B.R.S.M. The road to Tet. Lett. Is paved with good intentions


And Now For Something Completely Different 10: Don’t Buy Your Undecacycloicosane From Sigma-Aldrich

A funny thing happened the other day: I went onto the Sigma-Aldrich website to order some undecacyclo[,11).0(3,6).0(4,9).0(5,8).0(7,10).0(13,16).0(14,19).0(15,18).0(17,20)]icosane, and was amused to notice a rather M. C. Escher-like rendering of the structure:


Looking for alternative suppliers on Chemspider, I noticed it too had depicted the molecule in quite a strange way (although interestingly their 3D view of the molecule is spot on):

4788435 I guess that both these structures were probably drawn by computers, so I decided to see how Chemdraw's name-to-structure function would deal with such a complicated case. I was certain that the name would either be rejected or that some kind of tortuous hydrocarbon Gordian knot would result, but to my surprise Chemdraw emerged as the clear winner in this bizarre and impromptu competition:

icosane 2

More serious posts soon!

Filed under: ANFSCD, Fun | 18,573 views | 6 comments 6 Comments

And Now For Something Completely Different 9: Typographical Mistakes Of Yesteryear

Thanks to a co-worker, I recently became aware of a rather unique aside published within Thomas Tidewell's somewhat dated Tetrahedron Report on the Addition Reactions of Ketenes (Tetrahedron, 1986, 42, 2587–1613). Found spread over pages 2587–2588 is the following:


It turns out that this note originates from a satirical piece in Chemistry in Britain (Chem. Br., 1965, 1, 230) published some 20 years previously. As far as I can tell, the root cause was an unfortunate typo in a Chemical Abstracts entry (Chem. Abst., 1965, 62,1561d) report from Paris on the discovery of a new chemical species—namely "O-Silylated Vinyl Ketene Animals"—by K. Vijayakumaran. If only such errors were uncommon enough (and chemists good natured enough) for this kind of banter in the literature of today! Have a good weekend!

Filed under: ANFSCD, Fun, Literature | 26,930 views | 2 comments 2 Comments

Include Me Out: Mercury Azides

An interesting paper appeared in Angewandte Chemie yesterday detailing a re-investigation of a number of mercury azides that were—for reasons that will become apparent—not properly characterized when they were first reported in the literature back in the 1890s.[1] This publication is remarkable in a number of ways, not least that it has made today’s report on (trinitromethyl)borate synthesis seem rather boring and jejune in comparison.


"Always  look on the bright azide of life" —Image and pun from Angewandte Chemie, 2013, Early View

It turns out that Hg2(N3)2 and α-Hg(N3)2 are both easily prepared using reported methods and are display predictable instability/toxicity, but nothing to write home about. The most exciting part of this paper focuses on the alternative β- form of Hg(N3)2. The authors describe the procedure as follows:

“In analogy to the preparation of β-Pb(N3)2, a second metastable modification of mercury(II) azide, β-Hg(N3)2 can be obtained by slow diffusion of aqueous NaN3 into a solution of mercury(II) nitrate which is separated by a layer of aqueous NaNO3. Thereby, needle-like crystals of β-Hg(N3)2 start to form in the lower mercury(II) nitrate layer which is always accompanied by spontaneous explosions during crystal growth finally leading to a mixing of the layers and the fast precipitation of α-Hg(N3)… Slow crystallization during the preparation of α- or β-Hg(N3)2 leads to the formation of large crystals which are extraordinarily sensitive to all kinds of provocation (e.g. even detonate in solution) and therefore should be avoided by all means. Nevertheless, with extreme care, we were able to manually isolate some specimens of β-Hg(N3)2 under the microscope which allowed the characterization by vibrational spectroscopy, single-crystal X-ray diffraction, and the determination of the melting point.

Now, when people talk about metastability I think of things like diamond and Dewar benzene; substances that actually have an appreciable energy barrier to their decay. You know, the sort of thing where you can say “hey, check this out! It’s metastable!” without your statement being punctuated by detonations and the sound of breaking glass followed by screams. Seriously, how are you supposed to prepare a compound that detonates at random under its own weight during crystallisation?

That said, if you look at the detailed procedure for the synthesis of β- Hg(N3)2 in the paper’s supporting information and skip the line that cautions “during this period explosions frequently occur” (just keep calm and carry on), then once you’ve made and isolated the compound it does sound surprisingly stable. In fact, once dry and pure—and after some rather fraught measurements by one of the students—the group was able to determine that the compound was stable up to 180 ºC when it sublimed. One day, I would like to meet the kind of person that works on projects like this!


  1. Of course, charactization during  that period largely revolved around melting point, taste and combustion analysis, all of which are hugely inappropriate for explosive mercury compounds (although I don’t doubt that people tried; the Merck index includes information on the taste of pyridine, presumably obtained shortly after its isolation a few decades previously).
  2. Also, does this figure from the paper seem a bit strange to you?

Mercury azide owl

Alternative caption: Figure 2. Top: ORTEP drawing of Hg2(N3)2.

Thermal ellipsoids set at 50% probability at 173 K. Selected

structural data are summarized in Table 1. Symmetry code (i) x+2, y, z+1.

Bottom:  Owl in flight, seen during acid trip.

Filed under: ANFSCD, Current Literature, Fun | 22,414 views | 5 comments 5 Comments

And Now For Something Completely Different 8: Summarising Blogs With Wordle

Reading blogs is fun, but find new ones that you'll enjoy can be time consuming. Fortunately, there's a really useful tool to simplify the process: Wordle.[1] Just give it a URL or a block of text, and you get out a 'word cloud' that helpfully illustrates the frequency with which words are used.[2] This can give a useful flavour of what a blog is about! For example, entering the URL of this blog give the following:

'Synthesis' and 'reaction' are the most abundant words, and I think this gives a pretty good idea of what you'll find here on a typical day.If we subject Chemjobber to the same treatment we get the following (you can changes the colours easily):


Clearly, Chemjobber mostly writes about chemicals and percentages! Finally, I thought I'd subject Just Like Cooking to the same, rigorous analysis:

See Arr OHI'm not sure sure what to make of this one; it appears that the most common word recently used by See Arr Oh on his blog is 'really'![3] I wonder how this thing would cope with actual papers?

1. I got this idea by reading this post from Chemically Cultured this morning.

2. Apparently really common words like 'the', 'and' and  'a' are omitted to make things more interesting!

3. I think the program works by just pulling your RSS feed, so it only 'analyses' the most recent posts on a blog.

Filed under: ANFSCD, Fun, Not Chemistry | 22,829 views | 3 comments 3 Comments

And Now For Something Completely Different 7: XKCD-style Venn Diagrams

Update 03/04/2013: Chemjobber made a few!


Thanks to a recent xkcd comic I've just discovered a wonderfully concise new way to communicate – non-overlapping Venn Diagrams:

 From http://xkcd.com/1180/

For example, here's a statement my boss made last week expounded thus:


I quite enjoy the contradiction between the visual simplicity of displaying information in this way and the fact that it's actually a lot more effort to construct these than write a sentence that conveys the same information, as well as their highly inefficient use of space. There's  just something kind of amusing about them. Or I think so, anyway.


Give it a go, and share any good (chemistry related) ones you can think of in the comments. I've just put one in a talk I'm writing on acyclic stereocontrol for a group meeting; I'll let you know how that goes down next week!

Filed under: ANFSCD, Ask the audience | 23,589 views | 3 comments 3 Comments

And Now For Something Completely Different 6: Green Chemistry

Most of the credit for this one goes to occasional commenter Martyn!

Is it just me, or will green chemistry journals publish anything these days? For example, check out this paper published this morning in the Journal of Sustainable Agitation:


Unpowered Mechanical Stirring of Reaction Media Using Renewable Stirring Fish (RSFs). [PDF]


I couldn't make this stuff up!



Filed under: ANFSCD, Current Literature, Fun | 16,736 views | 6 comments 6 Comments

And Now For Something Completely Different 5: The Merck Index Challenge

Sorry things have been so quiet around here; it's been a hectic month! Here's something silly born of an unusual conversation over coffee.


The office microwave:  unnecessary chemophobia?

The Merck Index, along with Fieser and Fieser's Reagents for Organic Synthesis, Greene’s Protective Groups, March’s Advanced Organic Chemistry and Amarego’s Purification of Laboratory Chemicals is one of those books that any self-respecting organic research group will have a copy of. It’s an iconic reference work, although its usefulness has definitely waned in recent decades with the rise of the internet, Scifinder/Reaxys/Chemspider and Wikipedia. As Derek reported before Christmas, it was recently acquired by the RSC, who have just released an updated edition. I mostly use mine to pass the time waiting for NMRs to run, or when I need a more reputable reference than Wikipedia for a paper or report.[1] However, all of that changed last week when a tea break conversation sparked a bizarre new game: The Merck Index Challenge.

Anyone who’s ever flicked through a copy will probably have noticed that amongst all the drugs, solvents, salts and plants there are a number of… aberrant… entries. For example, Whiskey. And Lard.[2] And Raspberries. And Quorn. And Milk. Thus, the question arose: could a meal be constructed using only ingredients from the Merck Index? Better yet, could one manage three courses?

Filed under: ANFSCD, Ask the audience, Fun, Not Chemistry | 22,706 views | 3 comments Continue reading

And Now For Something Completely Different 4: Wikipedia Fun

Have you ever tried to look up famous chemists on Wikipedia only to end up misspelling their name or finding a more famous person who shares it?  Although sometimes this can be frustrating, it can also be pretty funny.[1] Here are a few amusing namesakes I discovered recently:


1. David McMillan

As well as being one of the leading figures in the organocatalytic revolution, according to wikipedia.org, "David McMillan is a British-Australian drug smuggler who is best known for being the only Westerner on record as having successfully escaped Bangkok's Klong Prem prison". A man of many talents. Apparently, Dave avoided recapture by his immediate acquisition of an umbrella once outside the prison walls... because escaped prisoners never carry umbrellas. Clearly a clever man.


2. Phil Baron

The real Phil Baran. Credit: Sexy Science

Although he tends to make the rest of us look bad and just won't stop writing review after review after review, I still  get excited whenever he publishes something. Apart from all that chemistry and reviewing, I have just learned from the Phil Baron wikipedia page that he's also a "voice actor, puppeteer and songwriter who voiced Piglet in the Disney Channel live-action/puppet television series Welcome to Pooh Corner". Where does he find the time?

Filed under: ANFSCD, Ask the audience, Fun | 25,548 views | 3 comments Continue reading

Four Days To Go!

From Chem. Soc. Rev., 2012, DOI: 10.1039/C2CS35116A

Just a quick post to remind you that I need your Colouring Competition entries by the end of Tuesday so I can write some kind of round up post in time for Nicolaou's birthday on Thursday. This weekend would be a good time to spend just 10 or 15 minutes messing around in Photoshop, the GIMP, or at a push, MSPaint. Heck, you can even print them out, colour them in and scan them if you don't have mad image editing skills. Not that it matters; I certainly don't. Give them to your children! If you're short of inspiration you can check out the entries from See Arr Oh and DrFreddy, or look at the latest Nicolaou review above.

Filed under: ANFSCD, Ask the audience | 11,085 views | no comments No Comments

Conditions You’ll Probably Never be Desperate Enough to Try

Or: Somewhat Like Cooking

We all know what it’s like to be desperate for a reaction to work; to need a result so badly, or to have a supervisor breathing down our necks, telling us that something must be possible. I’m sure all bench chemists can remember searching the literature for a procedure to prepare a given compound, only to find one, read it and then discard it for being too dangerous or just plain ridiculous. We can all probably think of a few procedures that we're just not paid enough to follow. For example, before Christmas I wanted to make some of this carboxylic acid.

Easy, right? Surely you just oxidise the 2,5-hexadienol that you can get in one step from allyl bromide, unprotected propargyl alcohol and indium? Nope, there are numerous preparations reported, and they all use either tin, or worse, nickel tetracarbonyl. A thing that myself and Derek Lowe definitely won’t work with.[1]

Yup, chemists love to talk about dangerous procedures. But what about ridiculous ones? I once heard an academic tell a story about his time as postdoc with Steve Ley. In his first few months in the group, another postdoc whom he referred to as ‘Crazy Norman’ had been working out the last few steps in a natural product synthesis. The final reaction was the selective reduction of one of three or four double bonds in the molecule by hydrogenation. Norman performed this reaction once on a small scale, got some NMRs and then left and moved on. After he was gone, Ley set another postdoc the task of making a little bit more of the natural product, by repeating Norman’s final step. But they couldn’t. The particular selectivity that Norman observed (and had the NMR data to prove) was never seen again. His successor tried everything – different catalysts, solvents and temperatures. New glassware, clean stirrer bars, old glassware and dirty stirrer bars. They stirred clockwise and anticlockwise, by the window and in the dark. It was rumoured that someone in the lab might have been doing some sulfur chemistry on the day when Norman did his reduction, so they tried even tried wafting some thiols at the flask full of catalyst and solvent, to maybe poison it just a little bit. Eventually, they rang up Norman to ask if he remembered doing anything – anything at all – unusual when he ran the reaction. He thought for a while and then replied, in total seriousness, “I think I might have washed the glassware with Vimto”.[2]

Image from americansweets.co.uk

Give that man a Tet. Lett.! Here are a few other examples of ridiculous things you’ll never try:

Filed under: ANFSCD, Current Literature, Fun | 152,654 views | 41 comments Continue reading