. The default value is 0 dB. Do not adjust.

T aq -- Total acquisition time for the experiment, given in seconds. This is calculated from the values of the data acquisition parameters.