Christmas decorations for chemists

As I was decorating the Christmas tree today I found some of my chemistry contributions to the festive season. First up is my carbohydrate paper cone that I received as a gift some years ago:
And then there's this very old distillation receiving flask that looks great on the Christmas tree: Notice how they have marked each of the receiving arms with small blue coloured glass bumps. Okay that really is it until next year. Merry Christmas and Happy New Year. D!

+PLoS+

Some time ago when I was ranting about papers, authors and so on I promised a post on open access journals, more specifically PLoS: Public Library of Science. I'll leave the Open Access issue for another day, suffice to say it's something I like very much. Anyway, the PLoS journals have several neat features:

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(1) Upon submission of a paper to a PLoS journal each author receives an email from the journal where (in detail) they have to justify why their names are on the paper. Until this process has been completed the paper will not be considered for publication.

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(2) If the paper gets published it will contain an account of what each author has contributed to the paper.

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This is all about transparency and not getting on the paper for doing routine work or just as a favour to a buddy. Obviously, the system still isn't perfect but it applies some pressure on the authors. It makes them think about the whole process and I bet that it gets rid of most of the crap you get in ordinary journals.

And there's more:

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(3) PLoS journals have good to high impact factors. In other words people contribute good work to these journals.

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(4) Readers can post comments and questions on the paper and the authors can respond. Just like a blog.

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(5) If the authors make an important discovery relating to the paper they can add more data to the original publication. How cool is that? I wish I could do that with some of my publications. The extra data still has to go through peer review which makes it even better.

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So why am I not publishing all my papers in open access journals. Well chemistry still hasn't caught up with things in this area. There are things happening but compared to what's going on in biology we have a long way to go. However, this is the way of the future and the journals know it so they will have to adapt. Recently, a bill that required all NIH funded research to be published in open access journals was vetoed at a late stage by President Bush so things are certainly bubbling away in this area.

Merry Christmas and Happy New Year people. No more posting this year. See you in 2008 and thanks for all the interesting and very encouraging emails. D!

Colourful Chemistry

I'm doing lots of new chemistry in my new job which is great. Since I started my career as an organic chemist more or less everything has been supposed to be colourless or white.
What makes the chemistry I'm doing now even greater is that it has colour whilst still being organic chemistry.

Here's some recent pretty pictures. Check out my beautiful green reaction.
And how about this product from another reaction? Initially I assumed that the product was impure but what do you know it's supposed to like like this.
In your face inorganic chemists! Can anyone guess what I made? It is a classic reaction taught in first year university organic chemistry. It's nice to see the chemistry I have been teaching undergraduates is useful and actually works in the lab. D!

Compound Characterisation in Industry

As I have mentioned previously I'm back working in industry/biotech. One of my colleagues asked me an interesting question today:

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What is the golden standard for compound characterisation in industry?

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Where we work now we only do 1H NMR and LCMS. However, in my previous industry job we also did 13C NMR, full on 2D NMR and elemental analysis. What are you industry people out there doing and what are your views on this issue? D!

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!