Open Access Journals - Beilstein Journal of Organic Chemistry

It's amazing how unpredictable life is. Only four months after I started my job in biotech I'm heading back to academia. Not that there was anything wrong with the job but I've been given an opportunity to return to Denmark (which always has been the long term plan) so I'm going with the flow. I recently had a post on open access journals and was moaning a fair bit about how we don't have any decent chemistry open access journals yet. Well I was wrong. A colleague alerted my attention to Beilstein Journal of Organic Chemistry (BJOC). This is the best attempt I've seen yet. They are publishing a reasonable number of papers, the quality of the material is good, the journal gets indexed by all the important organisations and it is absolutely free. The impact factor is still low (ISI WoK: 0.35) but this should improve with time. So check it out.

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The past year I've been involved in setting two labs up and whilst searching for information on equipment etc. I've been quite pleased with the Google adds people have on their web sites. I found a fair bit of the stuff I needed this way so I've decided to give it a go here at Curly Arrow. So sometime in the very near future adds will start appearing on Curly Arrow that should be useful to people interested in purchasing lab equipment. D!

Catalytic Hydrogenation - now fire free

In my experience you should not do synthetic organic chemistry if:

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(A) You are drunk (or the following day when you have a hang over)

and/or

(B) You are in a hurry

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Recently, I violated Commandment B and decided to put a large scale catalytic hydrogenation on really, really fast. Bad idea!

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Now hopefully most of you realise that the addition of palladium on charcoal (or charcoal alone) to organic solvents can result in instant bonfire. Unfortunately the chemists hand is often right above the flask as the catalyst gets added and some very nasty burns can result. Even worse the whole thing may take off and you'll frantically be looking for a fire extinguisher (Always know where the fire extinguisher is. You will need it one day).

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There is an easy way to avoid this problem. If you first remove all atmospheric air inside your flask there will be no fire. In other words what you have to do is flush the flask with nitrogen or argon. I normally hook my flask up in such a way that I can evacuate it with a pump and fill it with nitrogen. I've shown one of my recent setups on the picture. You can obviously connect things in many different ways depending on what equipment you have available.

I normally evacuate the flask and fill it with nitrogen at least three times. Only then do I proceed to add my catalyst. After addition I repeat the evacuate the flask procedure but this time I flush the flask with hydrogen and at the end I attach a big fat balloon with hydrogen gas and stir the reaction mixture vigorously.

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The other day when I was in a big hurry I decided to skip the flushing with nitrogen step (for the first time ever) and as a consequence I had my first Pd on charcoal fire. I was very lucky and didn't burn myself because the weighing paper was shielding my hand. The drama was quickly over as I had my lab book handy and sealed the flask with it. The hydrogenation worked fine and I made it in time to the pub. However, next time I think I'll skip the first pint with the boys and flush that flask as I normally do. D!

Recycling Silica Gel

Insert usual excuse for infrequent posting here: .....

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I recently received the following email regarding recycling of silica gel:

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"In the past we used to regenerate SiGel with fuming nitric acid, much as you do here (refers to previous post - D!) .Place the coloured, used SiGel (which of course must be uncoated and completely dry) in a large beaker. Approximately a third full. Place it inthe fume cupboard and pour in the nitric acid so the SiGel is completely moistened. If necessary, stir it. After a possible initial fuming has stopped, heat it on a steam bath for 10 minutes - leave it overnight. Next day, fill up with water, stir and let it settle. Wash 3 more times. At this point, it should be colourless, if not, repeat with more nitric acid. Then wash with satd. sodium bicarbonate until neutral and filter on a Buchner funnel. Wash with water, methanol and acetone and let it suck completely dry. Finally, activate by heating it in an oven overnight at 100-120 C.This way, it is as good as new for most purposes."

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This may be of use to some chemists working at institutions where money is very scarce. However, considering the amount of time and large volumes of solvent required to do this I think it can be classified as historically interesting but not practically useful to most of us.

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Nevertheless thank you for the email. I have wondered exactly how you would go about recycling your silica gel.

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Speaking of silica gel and techniques that are disappearing from the chemists hood check one of the most recent posts at In the Pipeline out. Derek seems to think that TLCs are on their way out as LC-MS is becoming more and more common. I believe that it will take several decades before Derek's predictions come true (especially in academia) but he does have some very good points. D!

How to clean your sintered funnel

Lately when I have been cleaning my sintered funnels people have stopped and asked me what I was doing. To my surprise many chemists don't seem to know how to take a nasty, dirty sintered funnel and making it nice, white and shining again in about 15 minutes.
These days I'm doing lots of old school chemistry that involves heating the crap out of the components using for example conc. sulfuric acid as the solvent. Needless to say things are polymerising and decomposing left, right and centre and when you filter it through your nice white sinter it ends up looking nasty (see picture above). The stuff doesn't go anywhere with acetone, water, 2M sodium hydroxide or hydrochloric acid etc. so what should you do? Before I proceed please note that if you attempt any of the following you must:

(1) Wear a closed lab coat, safety glasses and plastic gloves

(2) Conduct the cleaning in a fume hood with the sash down at all times
(3) Ensure that all the glassware is clean and doesn't contain residual organic material such as acetone
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Please take the above advice seriously. People have had nasty accidents doing the following because they weren't careful.
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There are two common ways to get your sinter clean:
(1) Conc. nitric acid, or
(2) Conc. sulfuric acid and hydrogen peroxide
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Nitric acid is the easy solution and more often than not it does the trick. However, occasionally it is necessary to use more vigorous conditions. I have never had a sinter that didn't become white after treatment with conc. sulfuric acid and hydrogen peroxide and this is generally the method that I use because I know it works every time.
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Procedure:
(1) Fit the funnel to a Büchner flask attached to a vacuum that you can control easily
(2) Add a small amount of conc. sulfuric acid so that it covers the surface of the sinter
(3) Add a dash of hydrogen peroxide and stand back. Things get pretty hot, bubbly and exciting at this point (See picture above).

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(4) When the ingredients have been cooking away for a minute or so apply a very gentle vacuum briefly. This should be sufficient to suck the sinter dry (See picture above),
(5) Allow the cocktail to settle down and cool off and clean all the equipment with lots of water taking care not to pour the contents all over yourself. Your sinter will now look like this.
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Too easy but please do be careful guys. D!

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!