Two-headed chemical mayhem!

Possible answer to Sam's question

2007-03-10T09:24:00.000+11:00

One of our loyal blog readers, Sam, wished to know how primary alcohols were iodinated using triphenylphosphine, iodine and imidazole. Here is it, courtesy of petr: In any case have fun in the thursday morning seminars, Samuel! I wish I was there to see a certain first year PhD student write his messy structures (if you can call them that) on the board together with sound effects. Bob Woodward would surely be turning in his grave!

-Bkr

Interesting chemistry articles

2007-02-18T19:25:00.000+11:00

So I thought I might post something chemistry-related - something I haven't done in a while. Below are three papers I have read recently.
After reading almost any of Fujita's papers, I always think to myself "wish I would have published that". His work is simple (in theory), which gives it an intangible elegance. Here (J. Am. Chem. Soc. 2007, 129, 1850) he uses light to labilise his Pt-pyridyl metallocyclic systems to give the thermodynamically more stable (due to hydrophobic effects/pi-pi stacking) catenated dimers. This takes only minutes under UV light, whereas days are required if it's heated instead. Not a new concept, but nice application and mechanistic insight (photochemical mechanism is dissociative, thermal one is associative, which is of course most common for square-planar complexes).
Another cool paper, also in the field of coordination chemistry, is a recent review by Nitschke (Acc. Chem. Res. 2007, 40, 103) highlighting some nice dynamic combinatorial-style work. Most people (myself included) just abhor the prospect of a mixture of products from a reaction - this guy (who, like many top supramolecular chemists, is of the Lehn pedigree) loves them! Anyway, the point of this work is that, unlike Sanders or Fujita (whose work primarily uses labile covalent and coordination bonds, respectively) Nitschke uses a bunch of very labile interactions and can, depending on the product distribution, quantify and rationalise these contributions.
I'll finish with a paper published by none other than F. Albert Cotton, who recently passed away at the age of 76. The guy was a powerhouse of inorganic chemistry and most undergrads would have consulted Advanced Inorganic Chemistry (co-authored by the Nobel Laureate Geoffrey Wilkinson) at least once during their studies. A 2006 Dalton paper from Cottons group (Dalton Trans. 2006, 3900) is a great read and is perhaps the most thorough analysis of a square/triangle equilibrium to date. The crystallisation of the square and triangle components, along with their X-ray and NMR characterisation (they can each be dissolved and an NMR spectrum acquired before substantial interconversion) allowed for the mixture to be analysed quite simply. While many people give a half-arsed argument when considering such equilibria (triangle formation leads to an entropy increase, due to the formation of more particles, but is higher in enthalpy owing to angle/steric strain) Cotton has done all the work and gets all the thermodynamic numbers out. Full marks to him!

Peace out,

-Bkr

Tasmania =)

2007-02-17T12:43:00.000+11:00

After a long hiatus from blogging, Beaker has returned to report on his expedition to Tasmania, the Island state, which would be hosting IC07 (a meeting of inorganic chemists in Australia). Here is a map for ppl not familiar with Australia:Beaker conducted this journey with certain other chemists from the University of Sydney - as if seeing these nerds every week at uni wasn't bad enough, spending every waking hour around them was more than sufficient to drive him nuts. What was cool, however, was walking around in world heritage areas (which, along with reserves and National Parks account for 36% of Tassie) all day. In particular, our day in Cradle Mountain during which the weather was awesomely fine (this apparently only happens once every ten days), was pretty sweet. Apart from being overly sunburnt, Beaker enjoyed it - here are some pics:We would then journey to the west coast of Tassie, namely to a small (~1000ppl) ex-shipping and convict town called Strahan. The easy-going and laconic nature of this place went down as brilliantly as the local beer - we felt the best way to see this place was on a relaxing cruise around the harbour. What was less relaxing was being in a car with a certain Irish postdoc who, despite his strong stance on lab safety, felt no need to drive in anything other than a suicidal manner. Of course, he turned out to be an awesome quadbiker!
Our last port of call would be sunny Hobart, the location of the inorganic chemistry conference. Hobart has many features that distinguish it from more civillised cities. It appears that the local children have not heard of the concept of attending school. Either that, or school there only really takes up a small fraction of their time, the rest of which may be spent playing with their pet tasmanian tigers, frequenting Legs 'n' Breasts (the local chicken shop) or having a few Cascade Lagers. The scarcity of public transport was also disappointing, with no trains and very few buses/taxis. Having said that, we could walk from our motel to the convention centre, pictured below.
While I probably didn't learn as much stuff or meet as many new people as I had at previous conferences, I still enjoyed myself. The talks I attended (which may or may not represent a small fraction of those I should have attended) were pretty good. The plenary lectures given by Schrock and van Koten turned out to be pretty interesting, as I had expected. The former presented work on the catalytic reduction of dinitrogen (most ppl would have read of this, it's been out for a few years: Science 2003, 301, 76) which may see him get a second Nobel prize if a practical version of his Molybdenum-containing system is developed...

...Anyway, so I'm back in Sydney, in my 3rd year of a PhD...
my work certainly won't lead to any Nobel prizes, I really just want to get done and move on. It's that feeling I always get after conferences - possessing new ideas and a renewed urgency to develop them.

Keep it real, be yourself and stay positive :)

-Bkr

The FANTABULOUS lab timer

2007-01-15T22:13:00.000+11:00

A most fantastic device has been invented in our lab recently. It is the all purpose chemistry 4 and a half minute glass! Here is how you too can make your very own device. All you need is two bottles of your choice (preferably empty, but whatever floats your boat), some superglue, some sand, and lastly a piercing implement!

Who really needs an hourglass anyway. An hour really isn't a very practical time period. However 4.5 minutes seems to be the ideal amount of time to do many many lab related things! For example, ever come back to your bench to find your t.l.c plate has overrun? Well no more! With the 4.5 minute glass your t.l.c plates will be full of t.l.c goodness when you return to your bench. (Of course, the 4.5 minute glass has been specially designed to account for variables such as solvent system, plate size, wind velocity etc.)

Here are some other lab related activities you can do in 4.5 minutes:

1) Annoy evil lab mates
2) Set up a column
3) Decide to quit your PhD
4) Act like an idiot and get your friend to take a photo (see picture below)

Of course there are many more, but I will leave suggestions up to our valued blog readers.

Beaker faces wrath of Dimroth rearrangement

2007-01-02T20:10:00.000+11:00

At the end of 2006 I was messing around with some 1-alkyl-2-aminopyrimidinium-based ligands of type 1 in aqueous solution. For some reason, my ligands were giving weird NMR spectra after heating in water. Turns out Beaker the ignoramus was unaware of some old-school chemistry pioneered by Dimroth in the early 1900's, which predicts the formation of rearranged product 2. This has the alkyl group now stuck to the amino nitrogen atom rather than the pyrimidine nitrogen. The simple hydrolysis and condensation mechanism is depicted below.The reaction is very general - it can occur in a heap of nitrogen heterocycles in which an amino group is alpha to an endocyclic nitrogen atom. So yeah, its back to the drawing board for me =(

-Bkr

Happy New Year!

2007-01-01T11:15:00.000+11:00

Well, just in case it wasn't already obvious, Sydney is THE New Year's Eve capital of the world. Here is some proof:

I didn't take the last picture, which explains why it's halfway decent. The thing lit up on the harbour bridge is a gold emerald (i dunno why it's not green). Emeralds evoke ideas of the Emerald City from the Wizard of Oz, which, in turn, alludes to Oz = Australia. I'm sure you'll agree that the logic of our totally awesome country is impeccable!

Heaps of chemical mayhem will be in store for 2007 =)

-Bkr

Festive Season Wishes for One and All

2006-12-22T08:33:00.000+11:00

Hi Everybody!

Bunsen and myself are very happy that there are actually people other than us two muppet scientists visiting the blog!

2006 has been a very cool year indeed!

Now Beaker has been talking to Santa the past couple of weeks and has come up with a list of the most popular things people have wished for this Christmas. Check it out:

10. David Hasselfhoff - Pip, a young Kiwi lass in our group has been craving Mitch for quite a while now.....apparently, she's not alone.

9. Tickle me Elmo - A regular favourite

8. Beaker - Shocking, I know!
7. Bunsen - Not so surprising

6. Jackson SLS - The ultimate axe....I want one soooooooo badly

5. You want that reaction that you've been working on for ages to actually work for once!
4. Some B19 glassware

3. Toyota Celica - A sweet-as ride...

2. XBOX360

1. Cork Rings!!!!!!

Bunsen and Beaker wish everyone a Merry Christmas and a Happy New year. We hope everyone gets what they wish for and that nobody receives lumps of coal. 2007 will be an awesome year. Bunsen and Beaker will be in their 3rd yr of PhDing, the make or break year. May next year bring awesome results to your experiments and fun times =)

l8r,

-Bkr

Gigantoid lab

2006-12-21T21:11:00.000+11:00

Following on from the anti-Newtonian lab post, we have successfully begun work towards creating a super gigantoid lab. This lab will contain all the usual chemistry bits and pieces EXCEPT everything will be MASSIVE!

We have begun our quest by growing average garden variety pipette teats and suba seals to an amusingly large size. All you have to do is soak the pipette teat/suba seal in DCM overnight and there you have it!

Here's how much we managed to grow a pipetter teat:

If you think that's cool, you should see the gigantic suba seal we made. The first picture is a before and after shot, and the second is a comparison with some common normal sized lab objects:

Chemistry mythbusting

2006-12-21T20:50:00.000+11:00

I have been told by several independent sources that if you microwave your molecular sieves for too long then you are left with a molecular sieve block. Molecular sieve blocks sound fun, so we decided to test it out.

We took average 4 A sieves in a round bottom and microwaved the shit out of them for about 4 minutes until they smelled weird. We managed to get them white hot, but no luck with fusing the little buggers together. I believe a higher wattage is required, but that doesn't explain all the reports about the sieves unexpectedly melting. I think we need to investigate different pore sizes.

Bench Sabotage

2006-12-18T23:52:00.000+11:00

There are several clever lab pranksters in our research group. For example, one group member arrived in the lab one morning to find her collection of magnetic stirrer bars stuck to the vent (it always come back to the vent). There have been numerous pranks of this nature, which usually originate from the one source: an evil final year PhD student, which happens to be the same evil lab mate who stuck my hair to a lab stool with a magnet.

It appeared that it was time for some revenge. My prankster colleague and I found the perfect opportunity when this lab mate went away a couple of weeks back to a conference.

Ah...the possiblities were endless. This lab mate caught wind of the fact that his bench may be tampered with when he went away, and so in a fit of paranoia, he turned his lab drawers back to front, so that the handles were now directed towards the back of the bench. He finished it off with a laptop cable and a hefty lock so that the drawers could not be turned back around again by anyone but himself.

However, in our lab, we have two lab benches directly opposite one another. This meant that we were able to pull the drawers out from the other side of his bench and get to his drawers that way. Of course, we had to climb underneath the bench and avoid the 10 cm layer of dust and broken glass below that has probably been there since the 80's but it was worth it. There was a little bit of room to move the cable, and we managed to get to one of his drawers which contained his round bottom collection. It is this particular lab mate who detests B19 glassware, and has none of it in his drawers. So of course, the point of this excersise was to replace his round bottom collection with only B19 stuff. It was pretty funny when he went to get a flask!

For our next prank, we had gained some information that this particular lab mate absolutely hates the song 'angel in the centerfold'. I have to admit that it is quite possibly the worst song ever. If anyone even mentions the song it's pretty funny to see him go mental. With this information, we burnt that awful song onto several CD's which looked exactly like the ones next to the CD player, and then we copied the writing on the CD's. When he came back, I asked him to put some Kanye West on (yes, I enjoy a bit of Kanye), and instead of 'gold digger', out came that filthy song! He proceeded to scratch the shit out of that CD. That was pretty funny. We also masking taped a whole stack of his CD's together.....just for something extra.

Our last prank was very simple. We put our own lock over the top of his hefty lock so that he couldn't get to his drawers anyway when he came back.

Bad muppet bloggers

2006-12-18T23:28:00.000+11:00

Yes.....Beaker and I have been terrible bloggers. We promise to pick up the pace and post regularly from now on. Our excuse is that we have been too involved in our chemistry and couldn't possibly break away to do any blogging.........That's our story and we're sticking to it. Possibly Beaker has been busy setting up his chemistry fish tank. I on the other hand may or may not have been sabotaging my lab mates bench while he was away. (Pics to follow)

On the bright side, there is much excitingc chemical mayhem to be posted! I have diligently been keeping a record of all the mayhem that takes place in the lab, and I will be posting it all soon!

Here is a quick update on the blog polls so far. Well, it appears that everybodys favourite quickfit size is B24, and nmr is by far the favourite characterisation technique. It's followed closely by cork ring, which I believe is the only way to go.

More to follow!

Bunsen

2006-12-05T20:15:00.000+11:00

How would you figure out what you've got?
What is your favourite method of characterising a compound?

NMR
Diffraction
IR
UV-Vis/Fluorimetry/Chiroptical techniques
Elemental analysis
Electron/Scanning probe microscopy
Mass Spectrometry
Melting/boiling point
Taste Test/Smell Test
Cork Ring/Other

view results

PhD down the toilet - Stage 1

2006-12-03T18:28:00.000+11:00

Check out this cool little web game if you haven't seen it before:

Good Method of Procrastination

You get to draw a track for the little dude on a sled, and then he rides your track!

But BEWARE! This game can be super addictive. Maybe it's best for final year PhD students to stay away!

Current State of Affairs

2006-11-27T10:20:00.000+11:00

So this is our fishtank...it is empty, except for a collection of paper fish that we put in there to simlulate a thriving aquatic environment. Less realistic is the (barely visible) collection of pigs gathering around a candle. While fish probably don't want to live in this barren container, they certainly would NOT like to live in a coffee mug belonging to one of Bkrs office buddies. These are clean by his standards, I have once seen four shades of green (fungus) in there.

Bkr

Chemistry Fishtank

2006-11-26T10:56:00.000+11:00

Our research group needs a group pet or something...we don't even have any plants in our office. As a consequence, I have designed a fishtank incorporating quickfit glassware and fishtanks into one large fish playground! Food can be added via dropping funnel and, providing large enough joint size, the fish can roam around through the condenser.

Images of the current (empty) fishtank in our office will be posted shortly.

Bkr

What chemists do when they're not in the lab

2006-11-20T22:28:00.000+11:00

I saw U2 last week! They were really awesome. I was allowed out of the lab just this once so that I could go and see them.

Here's Bono

and here's The Edge

Well that's enough of the real word. More lab mayhem coming soon!

Bunsen

Sci-wine

2006-11-20T21:50:00.000+11:00

Chemistry is so 'vogue' these days that it's now featuring on wine bottles! Here's a Penfolds wine bottle that my lab mate found which has a periodic table AND a random chemical structure on the bottle. It appears to contain a five membered ring of some sort, with some very suspect looking bonding.

A periodic table on a wine bottle! It's ingenious! Maybe we could add some periodic trends on there too. This would certainly help the first years remember atomic radius and electronegativity trends alot better.

Bunsen

2006-11-16T14:45:00.000+11:00

Beaker in a tight spot!

2006-11-13T22:22:00.000+11:00

Hmmm yes.....Beaker has been a very bad muppet scientist! He has been arrested! This involves impenetrable keck clip hand cuffs, and a test tube on his head! Beaker has been accused of several crimes such as:

1) Leaving dirty syringes lying around so that they corrode
2) Releasing smelly substances into the lab
3) Blocking up all the needles in the oven
4) Not doing his lab chores

Let this be a lesson to all of you. Don't make the science police angry or your head will end up in a test tube!

Bunsen

Bunsen cooks Beaker

2006-11-13T21:53:00.000+11:00

Nano-(insert wanky name here)

2006-11-06T19:51:00.000+11:00

A self-confessed arachnophobe, I totally detest spiders... Having said that, I will now reveal the chemical structure of the smallest known arachnid, known as nanospider. I thought I'd contribute to the already burgeoning list of stupidly named molecules I've encountered including nanokid, nanoscholar and nanocar (Nano Lett. 2005, 5, 2330).

The cis-2,3,4,5,6,7,8,9-octaethylazacyclononane molecule (note the cis-stereochemistry of all the ethyl groups) incorporates 8 flexible ethyl legs as well as a pair of electronic eyes (I know spiders have eight, but meh..whatever) located in an sp3 hybrid orbital. In contrast to the Lewis structure I have given, Spartan predicts four of the spiders legs to be above the mean plane and four below it....making for a really uncoordinated look...so yeah...lets just ignore that! Nanospider loves organic media - it can spin graphitic webs of beautiful symmetry and high strength in no time ;)

The first person to prepare nanospider (pls send 1H NMR and ESI-MS spectra) will receive a free cookie from me...and if that wasn't motivation enough, you can be third author (after bunsen and myself) on the resulting Nature paper!

Bkr

bloggedy blog

2006-11-02T22:52:00.000+11:00

Here are some other chem blogs which Bunsen and Beaker have found.

The Chem Blog

TotallySynthetic.com

Sodium podium

2006-11-02T21:54:00.000+11:00

I think it's time to acknowledge the power of sodium metal. This is one cool element. I dare say it's a little promiscuous. It'll give up that electron to anyone who wants it! Yes, today we had a sodium fire. It was not the first. This lab has seen many a sodium fire. Last year I had to play fire fighter and put one out in the sink behind my bench. That was quite scary, as the waste non-Cl solvent container nearly caught on fire. Lucky it had just been emptied.

Today we were getting rid of some old Na noodles that were left in the bottom of a THF bottle. On inspection by a reliable post doc, it appeared that the noodles were no longer active. So this morning, we tipped them out into a plastic bowl. All was fine until a small tuft of smoke appeared. As we all lent over the top of the bowl to inspect the situation, the whole thing burst into flames. My guess is that that sodium wasn't dead after all! It was just hiding under a layer of NaOH. Sneaky. We all pottered around trying to find something to smother the flame with. We settled on a lab book, but this was too small to cover the whole bowl. By this stage, the flames had burnt several holes in the bottom of the bowl. In the end it just ran out of puff and burnt out. The sodium metal really taught that plastic bowl a lesson.

Here's a before and after shot.

And of course, it's now stuck to the vent.

Sodium is one reactive metal. If you don't watch yourself you might lose a head or two. I almost had some eyebrow singe action today. If it wasn't for my super sharp reflexes, I may be a few eyebrows short.

Bunsen

Nanoputians

2006-11-02T12:23:00.000+11:00

Chanteau's nanoputians paper (J. Org. Chem. 2003, 68, 8750) has been quite inspiring both to us and our chemistry collegues. In short, they spend their time making random humanoid-resembling molecules like "nanoscholar" and "nanokid".

Two things came to our minds:
1. How on earth do research groups get funding for doing this kinda stuff?
2. What if we could make moles and moles of nanopeople to make molecules for us - this means that we could spend all our time blogging instead of doing reactions! However, this may make synthetic chemists (like us) obsolete - so maybe it's best this doesn't occur.Bunsen and Beaker =)

Chemical Consumption

2006-10-31T19:14:00.000+11:00

Since all things edible and potable are chemical in nature, Beaker figures that consuming things from a chemical lab can't be all that bad - after all they are (or at least should be) pretty pure.

Given the anorexic nature of Beaker (it is rumoured that, with a lot of local anaesthetic, his head can fit into a test tube!)it was reasoned that drinking D2O instead of H2O would allow for some gain of mass. Well, Beaker has done that before, so he reasoned that adding some flavour, in the form of alpha-cyclodextrin was more appropriate. He reported the taste to be initally quite sweet, then it tasted like potatoes.

Interestingly, this cyclic molecular host (alpha-CD) may find use in chewing gums owing to it's slow release of (organic) flavour molecules. Beaker believes this to be a nice example of supramolecular chemistry in everyday life.

It seems that D2O is quite innocuous until half of your body's water is deuterated. Once you get to this stage, according to http://yarchive.net/med/heavy_water.html, cell division becomes inhibited and you die.

So now Beaker is looking for new candidate molecules to consume...suggestions welcome!

Beakie :-)

Anti-Newtonian lab

2006-10-30T22:48:00.000+11:00

Now that Beaker and I have officially intoduced our blog, I thought I would make my first individual post. I am the blogging chemist known as Bunsen, and I'm a female graduate student doing my PhD in organic chemistry. We have decided not to reveal our identities just yet in case this whole blogging thing turns out to be a complete disaster.

Well, here's my first lab story. I live on level 5 of the chemistry building, in one of the organic research laboratories. Some of the boys in my research group have been pulling apart dead hard drives, and removing the magnets. The magnets that come out of these hard drives are super strong.

This has led to two main observations:

1) Magnets are cool
2) They are even cooler if you can find something else magnetic to stick them to.

We had many many hours of fun sticking two magnets together and trying to pull them apart (this is really hard! They are some strong magnets!) When this got old, we took to using the magnets in more inventive ways. For example, one such evil lab mate of mine stuck a piece of my hair between two magnets, and then proceeded to stick my magnetic piece of hair to a lab stool. Being temporarily attached to a lab stool turned out to be pretty amusing, and so I didn't yell at said evil lab mate. I can get quite angry at times :-)

The discovery that followed is the basis for many hours of fun in the lab. Some genius discovered that the air conditioning vent that runs just below the ceiling in our lab is magnetic. We had magnets, and the ceiling was just waiting for some action. At first we just threw the magnets up and laughed when they got stuck to the vent. Then we took to sticky taping the magnets to random lab objects and then throwing these objects up. Now there is all manner of crap on the air conditioning vent. It may sound stupid, but seeing an empty chemical bottle/water container/random stuffed animals get thrown up in the air, and never come down is really hilarious! Who knew!

I thought it was necessary to share this discovery with everyone: What goes up doesn't always come down :-)

Bunsen

Sexy Science

2006-10-30T20:52:00.000+11:00

Just when you thought that the words "sexy" and "science" could never be mentioned in the same breath, it seems that, according to http://sexyscience.blogspot.com/, these two are not mutually exclusive!

In any event, it's good to see people discussing the lighter side of chemistry, so word to The Science Diva for her page.

Beaker

Welcome to our blog!

2006-10-30T15:58:00.000+11:00

Dear esteemed visitor,

Welcome to our first attempt at bloggifying! Our mission: To fill the web with chemical mayhem and other random stuff. Whilst we feel our way through the wonder of blogging, we appreciate your comments and feedback.

We are two graduate students at the School of Chemistry, University of Sydney in Australia. One of us is a synthetic organic chemist and the other an inorganic chemist. This is the basis for many hours of two-headed chemical mayhem, including doing fun and sometimes destructive stuff in our labs, as well as having endless debates about whether organic or inorganic chemistry is better.

It is our aim to bring attention to impressive synthetic feats, inept practitioners of synthetic chemistry, and general chemistry fun. We hope that this blog fulfils all your chemistry desires, and maybe you can learn a thing or two as well.

Yours sincerely,

Bunsen and Beaker =)

P.S. The bloggers welcome offers of post-doctoral positions from cashed up, hot shot academics around the world.