B.R.S.M. When all you have is a hammer everything looks like a nail

2Mar/146

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[10.8.0.0(2,11).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:

icosane

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 | 5,007 views | 6 comments 6 Comments
30Aug/132

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:

Aminals

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 | 12,966 views | 2 comments 2 Comments
28Aug/135

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.

mcontent

"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 | 9,211 views | 5 comments 5 Comments
18Jun/133

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:

BRSM
'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):

Chemjobber

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 | 4,266 views | 3 comments 3 Comments
1Apr/136

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]


Fish

I couldn't make this stuff up!

 

 

Filed under: ANFSCD, Current Literature, Fun | 6,625 views | 6 comments 6 Comments
27Mar/134

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.

DSC_0012

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 | 11,086 views | 4 comments Continue reading
16Jan/136

Who Ya Gonna Call? Blog Syn!

Ever see a reaction in the literature and think, "that seems a little too good to be true..."? Retro Baeyer-Villiger reaction? Quantitative cleavage of methyl ethers with Amberlyst-15? Catalytic reduction of alcohols to hydrocarbons with Dess-Martin? Bring it on! Ever struggle with a sensitive or fiddly reaction and wonder, "is it just me? Should this work?"? Well, now you don't have to! Thanks to a collaborative new website brought to you by See Arr Oh, with a little help from Organometallica, Mat Katcher and Myself. Now, if you find a reaction you can't reproduce or don't believe, simply head over to Blog Syn, and let us know.[1] Alternatively, if you think you'd like to be part of helping to make the literature a little bit more reproducible, pay us a visit and see what needs checking! If we all just run a few extra reactions a year we should be able to save chemists around the world many wasted hours and much frustration. You might even have some fun, make some new friends, and perhaps even learn some chemistry besides!

1. Or email See Arr Oh or myself

Filed under: Ask the audience, Current Literature, Fun | 5,035 views | 6 comments 6 Comments
9Oct/122

An Uncommon Lab Reference

Last Monday I set my MSci student the task of preparing the above compound and sent him off to do some literature searching. He quickly found a mention of it in a J. Med. Chem. paper, although the authors didn't give any detail themselves on its preparation, instead claiming to have used the method of Shulgin and Shulgin, described in reference 17:

That's right: a reference to PIHKHAL in the primary chemical literature! When I got over my initial surprise I did track down a copy (the university library didn't have it) to look up the procedure. Indeed, a very detailed and reasonable sounding synthesis of the compound is described under the chapter on the synthesis of 2C-T-2 (along with an evocative description of just how high you can get on it).[1]

There's lots of detail and the whole thing is done on sufficient scale to produce 10 grams of the desired compound. Perhaps not too surprisingly, the route starts with chlorosulfonation of 1,4-dimethoxybenzene, followed up with reduction (Zn in HCl) to give the thiophenol which is then ethylated. Easy. We're going to try it this week, and I will enjoy seeing PIHKAL referenced in a lab notebook. It's funny, I've been aware of this book for probably ten years or more - heck, I even gave a talk last year entitled 'Quinones I Have Known And Loved' - but I never thought I'd be reading it at work. Steven Weinreb once  said of Russell Marker: "There are more stories told about [him] than any other chemist. Although perhaps many of these stories are apocryphal, they are so fascinating that more of us cannot bear to stop repeating them... they are the campfire stories that bind our profession together",[2] but I think that the same could also easily be said of Shulgin. I mean, along with Humphry Osmond the man actually coined the term 'psychedelic'.[3] I learned today that there's even a Shulgin Index, written in the style of the more common Merck index, describing the physical and pharmacological properties of some of the psychedelics he and others prepared over the years. I hope to one day have the chance to read a copy.

 

Etc

1. More in this vein can be enjoyed in the digitised versions of Shulgin's lab notebooks. Although his handwriting, combined with the quality lost from storage and scanning, can make them quite hard to read in places they seem to be quite interesting and frequently amusing and insightful. Although the first entry in the first book describes his experiences of taking 400 mgs of mescaline sulfate and the results (which, including hallucinations experienced with eyes open and shut were 'very pleasant'), there's also some real explorative medicinal chemistry documented there. They're actually much better kept than the lab books of many PhD chemists I have worked with, and it's easy to forget that this work was largely conducted in a shed in California. If it wasn't, you know, for all the drug taking.

2. Chem. Eng. News, 1999, 77, 78; If you don't have access to that the article was also reprinted verbatim in The Journal of The Mexican Society the same year and can be enjoyed for free here.

3. It's interesting to note that this term come from the Greek for 'mind manifesting', which I think speaks of the pair's optimism for the curative power of such compounds. Hopefully I'll do another post on chemical etymology one day.

 

 

 

 

Filed under: Fun, Literature, Serious | 6,272 views | 2 comments 2 Comments
25Sep/127

Superlatives 1: The Heaviest Catalyst Ever?


While browsing through the Advanced Synthesis and Catalysis Early View today, I noticed this paper on a new Rhodium catalyst for the asymmetric conjugate addition of boronic acids to enones in water. Pretty standard stuff... until you look at the catalyst structure. Now, I'm not particularly up on phosphine ligand design but I don't think that PEG and geranyl geranyl geranyl geranyl geranyl chains are a common thing to include. I mean, I've seen BINAP derivatives with some pretty big polyaromatic hydocarbon groups bolted on (e.g. anthracene and pyrene), but this is in a class of its own. In fact, I think that I can safely say that this is the largest catalyst for anything that I've ever seen. I guess the logic is that if you can't have the organic solvent in the flask you can just include it in the catalyst itself by larding it with hydrocarbon and polyether chains, and it does actually seem to work. A possible drawback of this approach is that the darn thing weighs more than maitotoxin and takes a total of twelve steps to make; all that just so we can have another way to add phenylboronic acid to cyclohexenone. I'm making a note of this for the next time someone calls my total synthesis project useless. Or am I being too harsh?

Filed under: Current Literature, Fun | 5,604 views | 7 comments 7 Comments
23Aug/123

Holiday!

Not that it'll be particularly noticeable, but I'm on holiday from tomorrow onwards as I take my mountain bike over to the French alps for an exciting week of trying not to break anything that'll prevent me from working in a lab. In the meantime, please enjoy this extract from our old lab copy of "Purification of Laboratory Chemicals":

The urea can then be coughed up, and then purified as described on page 355. All in a day's work.

Note: It seems that this particular 'remedy' is missing from 2003 and later editions, probably for fear of lawsuits.

Filed under: Fun | 4,254 views | 3 comments 3 Comments