B.R.S.M. Home of Woodward Wednesdays

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 | 6,317 views | 6 comments 6 Comments
30Aug/133

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 | 15,430 views | 3 comments 3 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 | 10,675 views | 5 comments 5 Comments
5Jul/133

Non-Thermal Microwave Effects: Probably Still Bollocks

Thanks to Brandon and Martyn for pointing out these publications. Be warned, this post turned out seriously long and wordy!

mcontent

Almost since the dawn of microwave chemistry, which began in the 1980s with people simply putting Erlenmeyer flasks full of reactants in domestic microwaves, chemists have reported all kinds of improvements from heating in this fashion. To name a few of the more common ones, I've heard people claim higher yields, shorter reaction times, cleaner reactions, different selectivities, milder conditions and better overall energy efficiency. Microwave chemistry can be a good thing, and many of these effects are real, widely observed phenomena; the problem is that chemists disagree on their origins. However, comparison between microwave and conventionally heated reactions is fraught with difficulties. One obvious factor is that microwave reactions, at least in the organic chemistry labs that I’ve worked in, are inevitably conducted in sealed tubes, which makes direct comparison to the ‘open’ systems that are typically used in conventional reaction set-ups. Heck, even in open systems, superheating of solvents past their boiling points can occur if nucleation sites are lacking – even two reactions apparently refluxing in the same solvent can be at different temperatures! In fact, simply getting the temperature wrong is probably the major reason for the disparate results obtained when conventional reactions are compared to their microwave ‘equivalents’. This isn't helped by the fact that your average lab microwave only reads the reaction temperature by IR measurements of the surface of the reaction vessel; I’ve heard descriptions of this practice ranging from ‘optimistic’ to ‘demonstrably, hopelessly inaccurate’.

DSC_0012

I'm reusing this photo of a microwave just to break up the text a bit!

Because of these (and various other) hard-to-pin-down factors, it’s actually pretty hard to compare conventional and microwave heated reactions, and not everyone has the kit required to do so properly. This has led to numerous claims of so called ‘non-thermal’ or ‘specific’ microwave effects in the literature. These generally explain the apparent benefits of microwave heating by claiming that the microwaves don’t just simply heat the reaction medium (hence ‘non-thermal’), but instead excite (or even stabilise!) particular bonds or intermediates directly, in a fashion distinct from simple macroscopic heating of the reaction mixture. Such claims have been debunked for over a decade, and physical chemists will tell you—at least in the liquid phase—that energy is redistributed amongst the molecules in the reaction vessel on a much shorter timescale than the period of the microwaves used to excite them, making specific heating of one species over another unlikely. Certainly, temperature gradients and macroscopic hotspots may well exist (particularly in viscous/high dielectric/inadequately stirred media), and are readily measured with a temperature probe, but I’ve yet to see credible evidence for the molecular-scale thermal aberrations that are continually reported. It seems that, when investigated in detail, with care to eliminate other factors, claims of non-thermal effects have yet to stand up to scrutiny. In fact, I'm a little baffled as to why we see the continued reporting of results predicated on this phenomenon, with few proper control experiments. I'm not saying that they don't exist, and I'll happily accept their existence when sufficient proof is presented, but I think a lot of rubbish is generally talked on the subject.

One of the most prominent chemists to voice their disbelief in so called ‘non-thermal microwave effects’ is Austrian Professor Oliver Kappe, who's been countering such claims in the literature for at least as long as I’ve been a chemist. He periodically publishes smack-downs of claims of chemistry of this type, most recently in an Angewandte Chemie Essay that appeared just before Christmas (that I blogged about at the time). One of the groups whose work he criticised was that of Gregory Dudley at Florida state university, and things escalated this week with the publication of Dudley's reply to Kappe’s attack, followed swiftly by a further rebuttal by Kappe. The last ‘literature boxing match’ of this type that I can recall was the citalopram back-and-forth in OPRD a couple of years back, covered at the time by Derek over at In The Pipeline, and while the claims made by either side here are not in the same league of dubiosity there’s plenty of thinly veiled frustration and strained civility to enjoy!

Filed under: BRSM Reviews, Current Literature, Serious | 6,442 views | 3 comments Continue reading
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 | 4,745 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 | 7,417 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 | 12,577 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 | 5,480 views | 6 comments 6 Comments
15Dec/128

Non-Thermal Microwave Effects: Probably Bollocks

Update 1900: This was blogged earlier today by Tom Phillips over at A Chemical Education. Whoops!

For a related post on things to check before publishing your controversial results to avoid potential humiliation, see my old piece on 'metal-free' reactions.

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From Angew. Chem. Int. Ed. 2012, 51, 2.

It seems to me that people still talk a great deal about so-called 'non-thermal' effects in microwave reactions; i.e. some kind of mysterious rate acceleration that occurs from excitation (or even stabilisation) of particular bonds or intermediates directly, in a fashion distinct from simple macroscopic heating of the reaction mixture. One of the most prominent critics of those who claim to observe these phenomena is Austrian chemist Oliver Kappe, who's been debunking claims of non-thermal effects for at least a decade and he's just written an excellent Essay in Angewandte Chemie on the subject. Now, few people would argue that a lot of reactions work better in the microwave, but this can often be explained by rapid internal heating or increased pressure; that is, by thermal effects, however dramatic. An example from Kappe's essay illustrates the incredible magnitude of rate improvement that's sometimes observed:[1]

From Angew. Chem. Int. Ed. 2012, 51, 2.

Filed under: Current Literature, Serious | 17,310 views | 9 comments Continue reading
24Oct/120

Chem Coach Carnival: I’m A Postdoc and I Love It

Hi all, we* interrupt our* scheduled** programming to bring you an exciting** Chemistry Carnival entry! See Arr Oh recently had the brilliant idea of a Chem Coach Carnival, where people in different chemical careers describe their working lives to give others an idea of what it's like to be in their shoes. Here's my entry, which unfortunately seems to have turned out a bit too long:

What do you do?
As you might have guessed, I'm currently a 'postdoc' or post-doctoral research associate at a UK university. If you're not familiar with the academic hierarchy you can see where this fits in the academic food chain here, thanks to Karl Collins.

What does a typical day involve?
I'm one of three postdocs in a research group of around twenty people engaged in diverse projects across the spectrum of organic chemistry. When I was at school The RSC ran a campaign to tell people that 'not all chemists wear white coats', but I'm proud to do so for 90% of a normal day. At the moment I'm mostly working on a short-ish biomimetic alkaloid synthesis but in addition to my own project(s), I also get to field questions from PhD and MSci students, show people how to do stuff in the lab, write papers, work on my own crazy ideas, manage an MSci student and worry about what I'm doing with my life. I also do some teaching in the form of undergraduate tutorials, which is great fun. My job is essentially to solve an increasingly varied and intricate series of puzzles, and it's good.

How did you get where you are?
It sometimes feels like I've spent my whole life in full time education as I started university straight after school and my PhD a few months after I finished my undergrad. As it happens, I'm currently still at the same institution from which I obtained my PhD a few months back. Staying in one place like this is usually inadvisable, but it's not a bad university, there's a good climbing wall nearby, and my current position is really just a short term filler until I move to the US next year for a 'real' postdoc. Goodness knows what I'll do after that. Fortunately, thanks to the shorter British PhD, I've only just turned 26.

How does chemistry inform what you do?
I really can't know enough chemistry as it pervades everything I do at work. The deeper my knowledge, the better I'll be at my current job, and the greater the chance I'll have of getting another.

Pros and Cons?
It seems that this job combines most of the good bits of being an academic and a PhD student; on the one hand I get almost total freedom to do what I like, I still spend most of my time in the lab, I get to teach and I get to be familiar with all the stuff that other people in the group work on but I don't have to write grant proposals or a thesis, take exams, or attend many meetings. It's pretty much how I think being a chemist should be. The main problems with the job are that it doesn't pay that well; although money is rarely a problem for me, I couldn't start a family or buy a house; the hours are pretty long, and are only going to get worse when I cross the Atlantic; and it isn't a long term career, as doing more than a couple of one or two year postdocs is widely considered a bad idea. It can also be stressful and frustrating.

A funny story?
Reading through what I've just written I guess I come across as pretty keen on chemistry, but it hasn't been a lifelong interest of mine. I wanted to study physics at university but sucked at math so I ended up studying materials science. That turned out to be a little too last-but-one century for me; the amount of time we spent learning about steel and concrete really put me off. After a year I switched to chemistry, but was a mediocre undergrad as I spent most of my time running the university mountaineering club and planned to get a job in the outdoor industry when I graduated. It wasn't until my final year masters project that things changed for me. Although I usually did much better in inorganic chemistry, I chose to join an organic research group that looked interesting on paper, but to my surprise it turned out to consist only of one mostly retired emeritus professor and a young - but extremely talented - postdoc. To hear those two talk about chemistry was amazing; it was like listening to a conversation in another language, and as they swapped stories about this academic or that, discussed the latest Nicolaou paper or just stood around cracking jokes I realised that the world of organic chemistry was much more interesting than I'd ever realised. I loved the history, the in-jokes and the community. I wasn't a great masters student, but I doubt anyone else in my year learned as much as I did during their project. Four years later I'm still a chemist. And I'm not ready to stop learning yet.

 

*Majestic plural.

** This is not true.

Filed under: Ask the audience, Serious | 7,253 views | no comments No Comments