Getting Started

• 1: Launching OVJ
• 2: Tuning the Probe
• 2.1: Using the nanoVNA
• 3: Acquiring a Proton Spectrum
• 3.1: Processing 1D Spectra in DNPLab
• 4: Saving the NMR Spectrum

1 - Launching OVJ

Launching OVJ

OVJ can be launched in two different ways: 1) by double-clicking the vnmrj icon on the desktop or, 2) by opening a terminal window and launching it from the command line by typing:

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vnmr

Setting the Spectrometer Frequency

If this is the first time you are using OVJ, the spectrometer frequency has to be set to the correct value.

In OVJ, the spectrometer is historically set by setting the frequency of the deuterium (²H) lock frequency.

The ratio between the (¹H) and (²H) frequency is approximately 6.51. For example, to set the spectrometer to a ¹H frequency of 14.5 MHz the user has to set the spectrometer frequency to 14.5/6.51 = 2.227 MHz. To set the spectrometer frequency:

1. In OVJ go to Edit -> System Settings

   

2. In the window that appears enter the deuterium (²H) lock frequency in MHz.

   

Alternatively, the spectrometer frequency can be set from the OVJ command line using the lockfrequency parameter:

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lockfreq = 2.27

Next, you are ready to Tune the Probe.

2 - Tuning the Probe

Tuning the NMR Probe

To tune the NMR probe to the spectrometer frequency follow these steps:

1. Note down the spectrometer frequency. This does not have to be an exact value, but should be close (within 0.1 MHz of the operating frequency).
2. Switch on the nanoVNA and set the center frequency to the spectrometer frequency (set it to the frequency of the nucleus you want to observe, not the ²H lock frequency). Set the span to a value of 1-2 MHz.

3. Disconnect the NMR probe from the Bridge12 SCN spectrometer and connect it to channel 0 (CH0) of the nanoVNA.
4. You should see a ‘Tuning Dip’ on the nanoVNA. If you do not see a tuning dip try one of the following things:
   • Increase the span of the VNA to scan a broader frequency range
   • Change the matching on your probe
5. Use the slider at the top of the nanoVNA to move the marker to the spectrometer frequency (within +/- 0.1MHz). The marker will tell you the absolute value of the S11 parameter at the spectrometer frequency (see image below, S₁₁ = -7.8 dB).

7. Turn the tune and match capacitor of your probe to achieve a minimum reflection. In general, the tune capacitor will shift the dip up in down with frequency, while changing the match capacitor value will increase the depth of the dip. Optimize both capacitor values for a minimum in reflected power. The probe is tuned once you achieve the lowest value for S₁₁ (see image below, S₁₁ = -40.9 dB)

Next, you are ready to Acquire an NMR Spectrum.

2.1 - Using the nanoVNA

The Bridge12 SCN is delivered with the nanoVNA, a pocket-size vector network analyzer (VNA) to tune the probe to the transmitter frequency of the spectrometer.

The nanoVNA has two channel and has many different ways to display the (complex) S parameters. However, in the following we provide a brief set of instructions to setup the nanoVNA display to:

• Only show the reflected power from the probe (S₁₁)
• How to calibrate the nanoVNA.

The nanoVNA will store these settings, so you only have to go once through these instructions.

For a complete reference please visit the nanoVNA Webpage.

Setting up the Display

To setup the display:

1. Tap the touchscreen to show the menu
2. Tap the Display button (top right corner)

3. Tap the Trace button on the display

4. For convenience, select only Trace 0 by tapping on it. The selected trace is highlighted with a colored background (yellow for Trace 0). Unselect any other traces by tapping on the button.

5. To leave the menu tap somewhere on the touchscreen.

Setting the Frequency Range

1. Tap on the touchscreen to show the menu
2. Tap on the Stimulus button

3. Next, tap the Center button
4. On the next screen, enter the spectrometer frequency using the number pad and press the M button to indicate that the entered frequency is given in MHz.

5. Next, tap the Span button and enter the frequency range to observe the resonator tuning dip. Typically 1-2 MHz is a good range to start with.

Calibrating the nanoVNA

The nanoVNA is calibrated using a basic OPEN-SHORT-LOAD protocol. Three SMA connectors are included with the nanoVNA, used for calibrating the device (see image below).

• SHORT - Left, used to shorten the input of the VNA. This connector is all metal on the inside.
• OPEN - Middle, used to create an open port. This connector does not have a middle pin.
• LOAD - Right, used to simulate a 50 Ω load. This connector has a middle pin and a white teflon ring around it.

To calibrate the nanoVNA:

1. Set the center frequency and span to the desired range by following the instructions above.
2. Tab the Cal button on the display

3. Connect the OPEN standard to the CH0 port and press ‘Open’
   • The open entry is now black underlined

4. Connect the SHORT standard to the CH0 port and press ‘Short’
5. Connect the LOAD standard to the CH0 port and press ‘Load’
6. Press ‘Done’

The nanoVNA is now calibrated.

Charging the Battery of the nanoVNA

From time to time the nanoVNA battery needs to be recharged.

To recharge the battery connect an USB-C cable to the nanoVNA and plug the cable either into a USB charger or a computer.

3 - Acquiring a Proton Spectrum

This section provides a brief overview how to acquire a 1D 1H NMR spectrum. For this we assume that:

1. OVJ-B12 is installed on the computer
2. The hardware is set up properly
3. A sample is inserted into the probe
4. The NMR probe is tuned to the spectrometer frequency.

Acquiring a ¹H NMR

1. From the protocols tab drag the PROTON experiment into the plotting window, or double click on the PROTON protocol.

   

   Alternatively, the pulse sequence can be set using the OVJ command line:

   1	seqfil='s2pul'

   The PROTON sequence calls a pulse program s2pul. This is a general, two-pulse sequence used to run variety of different experiments such as a single pulse NMR experiment or an inversion-recover sequence.

2. Next, the user has to set the length and power of the RF pulse to properly acquire a 1D ¹H spectrum. In OVJ the pulse parameters can be changed from the OVJ command line or from the acquisition panel.

The length of the observe pulse is given by the parameter pw. From the OVJ command line set the pulse length:

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pw=3

corresponding to a pulse length of 3 µs.

3. Next some of the acquisition parameters need to be set. Go to the Acquire tab and click on Acquisition. Here, basic acquisition parameters can be adjusted. Alternatively, the values can be entered in the OVJ command line.

   • Spectral Width: Parameter sw
   • Acquisition Time: Parameter at
   • Complex Points: Parameter np

   For example

   1 2	sw=50000 np=4096

   will set the spectral width to 50000 Hz (50 kHz) and the number of points acquired in the time domain to 4096.

4. Set the number of transients (nt) to 4. In general, OVJ will add a CYCLOPS phase cycle to each sequence automatically to remove DC offsets and correct for phase imbalances. Therefore, the parameter nt should always be set as a multiple of 4.

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   nt=4

5. On the Acquire tab click Channels to set the transmitter offset tof parameter. To get started, set this value to 0

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   tof=0

   With the transmitter offset set to 0, the spectrum, if excited on resonance, appears in the center of the window. To center the spectrum adjust the tof value. Alternatively, you can click with the mouse on the peak (single red line cursor) and enter the command movetof in the OVJ command line. OVJ will automatically adjust tof so that the NMR spectrum in the next acquisition is at the center of the window.

6. Start the acquisition by either pressing the GO button or by typing

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   go

   in the OVJ command line. The acquisition will start and the data is displayed and processed on the screen.

Phasing a spectrum

Once the acquisition is finished, the spectrum most likely needs to be phased to show just the real part of the complex spectrum (see figure below). This can be done automatically using the autophase command aph or manually.

Using the Autophase Routine

To autophase the spectrum type the following command in the OVJ command line and press enter:

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aph

to autophase the spectrum.

Manually Phasing the Spectrum

Sometimes, the autophase routine fails and the spectrum needs to be phased manually. To manually phase an NMR spectrum:

1. Click the Phase button in the toolbar to the left

   

2. Click the spectrum with the left mouse button and keep the button pressed. Two red cursors appear to the left and right of the peak. Phase the peak by moving the mouse up and down. This will adjust the 0^th order phase correction (frequency-independent phase correction). Alternatively, the phase can be adjusted from the OVJ command line by typing:

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   rp=11.5

3. To adjust the 1^st order phase correction (frequency-dependent phase correction) click the Phase button in the toolbar to the left. Next, select the peak by moving the mouse cursor to the NMR peak and click the right mouse button. The point selected is the pivot point used to adjust the 1^st order phase correction. By moving the mouse up and down the phase of the rest of the spectrum can be adjusted. To adjust the 1^st order phase correction lp from the OVJ command line type:

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   lp=157

The proper phased spectrum is shown below.

Next, proceed to the next section to Save the NMR Spectrum.

3.1 - Processing 1D Spectra in DNPLab

DNPLab is a Python package to process NMR data. The software was developed by Bridge12 and is open-source, free to use. DNPLab can be used for offline processing of OVJ data.

Below, a brief example is shown how to load and process a 1D NMR spectrum. For a complete reference and many more processing examples visit the DNPLab Online Documentation.

Installling DNPLab

DNPLab requires a working Python installation and can be simply installed using pip:

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pip3 install dnplab

All requirements are automatically installed.

Processing 1D Spectra

A typical processing and plotting script is shown below:

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import dnplab as dnp

data=dnp.load('path/to/folder/PROTON_XY.fid')
data.attrs['experiment_type']='nmr_spectrum'

data=dnp.fourier_transform(data)
data=dnp.autophase(data)
data=dnp.processing.offset.remove_background(data,dim='f2',regions=[(200,320)])

dnp.fancy_plot(data)
dnp.show()

The general structure of the script is:

• Line 1: Import the DNPLab package.
• Line 3: Load the NMR spectrum. DNPLab can import many different spectrometer formats. The format is automatically detected and a dnpdata object is created.
• Line 4: The attribute of the spectrum needs to be changed to nmr_spectrum to ensure that the plot function fancy_plot works properly (this line will not be required in the future).
• Line 6-7: Fourier transform the spectrum and apply an autophase routine.
• Line 8: Remove DC offset from spectrum.
• Line 10-11: Plot the NMR spectrum

The result is shown below.

DNPLab has many more features for processing and analyzing NMR data. It can also be used to process EPR data. For more information check out the Online Documentation.

4 - Saving the NMR Spectrum

OVJ provides two different options to save the NMR data:

1. by using the OVJ GUI
2. by using the OVJ command line.

Saving Data using the OVJ GUI

To save the NMR experiment using the GUI:

1. Go to the Acquire Tab and select Future Actions
2. Click on save FID (see image below)

Saving Data from the OVJ Command Line

To save the NMR experiment from the OVJ command line:

1. Type the command save
2. Enter a name (e.g. mydata). Do not add an extension to the file name
3. Press return

The data will be saved and a study is created automatically.

Location of Saved Data

Assuming a default installation of OVJ, the data can be found in the ‘mydata’ subfolder in the vnmrsys/data folder:

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~/vnmrsys/data/