Question: I noticed you said you can see when you’ve made it in different ways , what are those ways ?

Kate McGonagle answered on 8 Mar 2019: last edited 8 Mar 2019 9:32 am

Hey, yeah this is a great question! These are things that I do everyday! There are a few ways I can monitor the progress of my reaction to see what’s happening in there and if I’m making the molecule I want. One way is by a technique called TLC – Thin Layer Chromatography – I spot a little bit of my reaction mixture on a silica coated aluminium plate and then sit the plate in some solvent. Different molecules with different properties will move up this plate at different rates. So, I can wait until the solvent reaches almost the top of the plate, take it out and so long as the molecule I’m making is UV active (most of them are) – I can visualise the plate under a UV lamp. If I spot my reaction mixture and starting material on the plate I can compare them – I can see if any of the starting material remains in my reaction mixture or if that’s all gone and there’s a new spot at a different place on the plate – maybe my desired molecule!
Here’s an example of a reaction monitor by TLC – you can see in the reaction (RXN) that there is both starting material and product – so the reaction is going well but it is not finished!

LCMS – liquid chromatography, mass spectrometry is like a technological advancement of TLC – TLC by machine, it runs a similar thing in a more fancy way and unlike just showing you the UV output like you get from TLC – you can see the molecular weight of the molecules under each UV spot! It’s amazing! This is vital info as by TLC, you have a new spot but there’s no way to tell what it is. If I’m making a new molecule I can calculate the molecular weight – so by LCMS I will know for sure if any new UV spot contains my desired molecules molecular weight.
This is an example of the output of an LCMS, you have the UV trace at the top and we can see the molecular weight of the molecule accounting for each UV peak;

After we have isolated something from the reaction – we think we can see our desired molecular weight by LCMS – we will perform an NMR experiment – Nuclear Magnetic Resonace – I will take a bit of the solid I have made and make it into a solution in some solvent and load it onto the NMR machine in a tube. This machine generates a complicated looking spectrum which contains so much information! Every peak in the spectrum tells us about a hydrogen atom in the molecule we have made – from this we can be certain of the structure of the molecule that this solid is made of!
Here’s an example of what an NMR of a certain molecule looks like;

Sorry for the massive answer, I know that’s a lot of info but I hope it kind of makes sense, if not please let me know! There’s a lot more information around all of these techniques, if you would like to know anymore again please just ask. Thanks a lot for all your amazing questions!