Well it’s that time of the week again ladies and gentleman so sit back and take 5 whilst I tell you all about another week in the PhD life. Apologies for the late upload, technical and logistical difficulties all weekend. Another week of long hours, shite MS data and a tonne of self-doubt.
I guess I’ll start at the start. The 5 step synthesis of my unnatural amino acid has been completed, high yielding (85% overall) with beautiful purity. It’s now sitting in a fridge wondering what the hell primers are and how it works in real life. Currently I intend to leave it to the bio kids to play with as I really I don’t understand it. I know only that it’s pure, dry, sexy and ready to rock. I also know it’s racemic… Apparently this is not an issue for what they want to do it for as they just double dose (? Don’t ask). I think an asymmetric synthesis is entirely possible utilising some fairly simple epoxide chemistry. The only real issue here is, would the face I synthesise be the face the enzymes need?
It’s also worth noting that in one step I added my reagents and some KI with the intention to sack off a Br. So why did I need 1 eq of this Iodide salt? Well little did I know that I was actually carrying out a Finkelstein reaction. This is essentially a conversion of any alkyl chloride or, as in my case, alkyl bromide to an alkyl iodide to increase reactivity. This then allows for the reaction to proceed more efficiently. Obviously I did not do this reaction, look at the reagents and think “hmm… Yeah obviously this utilises Hans Finkelstein’s chemistry to proceed, a substitutional bimolecular reaction involving halogen exchange”.
Above I have used a generic example to illustrate the point.
As I stated very early on in my blog posts, I would be completely open and honest on here about the PhD ups and downs. And now it’s time to discuss a downer from this week. Firstly, a relatively important reaction of mine failed to work.
My research presentation. The pacing was ok the volume was good, I didn’t swear too much. Obviously I just oozed calmness and confidence. But shoot. A couple of my chem draws were off and then I got asked about the mechanism for the Breslow intermediate. Remember that long ass one I put up a few blogs back? Well I got about half way through before I threw in the towel and allowed my supervisor to finish it off. I also then got asked very plainly and seriously by an academic “What are the advantages of C-H activation” Too say I was dumbfounded would be an understatement. The advantages are right there in front of you? C-C selective bond formation at the same position every time all the time in previously inert species. No functional groups needed. Very rarely do I find myself speechless. Again my sup’ saved the day because god knows what I’ve of said. The lesson here I learned is not every chemist gives a toss about organic might, and contextualisation is sometimes needed.
This was also when I was enlightened to my Finkelstein reaction because guess what… I didn’t know the answer to that question either! Obviously I intended for the talk to go much better than it did. I certainly didn’t knock it out of the park and the whole talk had a bodged feel about it all.
The pros? Errr…?
There were a few other chemical hiccups along way also, especially again on applications. As much as I’m a little afraid to present this to my second supervisor I at least feel his group won’t get too hung up on applications and instead focus on the actual chemistry being presented. Then scorn me on both no doubt ha-ha.
To clarify no one has actually come out and said well god damn Lewis that presentation was the drizzling shits and you need to sort your act out. Instead it’s been a mixture of well done here for this, that and the other and it was my first time up there etc etc. Sod that. I don’t need to be protected. I need that sledgehammer feedback to get myself straight. With that being said I think my second supervisor will be exactly that. Mean and cruel if required and will call a spade a spade which will allow me to fix up more efficiently.
Hopefully next week will be much better and I can get my life back in order… who knows.