Two weeks in the PZQ lab

02 Dec
Published by KatB


Rants, Miscellaneous

I've now reached the end of my second week in the lab working on the Pictet-Spengler route to praziquantel.
It's been quite a steep learning curve so far, particularly in terms of analysis and familiarizing myself with the lab.  I've had experience (if you can call it that) with NMR and MS before, but that was only in the sense that I prepared my sample in the tube/bottle and a week later, I got a spectrum on my bench.  Now I'm preparing NMR and LCMS samples on a daily basis.  I'm finding it much easier to use the LCMS (however, interpreting data is another matter), and I've been introduced to the procedure for recording NMR spectra.
I also believe I've uttered "Muuuurrrrray" in a whiny, I-don't-know-what's-going-on voice far more than other statement over the last fortnight.
I've discovered working on the "mg" scale and I've decided that I don't like it.  So much depends on that tiny amount.  I'd lose yield over a couple of steps and the next thing I know, I have 3 mg of product. 
That changed in the last couple of days when I started a reaction on a 20 g scale (KAB4-1).  For that particular reaction, I've also decided that I don't like it.  It's certainly nicer working on a larger scale, but the noxious nature of what I was handling has left my nostrils singed and a nasty metallic taste in my mouth.  I was also convinced the bus I went home on smelt like (2-isocyanoethyl)benzene.
I've wholeheartedly embraced the Open Science methodology and find that there are significant advantages of the electronic lab notebook (ELN), notably, the ability to post photographs.  It makes me think that all those times that I've followed a precise procedure where colour/precipitate/subtle changes in the reaction are mentioned.  It's rather difficult to follow "…added until just slightly faded from dark red."  What the hell does that mean??  Solution: take a picture.
I will admit, though, that I may have gone overboard with the photos and the posting.  But what I've realised, is that doesn't matter.  I'm not forcing anyone to read my notes, nor am I expecting people to read it.  But the information is there and could be of some use for someone later down the track.  I also have the ability to rant to no one in particular about a specific reaction/chemical/spectra when things aren't going so well.
The "electronic" thing is not without its drawbacks.  For one, the glitches in the ELN blogging have caused me to lose stuff I've typed up on a couple of occasions.  I've learnt to avoid those situations, but it was an exhaustive lesson.  Especially when I'd get enthused and type quite a detailed account of the experiment.  Another is the inability to "flick" through the pages.  You can't stick a pen in the page that you're constantly referring back to.  There have also been occasions where I've felt something should have been posted somewhere, but I couldn't work out exactly where its "place" was.  Lastly, I don't want to touch my computer after I've been handling chemicals and come into contact with who knows what.  It means that I'm going through gloves.  A lot of gloves.  (I've been encouraged to re-use them, but I keep forgetting which is the inside and outside…).
These "drawbacks" are addressable.  It's just different.  I'm finding the process to be quite flexible, and I definitely like that:
1.   I don't need to carry a lab book.  If I need to check something, I just open the web page.
2.   I can easily refer to previously performed, relevant experiments and the exact conditions and outcomes. Means that I'm learning from previous failures (although I don't think it should be called a "failure" as I'm benefitting from their experience.  Perhaps "lesson"?)
3.  The posting of photos.
4.   The ability to link between experiments/literature/anything-on-the-internet
5.  It's easy to keep up to date. 
Not sure how I'm going go when I need to keep a paper lab book again :S
As for the praziquantel project, I believe we're making steady progress.  Murray's getting somewhere with the sulfonamide catalyst (MNR20) and I'm on the way to making a bunch of Ugi-intermediates (KAB5-1 and KAB6-1), which I'm hoping to Pictet-Spengler cyclise and purify in the next two weeks to get sent off for bioactivity testing.  I should have a heap of Ugi-intermediates left over to get maybe get sent to whoever has a potential catalyst and is willing to give the reaction a go.  Either way, the next couple weeks surely going to be busy.  So many things to try/get done!
Things you find in the lab


MatTodd's picture

Sorry you missed out on lunch... 
That last link is broken for me. For those of you wondering about how Kat's new smelly large-scale reactions are going, here's one of them. Stirring over the weekend as I write.
Agreed about the lack of a "pen stuck in book" function in the ELN. Multiple browser windows?

No bookmark functionality? No bookmark bar, like a browser, on the interface? That seems like it shouldn't be too hard to implement in the software.

Links fixed + added for the reactions.
That's alright about lunch.  I really needed that time to run the second column, otherwise I wouldn't have got the NMR sample ready in time or those 2 reactions going for the weekend.
The only niggle I've got with multiple browser windows is that I tend to get lost in them.  Or I forget where I've "put" them.  It also means that I have to touch my computer to flick between them, although I've discovered that the mousepad still works with a piece of paper on top of it.  Might try plastic.  I wonder if foil will work...
Could work for when I need to check something, and the computer's gone to sleep, I can just bang on that.  Saves me from having to ask Angus to hit my keyboard for me.