Oct 29, 2009

Evil Lab Challenge

Today we had another of our patented Lab Challenges, and I'll tell you right now it nearly killed me. The Lab Challenge tests each individuals endurance and perseverance in the lab and tests both the nerves and the sanity.

It consists of the selection of a particular song (usually pop) which is then put on the lab music system and put on repeat. The song is then left to play consecutively until one person remains in the lab. However, as some daily duties require absence from the lab (e.g. toilet breaks, literature searches etc.) a tally is kept of each song listened to. This firstly makes sure you aren't tuning the song out but also makes sure you return to the lab.

As it was today, the song choice was Modern Talking's "You're my heart, you're my soul" (see previous post). Unfortunately, I found this song hidden in the depths of our lab music system's archives. I wish I hadn't.

It was HORRIBLE!!! We listened to that song from 10:00AM through to 5:00PM. I had to leave the lab several times, unfortunately the song could still be heard in the office. As a result I believe I have a tumour. The song's play length is 3:49. This means that the song was played approximately 110 times straight throughout the day. DEAR GOD!

At first, I thought it was OK, I was singing along to the music, but in the end I cracked. I still have the song running through my head. Apparently, tomorrow will be all German music all day, but not the same song over and over.

Oct 28, 2009

Ether peroxides!

I'm closing in towards my final target in my total synthesis, but I'm almost out of starting material for the key late stage cyclisation I've been trying to get going. Fortunately I had some more in the back of my freezer, but it was an old batch, and even though I knew it was clean because I remember running multiple columsn to separate it out from its close running diastereomer, I decided to check its purity by NMR anyway.

Sure enough, there was my starting material and all its familiar peaks, but I also saw two 2:1 ratio quartets at ~5 and ~4 ppm respectively. What the...

These peaks also reminded me of the strange peaks that I saw in the crude NMR spectrum of my previous reactions using the same compound. I knew it wasn't a degradation product of my starting material, so I simply thought it was something from the reagents and solvents. But when the same peaks kept turning up when I changed solvents and reagents, I knew something didn't really make sense. The only things common between those reactions were the starting material, and the work up procedure, and that's when I suspected that diethyl ether peroxides were in my crude.

This morning I checked my bottle of ether for peroxides using the KI solution test, and sure enough, there it was. Shaking a bit of my ether with a solution of KI resulted in a pinkish orange organic layer (due to the peroxides oxidising the iodide ions to iodine), and a yellow water layer (due to the I3- ion). Testing various bottles around the lab, it seems (from qualitative observations) that my bottle actually had much more peroxides than others. I guess it's probably due to my habit of having my own bottle of ether. B, probably due to the nature of his chemistry, almost never uses ether since it's not polar enough. P just grabs a bottle of ether on the shelf whenever he needs it, so each of the bottles on the shelf roughly gets the same exposure to air and light. Since I have my own bottle, my ether gets much more exposure to the elements than the other bottles. And since I've been doing <10mg reactions, the small amounts of peroxides show up very well in my crude NMR, as I don't necessarily scale down work up procedures proportionally. If I did I would be extracting with 0.5mL to 1mL of solvent which really isn't practical. B and I washed every single last drop (well not really) of diethyl ether in the lab with KI solution, then washed the ether with sodium thiosulfate solution. Drying with sodium sulfate then distillation gave (hopefully) peroxide free diethyl ether. The question is: why did my starting material, which was columned and dried and stored under argon in the freezer, have diethyl ether peroxides? I think it's because I wash my NMR tubes with water, acetone and diethyl ether successively before drying in a warm oven. The ether I used must have had peroxides. Either that or it was from the solvent used in the column in which I purified the starting material in the first place. All the more reason to change the purification protocol of this compound from an ethereal solvent system to a hexanes/EtOAc one. Unless an ethereal solvent system gives improved separation over a hexanes/EtOAc system, or unless there are problems with volatility, why use an ethereal solvent in the first place. Sure, you can rotavap the stuff off a bit faster, but it's so much more expensive.

Oct 27, 2009

Modern Talking

Today W introduced us to possibly the greatest pop band of all time. Or at least in Germany. Those crazy German's love their music and while they are possibly the most straightforward people on earth their music is absolutely NUTS!!! Or as W points out, "Straightforward nuts". Check out these film clips for music that hit No. 1 in the 80s in Germany.

Thankfully, I wasn't alive at the time of these SUPER tracks. But Dieter Bohlen, the blond guy with slightly less makeup made Billions of Deutschmark on this kind of crud and is still a massive celebrity in Germany. NUTS!!!! (He now wears more makeup).

Thomas Anders, the scarily androgenous guy in these clips is HILARIOUS and I recently dug up that he had a concert in July THIS YEAR!!! ZOMFG! Who the hell pays for this stuff??!!

Anyway, that was the highlight of my day today and I thought I would share that small amount of joy with whoever reads this.

Oct 26, 2009

Student Reports

So today I began the arduous task of marking the 40-odd reports that have piled up on my desk over the last few weeks. It isn't actually that many and I could probably do it in about 2hrs if I could abide all the stupidity that is ingrained into so many of them.

Don't get me wrong. Some students are a delight to teach, fun to talk to and very intelligent. But there is always another end to the spectrum. Where the student ignores your instructions, cuts themselves and bleeds all over the lab. Or simply falls asleep in the fume hood (ask MSG). Anyway, it might seem that with these students that their reports will follow a similar pattern in which they neglect to read the instructions on writing up the report.

However, this is usually not the case. Where you may have a sociable, smart student in the lab it is often the case that they are sloppy with their reports and neglect to read the instructions carefully. Which is a shame as they are only marked on their reports. Conversely, the crazy ignorant student somehow garners enough knowledge of the English language to produce a decent report.

This isn't the case for all the students and is just an extreme case but it often makes me laugh, then cry then repeat the process as each surprise appears. I hate to admit it but by the end of this marking session I will probably be a deranged quivering heap incapable of human conversation. This is most likely also going to be due to the lack of assistance we have from teaching staff who lump the pracs on us and tell us to mark them without a marking scheme. I mean, sure we know how to run the prac, but c'mon, that means we have to actually do some work and figure out some answers. Seriously, don't these guys know we have blogs to write and facebook to check.

Just to make matters worse I have to feel sorry for the students who get poor marks so that I go back over the damn thing to see if I missed something only to find out that 'Nope, he's just an idiot' or 'nope they didn't just fill out the answer sheet and now I have to go read through the whole thing to find their answer'. I swear to god if the chemicals don't kill me this probably will or at least age/jade me to something more like the PhD students I remember coming through as an undergrad.

Oct 25, 2009

Undergrads' shenanigans

The second semester of 2009 is drawing to a close. During this semester of 2nd year lab tutoring, I've certainly been impressed with some of the undergrads' efforts, but I've also witnessed a lot of idiotic behaviour, both in lab work and in their report writing.

Asleep at the fumehood
Why would you bother turning up to labs if you're just going to fall asleep. And is there a worse place to fall asleep than with your face planted on the bench inside the fumehood? "Dude, wake up, you can't sleep there" I exclaimed, but to no avail. "Hey, you get up, you can't sleep there" I shouted this time, but he didn't respond. By then another student required my attention, but fortunately for our sleeping student here, he was awake by the time I got back to him, about to physically pick him up and get him out of the lab. Fortunately it was only a flash column being run in his hood, nothing too dangerous.

Recrystallisation or evaporation?
The students really seemed to be confused as to what recrystallisation meant. As the title suggests, they thought that by simply dissolving the crude product and evaporating it, the Law of conservation of mass would somehow not hold true for the tiny piece of the universe inside their conical flask, and the brown impurity would simply disappear.

One of these students was both arrogant and ignorant. "Tutor, how do I evaporate this solvent faster under a stream of nitrogen?"

I didn't remember this being part of the procedure, so I asked "why do you need to do this?"

Student: "I'm trying to evaporate the solvent and I need to do it faster"

Me: "But why are doing this?" (By then I realised he was trying to do a recrys, but was trying to ask him questions so that he would understand the error of his ways)

Student: "I need to evaporate this solvent but it's very slow. I just need to do this ok? Can you just tell me how to do it faster?"

Me: "But stop for a sec, why are you doing this? What is the point of dissolving something and just evaporating the solvent?"

Student: "Can you just tell me how to evaporate this faster? That's all I need to know ok?

Me: "You're trying to do a recrystallisation, so what you need to do is dissolve it in minimum amount of boiling methanol and then let it cool slowly. You DON'T want to just evaporate all the solvent."

Student (dismissively): "Are you sure? Can you just tell me how to evaporate the solvent?"

Me: "Look, you can do whatever you like, but at the end of the day, the melting point doesn't lie. If you don't do it properly, then you're only kidding yourself because when the lab technician runs your melting point it's going to be horrendous."

Student finally realises (or did he?) his mistake but walks away without a word. He does the recrystallisation as I requested.

Each of the tutors was responsible for marking the reports of a particular experiment for the course. I was marking one where they had to find the ratio of oxygen uptake per mole of a particular transition metal. Now everyone knows the answer was 1 oxygen molecule to 2 metal ions. As one might expect, not every student obtained experimental data that corresponded to this. Here are some of the most frustrating explanations... or the funniest explanations... and if you've been marking reports for the last 5 hours it's definitely the former.

"The ratio obtained was 1.4 to 1. Since 1.4 is closest to 1.5, the ratio can be taken to be 1.5 to 1. Therefore the ratio is 2 to 1 since 1.5 should be rounded to 2."

"The ratio determined was 2.7 to 1. Since 2.7 is not quite 3 , the ratio is therefore 2 to 1"

"The amount of oxygen was 0.0018, ~0.002. The amount of {metal} is 0.0014, ~0.001. Therefore the ratio is 0.002/0.001 = 2.0" (FYI 0.0018/0.0014 is 1.3)

How awesome is this for a reference to a melting point


This is the 7th entry in google when you type in the search terms salenh2 melting point (as of time of writing)

I told the students specifically that wikipedia is not a valid reference. So how surely this would be ok right?


Ahhhh undergrads...

Oct 24, 2009

Fantastic scenery in organic chemistry

Contrary to the media's portrayal of chemistry, in organic chemistry, the only colours a chemist comes across are yellow, black, or colourless (which is of course not a colour). Unlike its inorganic counterpart, organic chemistry is typically visually boring. There are notable exceptions though.

For me, it is so pleasing to the eye when you load a flash column with a solution of brown crude product from a reaction, and the brown junk gets stuck at the top. Of course, that joy is short lived if you find out that you failed to achieve good separation, or that the brown junk accounted for most of the weight of your starting material...

More visually spectacular however is the colour of a sodium benzophenone still. For those not familiar with this, the sodium and benzophenone system is used to dry (remove trace amounts of water from) a range of organic solvents, such as diethyl ether, benzene, tetrahydrofuran (THF). Thinly rolled (or drawn) sodium is added to the solvent along with benzophenone. When water is still present in the solvent, the solvent/benzophenone mixture is yellow. However, once the solvent is completely dry, the colour turns to a deep deep blue colour. The sight of a deep blue solution of THF with bits of metallic silver sodium bobbing up and down as the solvent refluxes brings tears to my eyes. Well not really, but it's a pretty awesome sight.

My all time favourite (for now) is in distillation of reagents. I had to distill TMSOTf the other day. Actually you'd think it shouldn't be yellow considering it was stored in an ampule. In any case, I distilled the stuff across into a Schlenk flask nice and clear, leaving the yellow residue behind. Beautiful!

Oct 20, 2009

Walking around on two broken legs

Well, while it is not uncommon for some chemists to explore the world around them I am sure they have been a bit smarter about it that W, P and myself over the weekend. Deciding to climb up Mt. Barney was a good idea, but via Logan's Ridge may have been a bit too adventurous.

As it is we are a still alive but all three of us are hobbled. I personaly have named the double blisters on both my feet and look forward to having some intimate alone time with them for the next week or so.

P on the other found a tick today and decided that the best method of tick removal is nitric acid. After some convincing we got him to just pull it out but we couldn't stop him for sending the little fella into a nice little spa bath of nitric. Needless to say the tick died.

Anyway, finally managed to crawl out of bed this morning and put some shoes on so I can get in the lab. After a bit of literature searching I found the reaction I am going to do today and will hopefully lead me to an improved method for my drug. YAY! Just me and J in the lab today methinks.

Oct 16, 2009

Welcome to RBF

Hey first post in RBF ;) We're a bunch of PhD students doing synthetic organic chemsitry in the land Down Under. We hope to share some of our stories and experiences with fellow graduate chemists around the world. We would be glad to receive advice and comments from more experienced chemists of course ;)

Looking forward to our 'real' first post!