# NMR Checklist

## Before Pulsing

Make sure:

1. The power levels and pulse durations on all channels do not exceed safe levels.

2. The duty cycle of the pulse sequence experiment is not above 5%.

## After the Experiment has Started

Make sure:

1. There is signal in the FID. There is no point in running the spectrometer if there is no signal.

2. The water signal is properly suppressed. You will have to stay for a few FIDs to make sure the water suppression is consistent as the phases of 1H pulses are being incremented.

3. The receiver gain is above at least 64 without saturating the digital receiver. The signal-to-noise ratio goes down as the gain goes down. Typically your water suppression isn’t good enough if the RG is below this value.

4. The receiver gain is not too high. Monitor the level of the digitizer limits, and set the gain to a level in which the FID is not greater than 1/2 of the digitizer limits. ‘rga’ sets this automatically, but you should not set the gain to a level higher than 512 to avoid the possibility of overflowing the ADC.

5. The temperature is set to the desired temperature. The distribution of conformers changes with temperature, and therefore chemical shifts change with temperature. Spectra at different temperatures may not be directly comparable.

6. The lock signal is aligned to one of the horizontal grid lines in lockdisp. A change in lock level reports on changes in the shimming or B0 field during your experiment. If there were large changes, you should consider recollecting the experiment and alerting the spectrometer manager since the spectrometer could be seriously damaged.

7. Autoshim is turned on. This maximizes the lock signal, and concomitantly the FID signal, by making incremental changes to the shims. Our current setting optimizes Z and Z2 every 3 seconds. The exception to this rule is when you’re running liquid crystal samples since these might not be completely homogeneous over the sample volume.

8. The gradient pulses are pulsing. If your pulse sequence has gradient pulses, these pulses should dephase the lock signal, which will then return to equilibrium with an exponential recovery. If the lock signal stays constant while there should be gradient pulses, then the gradient pulses are not pulsing.

9. The system is well tuned. A properly tuned and matched channel should reflect less than 5% of its power. Whenever the spectrometer is pulsing, check the amplifier control to ensure that the reflected power (red bars) is less than 5% of the forward power (green bars) for all pulsed channels.

10. Probe heating is minimal. Nutation pulses can have a strong electric field component that heats the sample. This can be monitored by decreases in the lock signal during the pulse sequence. If heating appears substantial, double check your power levels to make sure you are not decoupling continuously or using a saturating pulse at high power.

11. The cryogen levels are topped up.

# NMR Software Commands

## Starting an Experiment

• xwinnmr or topspin: start the NMR software.

• Lock lift: Eject the last sample, and insert your sample into the spinner.

• DO NOT INSERT THE SPINNER IN THE NMR WITHOUT AN NMR TUBE.

• Lock lift: Drop the you sample in the spinner. Check the sample temperature before dropping your sample.

• edte: open the temperature controller and set the temperature.

• lockdisp: open the deuterium lock display window.

• lock: select the deuterium solvent to be used in the experiments (may or may not be needed).

• topshim or gradshim: open the gradient shimming procedure to shim the magnet. A manual shimming may replace or supplement this step.

• wobb f1: tune and match the F1 channel (1H) of the probe.

## Acquisition

• zg: zero-go. Start the data acquisition of the currently-opened dataset.

• gs: Pulse and repeat the first scan of the currently-opened dataset. This is used for tuning pulse acquisition parameters.

• multizg: zero-go multiple experiments in a row. If sequentially numbered experiments do not exist, the experiment will be copied.

• multi_zgvt: zero-go multiple experiments in a row. If sequentially numbered experiments do not exist, the experiment will be copied. Allows for the use of a list of temperatures and an equilibration period at each temperature.

• multizg_zgvd: zero-go multiple experiments in a row. If sequentially numbered experiments do not exist, the experiment will be copied. Allows for the use of a list of pre-acquisition delays.

• edlist: allows the editing and creating of variable parameter lists (e.g. vp, vt, vd).

• a: open the acquisition window for the experiment currently being collected.

• ased: edit pulseprogram acquisition parameters.

• eda: edit acquisition parameters.

• stdisp: open the shape tool.

• o1, o2, o3, o4, o5: Set the carrier frequency offset (in Hz) for channels 1, 2, 3, 4 or 5, respectively. This is relative to the spectrometer frequencies, SFO1, SFO2, SFO3, SFO4, SFO5.

• o1p, o2p, o3p, o4p, o5p: Set the carrier frequency offset (in ppm) for channels 1,2,3,4 or 5, respectively.

• rg: Receiver gain.

• ns: Number of scans.

• ds: Number of dummy scans—scans that aren’t saved.

## Processing

• edp: edit processing parameters.

• fp: Fourier transform and phase 1D spectrum.

• efp: Fourier transform and phase 1D spectrum after exponential apodization.

• qsin: Apply a sine-bell apodization window function.

• xfb: Fourier transform and process 2D spectrum.

• xf1 or xf2: Fourier transform and process only dimension one (xf1) or dimension two (xf2) of a 2D spectrum.

• stsi and stsr: Extract final spectrum starting from point number ‘stsr’ for a total number of ‘stsi’ points.

• rser: Extract an FID from a 2D spectrum for processing.

• wrp: Write a current processing of an FID to a specified processing location.

## Spectrometer Configuration (Advanced)

• wsh: write the current shim currents to a file.

• rsh: read the shim currents from a file.

• setres: edit configuration parameters.

• edasp: view or change routing parameters.

• setpreamp: view or change the pre-amplifier routing parameters.

• edprobehead: edit the current probe configuration

• ii: Initialize interface. This resets spectrometer computers and can help fix spectrometer problems. Try also using with the ‘restart’ parameter.

# NMR Reference Information

## Useful NMR Equations

Context Equation
Power level Calculation (dB) $pl_2 = pl_1 -20 \cdot log \left( \frac{\nu_1}{\nu_2} \right)$
Field calculation (Hz) $\nu_2 = \nu_1 \cdot 10^{(0.05(pl_1 - pl_2))}$
90º null pulse (rad/s) $\omega_1 = \sqrt{15} \Omega$
180º null pulse (rad/s) $\omega_1 = 3 \Omega$
T1 estimate (s) $T_1 = \frac{-1}{ln(1 - I(d1)/I(\inf))}$