1. NMR

General Info

For all NMR queries ask Alex Hayem ([email protected]) Lots of NMR information is on the team channel: Chemistry-NMR (https://teams.microsoft.com/v2/) which you should be added to once Bao requests this, and Alex actions it - I think. If you're not added ask Alex.

Machines

300 MHz - Located 1st floor - 1.07. Generally used for teaching labs. Operated as a walk-up machine. Also used for Li experiments.

400 MHz - Located 1st floor - 1.07. General day to day use NMR. You will be trained on this machine first, you can run all of your basic NMRS - 1H, 13C, HSQC, HMBC, COSY ect. It is also possible to run 19F and 15P NMR, any special parameters needed, ask Alex.

500-cp MHz - Located ground floor - G.07. Make sure to use 500 MHz specific tubes. Higher level NMR, you will get better resolution than the 400 MHz, good for ticky couplings, lower concentrations, better carbons and best for publications, you'll need to be trained on the 400 MHz first and use it successfully for a couple of weeks before you can be trained on the 500.

500-4c MHz - Located ground floor - G.07. Make sure to use 500 MHz specific tubes. More specialist NMR, you'll need additional training for this machine. You can run time-resolved and temperature ect. - ask Alex.

Training

All training is completed by Alex. You will first be trained on the 400 MHz. You'll need to complete this first then Alex should get back to you: https://teams.microsoft.com/v2/.

Sample prep

Dissolve 20 mg in approx 0.7 mL of deuterated solvent (found in the special solvents cupboard under the rotavap). We have MeOD, D2O, CDCl3, DMSO and more specialist ones. Make sure your sample is completely solubilised - we have filters if not.

Access / booking

Once trained Alex will give you fob access to the rooms. Bookings is done on the NMR Teams channel using the NMR Virtual Queuing System - https://teams.microsoft.com/v2/

Software

Mnova is currently what the department recommends.

Download from appsanywhere:

Stream from Cloudpaging player:

Should look like this, you can drag zip files directly across and they'll load:

Here is a helpful guide to using Mnova: https://leeds365.sharepoint.com/:w:/r/sites/TEAM-Chemistry-NMR/_layouts/15/Doc2.aspx?action=edit&sourcedoc=%7B1386d159-89f1-4748-bf38-79cefb2fe583%7D&wdOrigin=TEAMS-WEB.teamsSdk_ns.rwc&wdExp=TEAMS-TREATMENT&wdhostclicktime=1737732960228&web=1&clickparams=eyJBcHBOYW1lIjoiVGVhbXMtRGVza3RvcCIsIkFwcFZlcnNpb24iOiIxNDE1LzI0MTIwMTAwMjE3In0%3D

Topspin - Bao likes to use it but less people are available to help you with it and the university no longer provide a free licence but it does have some benefits.

Storage

Everything is sent via email but if anything goes wrong it is all backed up on the shared drives: CHM(\ds.leeds.ac.uk\Shared\Faculty-of-EPS\Research)(Y:) > NMR > (select the machine you used)

2. LCMS

General Info

The LCMS is located in G61. All information about it is on the Teams Channel - Chemistry - G61, https://teams.microsoft.com/v2/ (you should be added to this from the start). Contact Jeanine Williams / Stuart Warriner with any problems.

Sample Prep

Samples should be made up to 1 mg/mL in some polar solvent (MeOH is good), make sure no solid remains - we have little filters if needed.

Submitting Samples

All samples need to be submitted beforehand on remote analyser NOT ON THE MACHINE https://azchemspec.leeds.ac.uk/.

Add new sample:

Then change project to LCMS_G61. Experiment quickLC_Pos (standard LC method)

Put in your sample reference, leave barcode blank, leave injection at 1.0 and you can enter the target formula of you structure (this is not essential). Then hit submit. You should get an email with a barcode which you scan at the machine.

In the likely scenario you do not receive an email. Hit samples (the test tube on the LHS of remote analyser) then click on the barcode number and take a picture with your phone. Make sure to take your phone with the barcode and your sample in secondary containment to the machine.

Running the sample

The LCMS machine is sharp left as you enter G61. Scan your barcode using the scanner:

Once the barcode has scanned it'll give you a barcode position:

Place your vial in the correct position then hit confirm on the ipad:

Analysing results

Tracking of the sample and results can be found on remote analyser. Go onto your sample > Files > Open the report.pdf

3. HPLC

General Info

Located in the iPRD side room (B.37d). Mary Bayana ([email protected]) is in charge of training and any problems. You should not be putting any metals on the HPLC and avoid DCM.

Sample Prep

Samples should be made up to 1 mg/mL in some polar solvent (MeOH is good), make sure no solid remains - we have little filters if needed. ALways make up a blank sample to run first.

Instrument Booking

The HPLC is booked using Labshake (https://labshake.com/sign-in?next=http%3A%2F%2Flabshake.com%2Fuser%2Fmylab) which you will be added to by mary after you have completed training and RA's. You should book the HPLC but don't be surprised if others don't.

Sample Submission

You will get shown all of this during training but sample submission is a little more complicated than LCMS.

Step 1: Login in to the computer (Password: chem123!)

Step 2: Check reagent bottles match what the computer says and check that the waste bottle (under the desk on the left) is not full.

Step 3: Put your samples in the tray and make note of the positions (Letters left to right numbers front to back (1-10))

Step 4: Make a new folder for your data to go in. This PC > OSDISK (C:) > Users > Public > Public Documents > ChemStation > 1 > Data

Make sure to label it with todays date then if you like follow it with reaction number.

**Step 5: ** Load a new method: (You are welcome to use mine RNapier_GeneralMethod.M so long as you do not change it. Alternatively make a copy and rename it. This is a pretty standard method that should separate most things. For complicated separations consult Mary.

**Step 6: ** Load a sequence: (Again you are welcome to use one of mine 0108RN33.S but please make sure to not save it at the end (see below))

**Step 7: ** Next set the sequence parameters so your data goes to the right place:

Select the new data file you correct it should be near the top, then hit ok:

Step 8: Adding your samples next go sequence table:

This will pop up, sample location refers to where you put it in the tray and must be entered in this format, Sample Name is obvious, Method Name you will need to select the method you want (you can right click the one at the top and filldown) leave everything else except sample type:

Use the little buttons at the bottom to add or delete lines:

Once you're done hit run in the bottom right corner and you're done. But make sure to hit NO when the next thing pops up (unless you want to overwrite your own sequence but not if you're using mine)

Obtaining and Analysing Results:

To get your results you will need a memory stick, just drag the data file you created across.

You will need to download OPENChrom: https://www.openchrom.net/. (You may need to overcome uni IT). Once downloaded it should open up and look like this:

Click data analysis. Open your file by locating either in Drives if its on your memory stick or Home if you've moved it across on to your computer, locate the file and double click on the CSV, and your chromatogram will open up.

4. GCMS/MS

General Info

The GCMS is located downstairs in the iPRD. Mary Bayana ([email protected]) is in charge of training and any problems. Not many people use the GCMS so it is nice and quiet. You should not be putting any metals on the GCMS. Things with very high BP. or MW will not come off (so use HPLC instead) and anything with a V.low MW < 50 will fly straight through the column and not be observed.

Sample Prep

Samples should be made up to 1 mg/mL in some polar solvent (MeOH is good) DO NOT USE WATER, make sure no solid remains - we have little filters if needed.

Booking the Machine

Booked using labshake: https://labshake.com/user/mylab.

Sample Submission

Once the software is open you should see:

Step 1: Load Method: Use GH_method this is a standard method that will separate most normal things. You can copy it and rename it if you like.

Step 2: Edit Sequence:

Step 3: Fill out sequence table: the following screen will pop up:

Change 'Name' column to sample name. Enter the vial position that you placed your sample in (the trays and plates are labelled on the machine). Make sure to select the correct method FOLDER (as shown below)

Make sure to select the correct method file (create new folder here in the correct month) and enter the label you would like the data file to be called:

Select sample or blank in 'Type' column. Then select the correct rack in which you have put your samples:

Leave everything else and hit OK bottom RH corner.

Step 4: Validate the sequence:

Make sure to change Data file Directory to your new folder. Label sequence comment to date and name, change operator name. Then hit run sequence, then hit no on the first window that pops up. Then hit yes on the sequence validation window:

The following window will pop up. Check the sequence file is correct and that the data path is correct and that the vial positions and names are also correct:

Step 5: Run the sequence:

The same window you saw before will then pop up hit run sequence and then your samples are submitted.

Obtaining and Analysing Results:

To get your results you will need a memory stick, just drag the data file you created across.

You will need to download OPENChrom: https://www.openchrom.net/. (You may need to overcome uni IT). Once downloaded it should open up and look like this:

Click data analysis. Open your file by locating either in Drives if its on your memory stick or Home if you've moved it across on to your computer, locate the file and double click on the .D file, and your chromatogram will open up. To view the mass spectrum double click on the peak, you can zoom in on the big and little windows:

5. Accurate Mass

General Information

Located in . Information can be found in the teams channel: Chemistry - G61 then on the LHS select the Accurate mass channel, https://teams.microsoft.com/v2/, you can find all of the information you need here: https://leeds365.sharepoint.com/:u:/r/sites/TEAM-Chemistry-G61/SitePages/Accurate-Mass-System-Training.aspx?csf=1&web=1&e=lMdec7. Training can be done by our very own superuser George or you can ask Stuart Warriner

Sample prep

This is an extremely sensitive bit of kit, samples must be weighed and prepared very carefully, you do not want to be the person that breaks it by overloading the column.

For all other information submitting/analysing samples go through: https://leeds365.sharepoint.com/:u:/r/sites/TEAM-Chemistry-G61/SitePages/Accurate-Mass-System-Training.aspx?csf=1&web=1&e=lMdec7