Low Vacuum Manifold

I couldn't believe my eyes when I saw this. The glass blower who made the manifold has missed the point. Five excellent high vacuum taps combined with a rubbish Teflon tap to produce a nice a shiny low vacuum manifold. Speaking of missing the point check this set up out using the same manifold. Spot 5 mistakes. D!

Sleeping with the stirring bars

Speaking of grease it appears that the spider mob has been busy again and sent one of their own to a greasy death. I'm sure that I'll have nightmares about falling into the massive silicon oil bath from hell for a while. D!

Grease

Some time ago I received an email from a reader regarding some problems keeping a constant vacuum during a distillation:

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"...What type of grease (if any) do you use for the ground glass joints during high (oil pump) vacuum distillation? I use the 'regular' Dow Corning High Vacuum Grease that comes in a funky aqua colored tube. Sometimes when I am carrying this out, all of the sudden partway through the distillation, the pressure will suddenly go from about 0.06-0.1 Torr (where it normally is) to maybe 0.6-1.0 Torr. It doesn't always happen but the effect on keeping track of the boiling point is irritating with the pressure all over the place..."

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This is a common problem and it's not necessarily a problem associated with the grease. Let's talk grease first. I have never used the grease mentioned above but I'm sure that there are many excellent greases available and this particular grease may also be good. However, I do know that if you stick to the correct Apiezon grease for your application you won't have any grease related problems. There is a whole range of Apiezon grease and for a high vacuum distillation I would recommend either Apiezon T or H. All the information you need to select the correct Apiezon grease is available here. Don't overdo it when you apply your grease otherwise you'll contaminate your material during distillation.

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Interestingly, I recently had a similar problem to that described above when setting up a high vacuum manifold. However, in this case the problem was not the grease but the use of inappropriate vacuum tubing. The vacuum I was operating at was much lower than that described above but the same vacuum surge phenomenon was observed. The solution to this problem is to buy Tygon tubing. It's expensive but it's worth all the money and you usually don't need more than a few meters anyway. Aldrich sell 10 foot pieces of Tygon. It's transparent, nonreactive, flexible, not brittle and doesn't leak. It's simply the best. There's a good post at Wikipedia on grease. Notice the smart way of applying grease using a syringe. Also if you are setting up a high vacuum manifold you should consider reading this post at Org Prep Daily. D!

Curly Arrow update

Apologies for the infrequent posting. I'm very happy to see that people keep coming to the blog despite this. So what's my excuse this time? Well I just started a new job. I have left academia (for now) and I'm working in a medium size biotech company doing some traditional medicinal chemistry to cure the world etc. However, I have been made an adjunct research fellow at the university and continue to supervise some students so I still have a foot inside the academia door. Also I have become a regular writer for the chemistry magazine published by the Danish Chemical Society which is quite exiting. Unfortunately this only gets published in danish so it won't be of interest to most of you guys. What's even more cool is that they have agreed to set up a blog on the magazines web page where the articles will also be published.
I'd like to thank people for the many emails I get with interesting questions and requests for paper reprints. Thanks for taking an interest. Curly Arrow has now been running for 1 year and seems to be a fairly popular blog (see some stats below). I've even reached the point where people are offering me money to place adds on the blog (You have to pay a lot more guys if you even want me to reply to those emails) and I have been blessed with lots of spam comments linking to porn sites (the pinnacle of my career). I almost clicked on cucumber sex to see what cucumber variety would be employed. D!

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From 18th October 2006 to 9th November 2007

Absolute unique visitors: 13,369

Total visits: 34,820 (89.47 Visits/Day)

Average time on site: 1:06 minute

The 10 most frequent visitors identifiable:

(1) Scripps Research Institute

(2) University of Cambridge

(3) Oxford University

(4) University of California

(5) Princeton University

(6) Columbia University

(7) University of Rochester

(8) Harvard University

(9) The Pennsylvania State University

(10) North Dakota State University

Authors - alphabetical vs. by contribution

After my first post on Authors and who goes on papers I have received quite a few emails from people and had some interesting discussions with some of my colleagues. It seems that everyone has a good story on this topic. Something that I've noticed can give rise to some heated discussions is whether authors should be listed alphabetically or according to how much they have contributed, i.e. the first author did most. From what I've gathered so far the alphabetical system seems to be a chemistry thing. When I mention this concept to people in biology/biochemistry they are outraged. In their area you really need to be the first or second author for the paper to carry any serious weight on your publication list. After thinking a bit about all this I have reached two conclusions that may or may not be right:

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(1) The alphabetical system only benefits the supervisor. The supervisor no longer has to have any troublesome discussions about who did what.

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(2) The contribution system also benefits the people that actually did the work. In many academic institutions and companies they look for first authorship's on papers. This is the only way they can determine if people did any meaningful science. From third author and down they could have ended up on the paper for close to nothing.

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And then there are the supervisors that mix things up:

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(1) Many supervisors will always put themselves last and everyone else by alphabet?

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(2) Others will always put themselves first and everyone else alphabetical (or by contribution). I suspect they do this so that the paper will be referred to as "supervisors name" et al. rather than "students name" et al.

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I have been through two alphabetical places and four by contribution places and I have reached the conclusion that if you want your name at pole position (at the alphabetical places) you just have to do all the work yourself. And finally just in case anyone thinks that I'm moaning and I'm unhappy about how things have panned out for me - I'm not - I just thought the topic was interesting. D!

NMR tube cleaner

I have a lot of NMR tubes and as a result I don't clean them very often and when I eventually decide to do something about it I'm faced with something like 30 dirty tubes. Now firstly if you work this way you have to soak the NMR tubes as soon as you are done with them. If you just let them evaporate to dryness you are in trouble. I normally just empty the tube and fill it to the lip with acetone and cap it. This way it wont dry out for months.

When I was cleaning my tubes the other day I had three synthetic organic chemists from three different countries walk up to me and ask what I was doing. This was somewhat surprising so I've decided to share with you what I thought was common knowledge: The NMR Tube Cleaner. These things are commercially available (expensive) or you can have your glass blower make one at a reasonable price. You can see my set up on the picture above. This is how it works:

(1) take the cap of your NMR tube and attach it to its base

(2) stick the tube in the cleaner (see picture) so that the cap seals the opening at the top

(3) squirt solvent(s) into the solvent opening (see picture).

The system is under vacuum and the solvent gets sucked through a thin tube that goes to the bottom of the NMR tube. It is very effective and I usually do a combination of solvents to get rid of everything. Its smart to have a three way tap between the cleaner and the pump so that you can let air into the cleaner without having to turn the vacuum off all the time. There's an NMR tube entry at Wikipedia that also describes the NMR tube cleaner. D!

Authors - who goes on the paper and why?

Yes I know! It's pretty quiet around here. My Internet connection at home is dead. I'm on the phone with my Internet provider every day to resolve this issue but it is a slow process.....So I guess a bit of blogging from work is required (Sorry boss. I'll run that column in 15 minutes). I'm writing papers at the moment and this always brings up the issue of authors. Who's on and who's off? Over the years I've experienced some pretty disturbing things in this category:

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(1) You send the paper off to your boss for proof reading etc. and it comes back with another name on the paper! Why? The boss feels bad about not giving that person credit for something completely unrelated and is trying to make up for it.

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(2) People doing routine analysis go on all papers. This category is a bit of a grey area as some techniques may be routine to the person doing it but does require years and years of experience. An interesting issue in this category is X-ray crystallography. Many older scientists (50+ years) don't realise that this has become a routine operation and religiously put the x-ray dude on all papers. Granted in the world of small molecule X-rays the crystallographer should go on sometimes when things aren't trivial. However, 90% of the time this is definitely not the case.

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(3) Everyone in the lab goes on all papers! This is really far out but nevertheless the policy in some labs. By everyone I also mean the technician making up the solutions.

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(4) And then there are the totally reasonable, serious scientist that will actually ask to have their name removed from the paper as they don't think they have contributed enough. I like this person much more than the evil pseudo-scientist snake that will do anything to sneak their name on a paper.

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There's much more where this is coming from. Another post on the topic coming up shortly. D!

Pay Rise Cake

Regardless of whether you are working in industry or academia there will be occasions where you will have to supply cake (If this isn't the case you've got it all wrong and should bring some cake to work tomorrow). Now I will concede that there are decent commercially available cakes that I will eat with great pleasure. However, if you consider yourself a synthetic chemist, be it organic or inorganic you MUST make the cake yourself. It's way easier than synthetic work and the final product doesn't require chromatography, tastes great, won't kill you and will make people happy. So here's a recipe to help you guys out if you have no idea what to bake. It's the cake that a friend of mine has named the pay rise cake as you are guaranteed to impress your boss with it. It's a fairly expensive cake to produce but believe me its worth it.

Banana and Chocolate Cake aka Pay Rise Cake [Serves many, 20+]
Ingredients
Flour (500 g)
Sugar (500 g)
Quick oats (50 g)
Butter (300 g)
5 x 50 g eggs
8 ripe bananas (ca 700-800 g when peeled)
Skim milk (150 ml)
Vanilla sugar (5 tsp)
Baking powder (5 tsp)
Salt (3 tsp)
Dark chocolate (300 g, Don't be a cheap skate and use good stuff. For example Lindt 70%)

Procedure
(1) Melt the butter - do not reflux
(2) Beat the sugar with the melted butter
(3) Add the eggs (not the shells) and beat
(4) Add milk and bananas (mash the bananas first) and beat
(5) Add flour, quick oats, vanilla sugar, baking powder and salt and beat
(6) Chop some of the chocolate (200 g) and mix it with the dough (don't beat it at this stage)
(7) Transfer the dough to a large baking tray (eg. 30 x 30 x 5 cm) and bake in the centre of the oven at 180 oC for 40-45 minutes. When the dough doesn't stick to a metal object it is finished (you basically insert a metal object such as a knife into the cake and check if anything is sticking to the knife). It is a good idea to check on the cake after 30 minutes as ovens vary greatly in performance. The cake approximately doubles in size depending on the baking powder used.
(8) When the cake has cooled to room temperature cover it with a thin layer of melted chocolate. You have to be careful when melting the chocolate. First chop it up (100 g) then put it in a suitable container (eg beaker) and melt it using a hot water bath whilst stirring. Do NOT add water, milk or anything else. Simply use good quality dark chocolate with a high cocoa content and you are in business.

Enjoy the cake - it is really nice. The cake is excellent for freezing and I generally have some tucked away at -20 oC for "emergencies". If a pay rise isn't enough and you are going for a promotion then you may consider serving it with some fresh strawberries. D!

Retraction - Azepinoazepine or Viologen?

I believe a new post is way overdue. Since my last post I almost ended up becoming a regular writer for a chemistry magazine and I have been reading an excellent book: Organic Synthesis - Strategy and Control. In due course I'll post a review of this most excellent book. Anyway, let's get to the point. Additions and corrections to papers are quite common in organic chemistry but you don't see retractions very often. Well it appears that Yamaguchi, Tsutsui and Sato where getting a little bit too excited about their synthesis of azepinoazepines (1). However, after the paper was accepted in Angewandte Chemie someone (probably Thomas Vaid, Washington University, US) was kind enough to point out that they had in fact made some viologens (2) (See Vaid's paper on viologens here). I guess that paper didn't last long on the CV. In Yamaguchi's defence I will say that it isn't entirely trivial to sort out the 13C NMR spectra of these compounds and when you are actually trying to make something specific you have a tendency to get carried away at times. I just hope this sort of thing never happens to me. On a similar note someone I know recently had a rather controversial opinion paper accepted in a high impact journal. However, whilst making changes suggested by the referees she came to the realisation that they couldn't actually draw the conclusions they had been making in the first place......I guess that's better than having to retract it later on but it's gotta hurt. D!

Behold cyclohexane!

Recently I was flipping through a magazine published by a learned society and my eyes were caught by this rather interesting picture. The aim of this photo is to encourage scientist to publish in certain society journals. Firstly, it seems rather lame that the teachers is pointing at cyclohexane that appears to be in its perfectly flat conformation? Is that the most acidic proton he's pointing at? Secondly, what is going on with the students. I have a feeling the guy to the left is a werewolf. Or maybe he's just split up with the girl to the far right which would explain why she looks like she's about to commit murder. And what's going on with the woman in the background? It's cyclohexane people and not Brevetoxin so stop looking at it like that. D!