Jan 29, 2010

Beds in the office

I have always been a firm believer in having beds at the university somewhere. Just somewhere you can go to have a quiet comfortable nap. Like right now I am suffering from a severe food coma and need a nap so I would go have a nice lie down for 30min or so just to catch up and then be ready to go again. 

I know this has been proposed before and one company takes it to the extreme. But seriously, I get tired after lunch and would love a nap. I think there ought to be some more sleep time factored into work. Although, this blog is sending me to sleep right now. Better just to get back in the lab and clean up. Friday is so not fun, until you leave.

Jan 27, 2010

Australia Day = Awesome

So yesterday was Australia Day. Normally, I wouldn't really have anything grand planned for it but this year it was different. This year it was proposed that the back hill in my mum's house would be perfect for a slide. Couple this with a pool and you have some wet and wild fun just waiting to be had. So after searching for hours trying to find a suitable sheet of plastic for a slide we came across a giant tarp in mum's garage, some tent pegs and 2 or 3 bottles of $1 dish washing liquid. Then it was just add water (and beer). We set up a sprinkler hose down the length of the tarp, pumped some tank water through it and then it was game on.

Here is how to have a blast on Aussie Day:
Crack a beer, drink half, down the slide, drink some more, down the slide again, drink, then jump in the pool. Rinse and repeat. The BBQ was fired up and some well marinated sausages and onions were fried up with plenty more beer and the party was definitely in full swing. Some rest time after eating, have a chat over beer then watching some cricket in the street out the front of the house. PERFECT AUSTRALIA DAY!

You can't ask for a better set up - public holiday on a tuesday where you are almost expected to be shady at work the next day. Lots of sun, lots of beer and tons of fun.

Any of you out there keen to share your day post it up, I'm keen for some more ideas for next year.

Jan 25, 2010

Super ASAP

Now THIS is what I call ASAP (ACIEE paper on ent-Hyperforin):

Jan 23, 2010

RBF Teaches: Lab Safety

While it really is impossible to go through all aspects of lab safety in the space of one short blog I still find that it is indeed quite necessary, especially when you lay out a number of reaction procedures initially and direct young chemists to your site for demonstrations and support on fundamentals on lab life. I also was greatly inspired by excimer and his fellows and followers at CBC who recently compiled a great topic on lab safety which ranged through various points and all of them very valid. So, for those of you who want a straightforward rundown of exactly what was covered in that blog I hope that you will find that here. Along with (hopefully) a few pointers from MSG who, IMHO, is perhaps one of the most pendantic, but also the most safe and efficient chemists I know [MSG edit: why thank you ;)]. So let's get started.

  1. Cleanliness is next to godliness in the lab - In my opinion it is vital that you have a clean area before you start work, this will prevent you accidentally bumping over glassware, spilling solutions and give you a good idea just what things are needed in the hood for the reaction to begin. [MSG edit: the best time to clean up is when you're waiting for your reaction to finish (rather than heading straight for the next free computer to play restaurant city on facebook). Clean up whatever glassware and equipment you used and any mess you've made. Then read ahead and prepare whatever pieces of glassware, reagents and equipment you need for your work up. This will help you save time (so you can go home and play restaurant city), get your experiment to run more smoothly (which means better marks), and being organised means less likely to rush and get into accidents.]
  2. Preparation is key -Before you start, before you even enter the lab, know what you are doing and know it well. It is ok to have your reaction procedure with you while you are doing the experiment but what is more important is knowing what each step means in terms of the reaction (e.g. why do you add the water slowly, to quench? so it doesn't explode in your face! That's why!). If you are planning on scaling up a reaction then remember that the bad things that can happen on a small scale can increase exponentially on large scale.
  3. Always do your MSDS - this is important to understand what you are working with and although it is on an industrial scale and a lot of the time not relevant to lab scale it still outlines the dangers of chemicals, sometimes it may be wrong or leave out important facts. [MSG edit: puuuhlease use the fumehoods!]
  4. Lab safety equipment is vital - I know it can get hot or the goggles can hurt your nose but imagine losing your eye because a piece of glassware explodes or you spill a solution of corrosive liquid on you and the only barrier is your shirt. Therefore, Labcoat, Goggles and Gloves are all VITAL! [MSG edit: Ok guys all this gear is not just for show - you've gotta be a complete idiot to think you're invulnerable coz you're not! From most important to least important, I'd say it goes goggles, enclosed shoes, gloves, labcoat. REMEMBER, you can be the safest chemist in the world, but you still need to protect yourself against accidents caused by people around you!]
  5. Check your equipment - Star cracks in RBFs are a good one to look out for (implosion from high vac is not something you want to experience). Make sure your heater stirrer is working (this will save time if it isn't and you have to rearrange your whole experiment). Blocked needles can lead to big problems (don't force a syring if it isn't moving, you will probably end up with a facefull of reagent).
  6. Know your exits, showers, eye wash stations and fire extinguishers - May sound simple but the nearest shower may save both your skin and your life, just pray it never comes to that. Make sure before you use any lab that you know where they are so that you can find them with your eyes closed...literally!
  7. Never work alone - This is one that is often not obeyed by organic chemists. It is never wise to be in a lab on your own. That other person in the lab may just be the only one capable of pulling your arse out of a really bad situation. If they aren't there and things go wrong start praying.
  8. Ask! - If you haven't done a procedure before and you are unsure, a second opinion is great to have. Whether its an experienced post-doc or even a co-worker to just watch over while you do it, it is better to have someone else there if you are not confident.
  9. Don't Rush - The expression haste makes waste is often used and seldom heard. If you are rushing an experiment to get home on time you are more likely to break something and cause yourself more time and potential danger. Take it slow and get it right and don't feel that you are too slow, there is no such thing in chemistry. [MSG edit: In fact, if you rush, stuff up the experiment (which usually happens), you then need to repeat the experiment, which ends up taking up considerably more time than if you did it slowly but properly the first time around. 'Slow and steady wins the race'.]
  10. Documentation - Although it really isn't a safety issue, taking notes and making sure every step is documented is very important. It may be that another researcher will need your notes to do the same experiment, or you might one day want to publish your procedure, or if you make a mistake, you may be able to go back and see where you went wrong. Documentation people is what makes you a scientist! [MSG edit: Despite how hard you convince yourself, you won't remember what you did in the lab the day before (or even 3 hours before). Document what you did when you have spare time, for example, while waiting for a reaction to complete or while waiting for rotary evaporation to finish.]
  11. Checklist - This can be similar to your documentation but more of a mental thing. Go back over these points - do you know what you are doing? What can go wrong? What to do if it does go wrong? Make sure you can answer these questions before you start as well as while you are doing the experiment. You might feel indestructible but believe me you are flesh and blood and both of those can be peeled away with a spill of t-BuLi.
  12. Focus - stay aware of the experiment while you are running it. If you can leave it that is fine but remember it is there and what can go wrong and don't lose your focus on what you are doing, if something is bothering you fix it before you proceed. Don't get cocky. [MSG edit: Concentrate on what you're doing. If you're focused on your job, you're much less likely to be caught napping and panicking when accidents do happen.]
I know it all sounds very dramatic, and it kind of is, but remember its your life and your body on the line every day. It may sound like a dull job but the risks are there for the next careless person to find. (We really should get paid more) Get lots of sleep, stay focussed even if it is a boring column (these can shatter in your face) and at the end of the day always be wary of liquid oxygen in your cold trap.

[MSG edit: I don't know if you kinda got my drift, but safety and experimental success (at least in the undergraduate lab where every experiment is supposed to work) are strongly correlated. If you want good marks, then you want your experiment to go well, which means that you need to be prepared, focused, ask for help when needed etc. These are precisely the same sort of things you do in order to practice lab safety, so even if you don't care about your health or your colleagues', at least do the above for the sake of your own marks!]

Jan 22, 2010

I need sleep

I am struggling with the weather here in Oz, yes I'm Aussie but I still hate going to sleep covered in sweat. I haven't found much bearing in the whole drink warm milk thing, it's summer so I don't want to be drinking warm things. I wouldn't mind testing out the whole Turkey thing, tryptamines are pretty cool but I am still a student and affording all that turkey right now just isn't possible. Which brings me to the potential for drugs, I am totally not a druggo and I really haven't done anything hardcore at all, but there is something mildly alluring about doxylamine that makes me curious on whether I could possibly synthesise it safely in the lab.... I am pretty sure the answer is I could synthesise it but would I be willing to ingest it afterwards? No, I don't think so, not with the all the other stuff that might be in there.

So I go now to delve into scifinder. Maybe that will put me to sleep, but then again, maybe not.

Jan 20, 2010

More stink


Once more I have soiled the lab. I was doing my Barton decarboxylation once again and this time decided to show someone from another group how bad t-BuSH smells. I opened up my small plastic cylinder that I use for smelly syringes and the whole lab cleared out within 30secs. Thiols are so totally awesome.

Anyway, as promised, here are the pics of the setup. Its very simple. Large RBF, condenser, hot plate, oil bath, 240W lamp and retort stand. Argon feed in the top (i usually replace this line after the experiment as there is always some thiol stench in it, plus I vac the argon line to purge the system.) as well as the syringe with the acid chloride in it.

Voila, decarboxylating in progress.

Jan 19, 2010

Wooo free stuff

MSG, Thujone, P and I found ourselves jostling with a number of other fellow scientists in a biology lab that was closing down yesterday. All of us trying to find the best free stuff in their unfortunate lab. We came back with a mighty haul. After frantically scrambling over each other to get at the goodies (constantly wary of the Sodium azide jar complete with cracked lid) we raked in a large number of chemicals that were either in new packets, running low in our lab, or were known to cost a pretty penny.

Unfortunately, we missed out on the small Uranium sample that was up for grabs by mere seconds (this remains a sore point with Thujone). However, a number of cadmium compounds, some silver nitrate, a fresh 2.5L bottle of chloroform among other things, made up well over $2,000 worth of chemicals. The best part of all of it is that the lab was (as I mentioned previously) a biological one and I feel quite satisfied knowing I made them pay through the nose for once. And they provided me with a new 300W lamp for the lab which should be good for some of my photo-initiated reactions.

Take that Biology!

Jan 15, 2010

I hate patents

I have been slaving over these incomprehensible peices of crud for days. I seriously hate them with a violent passion. Nothing is ever straight forward and the crappy USPTO puts their patents up as quicktime images for crying out loud. Major fail. This means going to freepatentsonline.com and finding it there because SciFinder just links to the god awful USPTO website. Give me PDF or give me death. At least it isn't in Chinese [1].

Meanwhile, in the lab I have been synthesising more starting materials. On monday/tuesday I will be repeating the Barton decarboxylation so hopefully I will remember to bring my camera. Everything here is back in full swing. Even W is in the lab now and then, turning his pump on as well as the argon. It's good he enjoys a bit of time away from his calculations. I know I would. Those things are damn hard to understand.

The talk of the office is also hilarious, a co-worker was recently found to have been using her full name as a password. It was by chance that we found out, someone asked randomly if she did that and her suspect reply was enough to warrant an investigation which led to the discovery of the fact. Subsequently the password was changed after many hours of laughter at their expense.

Soon to come are some interesting experiments, we hope. A number of reactions that require a bit of technique and some clever thinking will hopefully be posted. Not by me cuz that's not my style, but hopefully MSG or Thujone will have a nice treat for you guys out there. I will be looking at posting some more RBF teaches soon which will hopefully help the undergrads out a bit as well as the tutors who teach them.

[1] and I finally get it translated only to find it isn't what I was after in the first place. Hooray for the little wanker who thought he was really smart by obscuring patents. I hope you are really proud of yourself. One giant clap for you buddy.

Jan 12, 2010

Can you have Mi Goreng with SOUP?

As you know, instant noodles are an essential part of grad students' diets. One particular favourite of ours is Indomie's Mi Goreng. Not only does it taste absolutely awesome, but it is unbelievably cheap, costing about $0.30 AUD per packet.

Mi goreng is malaysian for fried noodles. This makes it different from many other instant noodle brands in that you simply mix the seasoning and the flavour sachets with the moist but drained noodles. Unfortunately, SOME people in our group prefer to eat these awesome noodles in soup.

So if you've had these noodles before, it's time to settle this issue once and for all:


Hands up

Ok, so I have been thinking lately that a number of journals are becoming more electrosavvy and as such are including a nice little picture in the table of contents. And, while its not for lack of trying, a lot of our fellow researchers are struggling to produce a nice picture that truly represents the experiment and captures the reader's attention.

In the past there have been some really funny ones and I have no problem with, graphical abstracts that display the general reaction detailed within the paper, but to me something is really lacking. There is no pizzaz, no wow factor, no HOLY SH!T to the whole graphical abstract. I myself have struggled to produce a half decent picture for the intended use. So I feel that it is time someone steps up to the challenge and in doing so show the organic synthesis community how it's done. There may even be a business in it guys, design jobs are few and far between now and someone with a knowledge of both synthesis and graphic design may just find a niche market.

I have to admit though I have seen these graphical abstracts improving, combining pictures taken with cameras and some nice graphics are becoming more prevalent and some of the biochem papers have some nice rendered images but there must be something out there that can better this:

Also, if you can find any good ones guys let me know and I will post them up!

This one is so cool, even if it is biology! Super Macrocycles

And here is one that isn't the least bit confusing.... (Sarcasm much?)

 Now this one is getting there. I looked at it for more than a second so it caught my interest even though I don't really care about the topic.

Jan 11, 2010

Microwave Chemistry

I just thought I would put down a few lines on some microwave chemistry and hopefully gain some outside views as well. This all comes from a paper that my old boss recently published in Aust. J. Chem. regarding some pretty neat synthesis of quinolones and napthyridones by using microwave irradiation to replace the original FVT (flash vacuum thermolysis) methods.

As an undergrad I spent my honours year pounding on the CEM Discover microwave unit and I am so glad I did. The reactions I did in the microwave (when they worked) were so fast and I did so many more reactions in so little time that it really didn't seem fair on the other poor undergrads, like MSG, who had to do the good organic stuff in the fume hood. I kind of regret it too as I didn't really learn all that much in terms of lab technique among other things. However, I still love to use the microwave as much as I can, which is rarely now :(.

The use of the microwave for reactions such as simple esterification of carboxylic acids is a good example of MAOS (microwave assissted organic synthesis). The reaction takes no time at all and workup is no problem. But sometimes you just can't get the results you want from microwave reactions either. For example, some researchers in the past use trusty old kitchen microwaves for their MAOS and unfortunately this made replication of their experiments quite difficult in other labs. The generation of hotspots in the rotating microwave ovens is virtually limited in units like the CEM but at the same time the CEM is prone to generating a lot of heat in a short amount of time and you can really nuke a reaction and expensive materials if you aren't careful.

Another interesting part of the CEM discover microwave is the nitrogen inlet valve for "power cooling" the concept behind this being that if you cool the reaction while irradiating it you can put more microwave energy (in effect a greater vibration of the molecules in the reaction chamber) into the reaction and therefore speed the reaction up. However, in my experience the heat of the reaction was required to have the reaction proceed. Anyway, I am keen to have any outside input made as to how anyone else uses the microwave for reactions as this was deemed to be "the way of the future" in organic chemistry but we are yet to see the full implement of microwave reactions in our lab and I sure haven't been reading all that many journals with MAOS included.

Jan 7, 2010

Bringing back the stink

So today I am completing the final step in my nice little Barton decarboxylation. For any of you familiar with the reaction it is quite nifty and basically serves as a relatively straightforward method to remove carboxylic acid function from a compound. A quick search of our favourite cheat site OCP will show you that there are a couple of methods of performing the reaction either via a stannane or via the pyrithione. In both cases however a considerably stinky reaction ensues and if you are not careful (as I am often not) you could easily end up being the most hated member of your group.

I personally use the pyrithione method as I am really not fond of tin and the materials are quite cheap. However, in the reaction, which I will post a quite procedure for after the post ( I like to babble first), the when the radical of the pyrithione is formed the use of t-BuSH as a trapping reagent often causes quite a few groans from the rest of the lab. What's worse is that one time I was working up a courageous large scale reaction (>4g), which required a seperatory funnel and I inadvertently shook it too hard and ended up cracking the funnel on the fume hood door and spilling the contents all over myself. Needless to say I stripped off the lab coat but the smelly damage was done. I had to catch the bus home and I think I attracted a few admirers on the way. (By that I mean they followed me home waving flaming brands and tried to offer me a pitchfork, which I didn't need so I declined).

But seeing as though this is a chemistry blog and I feel like the few readers we have so far read this blog for some form of enlightenment I will share with you the procedure I follow. It is broken up into parts you need to prepare.


50mL RBF, inert atmosphere 

To a suspension of dry carboxylic acid (R-COOH, 2g) in anhydrous DCM (10mL) at room temperature is slowly added oxalyl chloride (1.5eq). The suspension is left to stir for ~30min until solution turns clear. The solvent is removed in vacuo ~40tor is usually good then 0tor for another 10min to ensure everything is evaporated. The white solid is then purged with inert atmosphere and anhydrous benzene (10mL) is added.


250mL RBF, reflux condenser, inert atmosphere

In a 250mL RBF is added ~1-1.1eq of dry and recrystalised 2-mercaptopyridine N-oxide sodium salt (you can use the non-salted version but I find the salt works better, this is also known as Omadine and apparently can be found in anti-dandruff shampoo). To this salt is also added ~2eq (~2mL) t-BuSH (the stink factor), 30mL of benzene and a catalytic amount of DMAP. The omadine should be shielded from light until you are ready to perform the reaction. Once you have your acid chloride solution prepared you can begin to reflux the solution and then irradiate with 250W tungsten light a short time before you begin to add the acid chloride.

Addition of acid chloride is a personal preference. In some instances when you have this under inert atmosphere it is probably a good idea to have a sulphuric acid bubbler attached to the system to prevent the stink from entering your argon lines. Also, I add the acid chloride via a syringe  in the top of the condenser and try to drip the solution into the soup without getting it on the sides of the condenser. Another method would be to use a dropping funnel but who really wants to clean up all that stinky glassware at the end of it all.

Anyway, dropwise addition of the acid chloride - you don't want to add it too fast or the formation of gas can cause a stink explosion- over about 20min. Follow this with a further 1hr irradiated reflux.

Cool the solution in an ice water bath and quench the stink with 10-15mL calcium hypochlorite sat. soln. added in portions to the vigourously stirring soup. Then extract the solution with 25mL ether and wash with 3x25mL water. Back extract the water with a further 25mL ether and dry the combined extracts with MgSO4. Run the decarboxylated product down a column and voila. You have made a mess a  lot of stink and some decarboxylated product. YAY!

Jan 5, 2010

Welcome 2010

Well it is definitely the new year, I know this because the boss is back and everything is in full flow again. The lab is humming with the dulcet sounds of high-vac pumps and the clink of clean glassware. Yesterday P, MSG and I (I mostly watched) decided that the THF still had looked like s#!t long enough and we should give it a clean.

What a mission that whole ordeal was, so much benzophenone and sodium crud settled at the bottom. We didn't know whether it would all react when we were adding some EtOH to quench it. We added it slowly but we weren't sure whether after adding small bits at a time, if there was a layer of crud covering a chunk of sodium, we would end up with a lot of EtOH and the sodium finally being exposed to the crud and the whole still going up in a giant bubbling ball of crud. We got lucky I spose but after we decided it was all quenched the crud was all clumped together making it nigh on impossible to simply tip it out into a waste bottle. After a lot of poking (with our patented lab-chopstick) P finally got the crud out and we could wash out the rest.

So that was fun, but now I find that to start up my reactions again I need to distill all my solvents (I say found out but deep down I knew). If there is one thing that makes me reluctant to get in the lab its the fact that I have to take around 2 hours just to set up for the reaction. Mind you this is large scale here and the solvents are definitely not the nicest. I have to distill t-butyl thiol and benzene and if they don't kill me then the rest of the guys in the lab will for the smell that always comes from it regardless of how careful I am. The tiniest drop inadvertently spilt anywhere causes an immediate reaction with someone else in the lab.

So here I go back to the lab, hope that my liver, which took a beating over the holidays, doesn't give up the ghost.