Training – Guide

Before you start to use the NMR facility, we want to make sure that you have understood all the information below. Therefore, your NOMAD account will initially inactive and you won’t be able to submit your sample.

Once you come with your first sample, please get in touch either with Tomas Lebl (tl12, room 129) or Siobhan Smith (srs9, office in the main lab – room 122) and we will quickly run with you through the workflow. You will also have opportunity to ask any questions you might have got and to become more familiar with us and the equipment.

Please don’t hesitate to approach us if you are not sure about anything in the lab or you need to any NMR experiments that are not currently available under automation.

  • There is a hazard of exposure to high magnetic field. If you have any metallic implants or pacemaker please do not enter the lab and get in touch with us via e-mail or phone first and we will take your case from there.
  •  We don’t take any responsibility for your belongings that could be damaged by magnetic field such as cards with magnetic strip, watch or electronic devices.
  •   Please, don’t wear lab coats and gloves in the lab
  •  The NMR facility operates 24/7. However, after working hours the doors will be locked. If you want to use the lab outside working hours, we can provide you with a punch code for the entrance door at your first visit to the lab. Please make sure, that the door is locked and lights are off if you are leaving the lab outside of working hours and nobody else is present.
  • Nitrogen fills are usually done on Wednesday morning. In normal circumstances we keep at least some instruments running but currently due to COVID-19 pandemic the main lab is going to be shut for roughly 2h from 9am.
  •  Due to COVID-19 pandemic there are additional general rules in place that are described in detail here.
  • Optimal sample volume should be around 0.6 ml.
  • Using larger volume samples is waste of resources and extreme cases could hamper sample automatic sample changer operation.
  • The sample should be homogeneous clear solution.
  • Bad sample preparation will result in poor spectrum resolution! 
  • Clearly label your sample by writing on the glass or cap.
  • Nonconcentric labels are not allowed.

To help with tracking your sample, use NMR tube caps of colour that have been assigned to your group (see the table below). Using different colour cap is the main cause for lost samples.

The instruments in the lab are equipped by three different types of sample changers.

For BACS and SampleXpress we need to apply some rules listed below that help to assure smooth operation of the instruments.

Bacs

  • Don’t use tubes shorter than 7’’. There is a 7’’ gauge at the entrance of the NMR lab where you can check whether your tube is long enough for BACS sample changer. The 7’’ tubes must be unspoiled and have no cracks at the top.
  •  If you want to insert your tube into a holder that cannot be reached you can move the conveyor belt by the buttons on the side of sample changer (see the red arrow in the picture below). If you do so, please pay attention. If the sample changer starts to operate release the button and wait until the sample changer finishes the operation.
  •  If you want to retrieve a sample that is just coming out wait until the operation is completely finished and the arm is in the upper position and pincers are closed.
  •  The BACS on Marcus has conveyor belt with 120 holders. Please pay attention to where you put your sample. The numbers 1-60 are in the inner ring and 61-120 in the outer ring. There is a sticker on the side of sample changer that helps to refresh you mind if you are not sure where to put your sample.

SampleXpress

  • Do not use any tubes that are longer then yellow mark at the inlet port of the sample changer (see the picture below). The tubes with Young’s valve must be 5’’. The longer Young’s valve tubes are too heavy and don’t get eject from the magnet.
  •  To add or remove samples use the buttons on the touch screen to bring your holder in to the right hand corner where you can insert your sample. There are also buttons that allow to add remove series of samples in consecutive holders.
  • Make sure that your sample changer has registered your sample (holder turned white). If your sample has not been registered take it out and put it back again.

How to operate the SampleXpress:

Add Samples

Remove Samples

Sample Case

  • SampleCase is very easy and intuitive to operate. There are no special rules.

Submission of NMR samples for automated acquisition is controlled by in-house build web-based software NOMAD. You can check the status in the NMR room at any time by going to the NMR Dashboard (st-andrews.ac.uk)

NOMAD 3 should already be running on the computer when you come to the NMR lab. You can see the status of each instrument – if they are green then they are available and if they are red then they are not. There is also a summary of when the machine is busy until and information on the length of queues for both day and night experiments (night experiments are longer experiments which run outside of usual operating times).

To book an NMR sample:

1) Click on book new job and then enter your user name and password when prompted. If this is the first time you have logged in then you will have to click the reset password link in order to set your own password.

2) Select a machine by clicking on it’s summary card or using the drop down menu and then select how many samples you wish to run. Click Book Slots.

If you would like to run more samples on another machine, you can select and book the slots at this point. You will now have a list of booked holders (this is the numbered position in the sample changer where you will place your sample).

3) Fill in the generated form for each sample with the relevant solvent, a clear title (lab book number or similar), select the experiment you wish to run and adjust any parameters. If you wish to run several experiments on the same sample, use the plus and minus buttons to add rows to the form.

If you are using Young’s valve tube on Marcus or Noah set the parameter ro = 0.

4) Once you have filled in information for all the samples and experiments you wish to run, press continue. You should see a “Success!” message and your experiments will be added to the pending queue at the top of the page.

5) The samples must be loaded onto a spinner. The next video demonstration shows how to insert your sample into a spinner in the way that minimises contamination of inner parts of the instrument. When you put sample into the depth gauge make sure that it is pushed all the way down and spinner holds your sample firmly.

Sample to spinner video

6) Put your samples into the correct holder on the correct machine (see the following section of instructions on how to use the automatic sample changers). Click on Pending Experiments, check the box next to your samples and press Submit. If you do not wish to go ahead with your experiments, please press cancel selected in order to free up space in the queue.

You should again see a “Success” message and your samples will now be in the queue ready to run.

Once all the experiments have been run on your sample, you will receive and email with a link to the data on NOMAD2

If you have submitted an experiment and change your mind, please cancel it – log in by clicking on the profile picture logo at the top right of the page, find the experiment in the queue list and check the box next to it, press the cancel selected button at the top of the list.

If your experiment is in the night queue, it will have a moon logo next to it in the list – this means it will run between 7pm and 9am the next morning. If the night experiments queue is longer than the 14 hours allocated then the samples will roll over to the next night.

  • You can come back and take your sample off the sample changer when your experiments are finished.
  • If you change your mind and get your sample back before the experiment/s start, then please cancel corresponding entry in the NOMAD system.

The sample changers are getting reset usually the first thing in the morning and around 4 pm. All samples remaining in the sample changers are transferred in the return racks. The racks are clearly organised by instrument and weekdays. The racks for lower field instruments (Marcus, Noah and Robbin) are on the desk near the entrance and for 500 MHz (Alec and Felix) are on the desk nearby the exit door. The return racks for 700 MHz instrument (Hector) are on the desk behind spectrometer PC.

Watch the following video to get yourself familiar with NOMAD database workflow.

NOMAD – database video