All your base are belong to JACS

This is a follow-up post to yesterday’s that looked at word clouds made up from the titles of JACS papers from the last 115 years.

Jake Yeston commented on Twitter about the lack of catalysis-based words in the clouds. This is something that also caught my eye and I’ve now had a chance to dig a little deeper into this.

The way the word clouds work (the ones you can make using Wordle at any rate) is by counting exact copies of the same word and then scaling the size of the word in the cloud in proportion to the number of times it appears in the input text. So, if you look closely at the word clouds from yesterday’s post, you will see ‘reaction’ and ‘reactions’ both appearing in the same word cloud. Similarly, acid and acids, complex and complexes, study and studies, and so on. Wordle also does not separate hyphenated words, so you will see things like ‘gas-phase’ and ‘electron-transfer’.

What does this mean for catalysis? Well, I started looking through the titles for the 2010-2014 data and found all of the following words (and there are probably other variants that I missed):

anticatalysis, autocatalysis, autocatalytic, biocatalysts, biocatalytic, catalase, catalysis, catalyst, catalytic, catalytically, catalyze, catalyzed, catalyzes, catalyzing, cocatalysis, cocatalytic, cocatalyzed, electrocatalysis, electrocatalyst, electrocatalysts, electrocatalytic, electrocatalyze, multicatalytic, nanocatalysts, organocatalysts, organocatalytic, photocatalysis, photocatalyst, photocatalysts, photocatalytic, precatalyst

This means that catalysis is being spread quite thin and not being lumped together as a single entry in the word clouds. But it gets worse. In the 2010-2014 cloud, if you look carefully you can find ‘palladium-catalyzed’… and remember what I said above about Wordle not separating hyphenated words? Not only is ‘palladium-catalyzed’ counted separately from ‘palladium’ and ‘catalyzed’, but also separately from things like ‘Pd-catalyzed’ too. And obviously you get lots of different ‘X-catalyzed’ terms, such as ‘gold-catalyzed’, ‘Rh-catalyzed’, ‘copper-catalyzed’, and so on. There’s an awful lot of catalysis going on, it just isn’t adequately captured in the word clouds. On the other hand, consider the word ‘synthesis’ — sure, it might lose some of its count to ‘synthetic’, but that’s about it; there aren’t anywhere near as many derivatives of ‘synthesis’ as there are of ‘catalysis’.

To get a sense of how much catalysis (in any and all of its guises) has been published in JACS down the years, I went back to the lists of titles and then searched for ‘catal’ as a fragment. For comparison, I did the same for ‘synth’ and what I found is plotted below.

catal_synth

In the 2000s, ‘catal’ words were almost level with ‘synth’ words, and by the end of the current decade, it looks very much like they will be in the lead. Is this the decline of synthesis?

Now, as I pointed out in yesterday’s post, it seems as though chemists really have something for acid and acids. Those words dominate the clouds in the early-to-mid part of the 20th century. On Twitter, Cafer Yavuz suggested that ‘base’ and ‘basic’ might be excluded as part of the set of common words, but I don’t think that is the case. Wanting to get a sense of acid vs base, I repeated the ‘catal’/’synth’ analysis for these words. The results are plotted below:

acid_base

The analysis is not perfect, partly because ‘base’ and ‘basic’ can have different meanings (more so than acid and acidic), and ‘base’ is also a fragment of ‘based’ which might be adding to its total. Nevertheless, something interesting appears to be happening. When it comes to acids and bases, it seems that the balance of power (in JACS at least) is shifting — where acids once ruled supreme, bases took the crown in the 2000s and seem to be consolidating their position in the current decade.

If you have any questions about the analysis (or other things you want me to look for in the titles), just leave a comment or drop me a line on Twitter. Similarly, if you want the raw data, drop me a line by e-mail, I’m happy to share.

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115 years of JACS titles

When Nature Chemistry celebrated its 5th anniversary last year, we put together a word cloud (using Wordle) featuring the 150 words that appeared most often in the titles of the papers we had published up to that point. That was a collection of just under 600 papers, but a clear winner did emerge — ‘synthesis’ was the word used in titles more than any other (excluding some common words such as ‘from’, ‘by’, ‘to’, ‘with’, ‘and’, ‘so’, ‘on’…). It seems that a large part of chemistry is still very much about making things, and that reminds me of one of my favourite chemistry quotes:

‘la chimie crée son objet’ (chemistry creates its object) — Marcellin Berthelot, 1860.

The Nature Chemistry title-word cloud was not based on a particularly large data set, however, and is also from a very recent period. I wondered if the titles of chemistry papers have changed much over time, and so I decided to look to a journal with a lot more history. I wanted it to be a general chemistry journal to ensure there was no intrinsic bias towards words associated with a particular sub-field within chemistry and so I turned to the Journal of the American Chemical Society (JACS).

The date range I chose is somewhat arbitrary, but round numbers have a certain appeal and so I started at 1900 and worked my way up to 2014, the most recent complete year of JACS papers. This amounted to a little over 168,000 article titles and just shy of 2,000,000 words in total. I may well do more analysis in time, but first of all I decided to break down the data into decades (including a half-decade of 2010-2014 to cover the most recent papers) and look at the most popular 150 words for titles in each given period (excluding the same common words as we did when analysing the titles of Nature Chemistry papers).

Note that the size of each word corresponds to the number of times it appears in titles in that period — the larger it is, the more it is used. I have not combined words with the same root and nor have I combined singular and plural versions of the same word. I have made everything lowercase for the sake of simplicity though (otherwise ‘Synthesis’ appears as a separate entry to ‘synthesis’). Also, the number of papers published varies a lot between decades, so comparing the sizes of words between different clouds is meaningless.

This is what I found:

1900-1909

1900-1909

So, chemists at the start of the 20th century (yes, I know the century started on January 1st, 1901, but just go with it) were a determined bunch who liked to study milk, oil, wheat, sugar and urine — perhaps not all at the same time. Also, note the presence of a decent-sized ‘sulphur’. Yes, sulphur, with a ‘ph’. And remember, this is JACS, with all its American-ness. There’s not a hint of a ‘sulf’ to be found in JACS titles in this decade!

1910-1919

1910-1919

Still a healthy dose of determination, but also a lot of acid. And now ‘sulphur’ has become ‘sulfur’ — in fact, there are 143 ‘sulf’-based words and only 17 ‘sulph’ ones in titles from this decade.

1920-1929

1920-1929

Acid still looms large, but a lot of derivatives and compounds now too. Note that there is a lot more preparation than there is synthesis.

1930-1939

1930-1939

Seriously, what is it with chemists and acid? Compounds and derivatives remain popular and it seems as though synthesis is catching up a little with preparation.

1940-1949

1940-1949

The age of synthesis is upon us. And note the appearance of the word ‘spectra’ too. Also, ‘esters’, what’s going on there?

1950-1959

1950-1959

Synthesis remains dominant, but words such as ‘kinetics’ and ‘mechanism’ are growing larger, suggesting that there is an increasing drive to understand reactions as well. And ‘stereochemistry’ rears its head in the cloud for the first time.

1960-1969

1960-1969

Synthesis is not quite as prominent in the 1960s, but still a popular word in the titles of JACS papers. A new (and quite prominent) entry is ‘resonance’, along with ‘magnetic’, and note that both ‘nuclear’ and ‘proton’ are there too, reflecting the growing use of NMR as a technique to characterize chemical compounds. Another notable entry: ‘carbonium’ (the old name for carbocations), which was an active area of research at this time.

1970-1979

1970-1979

Chemists’ fascination with acid finally seems to be wearing off somewhat. And ‘complexes’ is now much more prominent. I suspect that this is a result of host–guest chemistry really taking off in the 1970s and the word ‘complex’ being associated with many more things than just traditional metal-coordination compounds.

1980-1989

1980-1989

There’s a fairly sizeable entry for ‘total’, and the vast majority of time it is used in the context of ‘total synthesis’ — and ‘synthesis’ itself dominates once more. Also note that the popularity of the word ‘via’ is increasing and both ‘novel’ and ‘new’ are well used (‘new’ seems to be a fairly constant presence in titles throughout the decades).

1990-1999

1990-1999

There’s still an awful lot of synthesis going on.

2000-2009

2000-2009

Nanotubes and nanoparticles make an appearance in the top 150 for the first time — nano comes of age? Other notable first-time entries (although small) are ‘supramolecular’, ‘self-assembly’ and ‘quantum'; I’m a little surprised it took so long.

2010-2014

2010-2014

Synthesis remains at the top, but look at the topics creeping into the top 150. ‘Metal–organic’ and ‘framework’ heralds the growing popularity of MOFs and it’s easy to miss, but there is also a little innocuous ‘graphene’ creeping into the picture at the bottom. ‘C–H’ is growing in size too, which is usually found in titles in the context of C–H activation. And finally, chemists’ love of ‘via’ is sealed!

To summarize, here are the top-ten words for each period:

toptens

(EDIT added June 3rd: I forgot to mention when I first posted this that for the top-ten lists I did combine simple singular and plural versions of the same word, so ‘reaction’ is actually ‘reaction’ and ‘reactions’ combined. Same goes for study/studies, complex/complexes, acid/acids and some of the others. What I did not do, however, is go beyond that and combine words that share the same root, so ‘synthesis’ and ‘synthetic’ have not been counted together and nor have ‘molecule’ and ‘molecular’, for example.)

Just to give you a sense of scale, if you don’t exclude the really common words, the top-20 words for the last full decade (2000-2009) are shown below (and remember that the words are scaled relative to the number of times they appear – the larger the word, the more times they appear in JACS titles).

top20_2000-2009_common

So, the most common word in JACS titles is probably ‘of’ or, more meaningfully, ‘synthesis’.

(EDIT added June 3rd: there’s now a follow-up post, with some cautionary notes about word clouds and how they can miss some concepts…)

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The ups and downs of cyclohexane

Cyclohexane is undoubtedly an iconic molecule. Many of us learned to draw it (with varying degrees of proficiency) very early on in our organic chemistry classes as we were introduced to chairs, boats, half-chairs, twist-boats, cis, trans, A-values, conformation and, of course, axial and equatorial. Cyclohexane has six equatorial C–H bonds around the circumference of the ring and six axial C–H bonds, three pointing up and three pointing down.

It wasn't always axial (red) and equatorial (blue), you know...

A cyclohexane chair – it wasn’t always axial (red) and equatorial (blue), you know…

It turns out that it wasn’t always ‘axial’ and ‘equatorial’ though… and I only discovered this last week when I came across a 1953 letter-to-the-editor in Nature (Nomenclature of cyclohexane bonds) from Barton, Hassel, Pitzer & Prelog.

The letter notes (shown below) that the labels first suggested for the different C–H bonds on the cyclohexane ring were ɛ (epsilon) for what we now call axial, and χ (chi) for what we refer to as equatorial these days:

nature_barton

The citation (the subscript ‘2’ in the excerpt above) is to a paper by Odd Hassel published in 1943 in something called Tidsskr. Kjemi, Bergv. Met. which turns out to be the Norwegian journal Tidsskrift For Kjemi Bergvesen og Metallurgi (I’m sure that’s cleared it up for you…). Even if my Norwegian was up to scratch (it isn’t), I thought it would be somewhat tricky to track down a copy of this article to find out the reasoning behind the choice of those particular descriptors.

Fortunately, the article was later translated into English and published in Topics in Stereochemistry in 1971, along with an article by Derek Barton that had originally been published in 1950 in the journal Experientia.

Hassel’s paper — The cyclohexane problem — explains the origin of the descriptors as follows:

topstereo

For those of you paying attention, you may have noticed a problem. Whereas the Nature paper refers to ɛ and χ, the original Hassel paper refers to ɛ and κ (kappa). And based on the Greek origins of the descriptors, it is clear that it should be κ and not χ. Go back and look at the excerpt from the Nature paper above — even squinting a bit, it would need to be a very charitable interpretation to say that the symbol in question is κ and not χ. It seems that something went awry in the publication process (a couple of book chapters also confirm that the original descriptors were ɛ and κ).

One of these book chapters also pointed me in the direction of a 1954 Science paper, which shared the same authors (Barton, Hassel, Pitzer and Prelog) — and the same title — as the earlier 1953 Nature paper. On closer inspection, the letter in Science is, with one important exception, exactly the same as the one that appeared in Nature. See if you can spot the difference in this excerpt from the Science paper:

science_barton

So, Science got it right; a kappa (κ) and not a chi (χ) for the equatorial bonds. Perhaps more remarkable, however, is that both Science and Nature published the *same* letter (the Nature letter was published on Dec 12, 1953 and the one in Science on Jan 1, 1954) — I wonder whether the editors knew of the dual publication…?. Anyway, what was the ultimate purpose of this letter, this letter that was deemed so important that it should be published in both Science and Nature? Well, it was essentially just a proposal of new nomenclature for the different C–H bonds in cyclohexane.

After noting that the epsilon/kappa descriptors were difficult to remember, the authors pointed out that alternative nomenclature had been suggested by Beckett, Pitzer and Spitzer in a 1947 JACS paper. Basing their terms on geography rather than Greek, they had suggested the now-familiar ‘equatorial’ (e) for the C–H bonds around the equator of the ring and ‘polar’ (p) for the C–H bonds pointing either north or south away from the mean plane of the ring.

As highlighted in the Barton/Hassel/Pitzer/Prelog letter, however, the word ‘polar’ has another — very different — meaning in chemistry, and in an effort to prevent any confusion, they suggested that instead of polar, a better term would be ‘axial’. In another twist, the proposal to use ‘axial’ was actually made by Christopher Ingold who, despite this contribution, is only acknowledged in the Nature/Science letter (see below), rather than sharing in the authorship.

concluding para

Considering that ‘equatorial’ was already suggested in the earlier Beckett, Pitzer and Spitzer JACS paper and ‘axial’ is Ingold’s idea, the role of Barton, Hassel and Prelog appears to be one of making an authoritative plea (with Pitzer) to the community for a new standard to be adopted, rather than defining the new nomenclature themselves.

UPDATE 11/05/2015 – here’s an interesting post about Hermann Sachse and his attempts to get his ideas about the conformation of cyclohexane across to the wider chemistry community towards the end of the 19th century.

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A silicon spoof

This post is a follow-up to yesterday’s (did you notice the date?) that looked at an April 1981 paper by Dietmar Seyferth and James J. Pudvin published in the (now defunct) ACS journal CHEMTECH. This article reports the isolation of vacant 3d orbitals when tetramethylsilane is pyrolysed at temperatures in excess of 2,000 °C. Although a spoof, the paper is written so well, and with such attention to detail (the authors even include the supplier name and catalogue number for the ultrapure silicon tetrachloride that they supposedly used in their experiments), that the joke is not immediately obvious.

As I said yesterday, I’d never heard of the paper until Scott Denmark told me about it — and he was also the one who kindly provided me a copy (I doubt even #icanhazpdf would have worked for this one). I’ve had it sitting as an e-mail attachment for quite a while, but I figured the time had come to write about it — and looking at the calendar yesterday, I couldn’t resist. When putting the post together, however, I figured I would do a little more digging and see what else I could find out related to the article, and this post is the result.

Dietmar Seyferth

Although there are two authors listed on the paper, only one of them is real — and that’s Seyferth. Seyferth was the founding Editor-in-Chief of the ACS journal Organometallics and served in that position from the very first issue in January 1982 until 2010. In 2010, a special issue of Organometallics was published in honour of Seyferth (the Seyferth Festschrift) which featured an autobiographical essay entitled, ‘Looking Back on Happy Years in Chemistry‘. This 34-page article is remarkable in many ways, not least because the last 27 pages contain Seyferth’s detailed curriculum vitae (including full publication list)!

There are some interesting stories in the first 7 pages, however, not least the one about the Seyferth template (which ‘sold well for a number of years but ultimately was done in by ChemDraw’), but also one describing the story behind the CHEMTECH paper I blogged about yesterday — I reproduce that passage here:

Not all of my writings have been serious in nature. No. 353 in my publication list has the innocuous title “The Generation of a Highly Reactive Intermediate in the High-Temperature Pyrolysis of Tetramethylsilane” but really is a spoof in which I, with a fictitious coauthor, J. J. Pudvin, report the isolation and reactions of pure silicon 3d orbitals. I presented this orally at an organosilicon conference at Iowa State University in 1975 to the great amusement of my audience. Then there also is the only partly published (anonymously, without my knowledge, in CHEMTECH) “Researchmanship, Or How to Get Your Ph.D. Without Actually Working”, written in my younger years and modeled on Stephen Potter’s Gamesmanship, Lifesmanship, and One-upmanship books which were very popular at Harvard in the 1950s. Here J. J. Pudvin made his first appearance.

Using my highly advanced Internet-searching techniques (OK, I Googled it), I managed to find what claims to be the text of that other piece in which Pudvin first sprang into existence — it’s well worth a read too. Other anecdotes about Seyferth can be found on this webpage that lists the faculty members in the department of chemistry at MIT during the time that the class of 1964 were there. I particularly like this one:

When one of the new scholars asked him [Seyferth] how long it took a student to complete a Ph.D. in his research group, the answer was “The bad students — three years; the good ones — five.”

Anyway, back to the CHEMTECH paper and those 3d orbitals. Checking on Web of Science, the paper has apparently been cited just the once, but I’m not sure if the authors citing it are aware of just what they are citing… here’s the relevant passage in the citing paper (the bit in red is the reference to the CHEMTECH article).

A citation to a paper that suggests it is possible to isolate d orbitals...

A citation to a paper that suggests it is possible to isolate d orbitals…

There’s also a mention of Seyferth’s paper in the book Organic Chemistry: The Name Game: Modern Coined Terms and Their Origins in the context of other spoof chemistry articles (most of which are in German it turns out). By the power of Greyskull Google Books, you should be able find large chunks of the book here.

CHEMTECH

Another interesting part of putting together yesterday’s post was learning about CHEMTECH, an ACS publication that I had never heard of before being told about the Seyferth paper. It was launched in 1971 and ceased to be in 2001 (the last issue of CHEMTECH was actually published in December of 1999, but it re-emerged in 2000 as Chemical Innovation — although that only lasted until December 2001). The editorial in the last-ever issue spells out the reason for its demise:

If you are a subscriber or a reader of the ACS news department in Chemical & Engineering News, you already know that CI is closing shop. In these times of slow economy and greater attention to the bottom line, it was almost inevitable. Even the redesign and renaming of this magazine 2 years ago couldn’t reverse the decline in subscriptions, especially the institutional subscriptions that are necessary to keep a magazine like this afloat. So we take our leave. In the spirit of Rodgers and Hammerstein, I can say that all of my memories are happy tonight.

I beg your pardon.

I beg your pardon.

As with the launch of many new chemistry publications, the arrival of CHEMTECH (or Chemical Technology as was its official title back then) was heralded in the pages of Chemical & Engineering News. I’m sure that the ‘technology of urea’ and ‘the R&D and manufacturing of mothproofing substances’ would prove to be fascinating, but something else included in the description of what this new publication was going to cover was something that you wouldn’t (and shouldn’t) see today (that said, it wasn’t appropriate back in 1971 either). Just in case you were wondering, I’ve highlighted in yellow the offending bit in the passage I’ve grabbed from the pdf… yikes.

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Some surprising silicon chemistry

Ever since Scott Denmark told me about a gem of a paper back at the Bürgenstock conference a few years, I’ve been meaning to blog about it. Well, today is as good a day as any* I suppose, so here goes.

The paper in question appeared in CHEMTECH (I bet that’s one American Chemical Society journal that many of you have never heard of) in 1981 and was written by Dietmar Seyferth and James J. Pudvin. The fairly mundane title ‘The generation of a highly reactive intermediate in the high-temperature pyrolysis of tetramethylsilane‘ belies some truly astonishing chemistry.

The paper isn’t online, but here’s the Web of Science entry so that you know I’m not making this up.

It's a real paper, trust me.

It’s a real paper, trust me.

The article begins by noting a previous study that reports the pyrolysis of tetramethylsilane (and other organosilicon compounds) at temperatures of between 650 and 750 °C to form of ‘carbosilanes’ — compounds with Si–C–Si bonds. Seyferth and Pudvin point to their interest in reactive organosilicon species and suggest that the pyrolysis of tetramethylsilane at much higher temperatures than those used in the previous work could lead to even more exotic intermediates.

They then set about testing their theory and describe an experimental set-up that enabled them to pass a feed of pure tetramethylsilane (a whopping 6.81 kg in a typical experiment!) through a flash-vacuum-pyrolysis unit that was capable of reaching temperatures of around 2,250 °C. An elaborate system of cold traps was used to collect the products, which were then analysed with a comprehensive range of techniques.

Perhaps unsurprisingly, large amounts of hydrogen and methane were formed, along with other higher hydrocarbon products. That didn’t account for the silicon atom sitting at the heart of each molecule of starting material, however, but that was recovered as a mixture of silicon carbide and elemental silicon. After fractionation of other residues condensed in the liquid-nitrogen trap, just under a quarter of a gram of an amber liquid (let’s call it compound 1) was obtained — and this is where the fun/weirdness began.

Three separate attempts to determine the elemental composition of 1 suggested that it contained no carbon, hydrogen or silicon. Molecular weight determinations gave a range of results (and were solvent dependent) and NMR spectra recorded in hydrocarbon solvents — even 50%-by-weight solutions of 1 — did not reveal any resonances (1H, 13C or 29Si) other than those arising from the solvent itself. What was strange, however, was that this mystery compound was interacting with the solvent, leading to shifts in their expected NMR signals.

It was also noted that compound 1 exhibited some unusual reactivity — when dissolved in carbon tetrachloride in the open laboratory, both hydrogen chloride and carbon dioxide were observed to be formed. On further investigation it was found that solutions of 1 in carbon tetrachloride reacted with water (or dilute sodium hydroxide) and that all of the carbon tetrachloride was consumed in these reactions.

Left somewhat perplexed by their inability to characterize compound 1, Seyferth and Pudvin decided to look at the silicon-containing products formed during the pyrolysis process. Chlorination of the mixture of elemental silicon and silicon carbide resulted in the formation of silicon tetrachloride and carbon tetrachloride, which were then separated by distillation. This led to the surprising finding that, “The carbon tetrachloride obtained was unexceptional, but the silicon tetrachloride had anomalous chemical and physical properties.”

It was found that the silicon tetrachloride was unexpectedly resistant to hydrolysis; even the reaction with boiling water was slow. The 29Si NMR spectrum of this silicon tetrachloride was also very strange in that the single expected resonance was shifted upfield by 0.15 ppm compared with a ultrapure commercial sample of the compound — and this observation was consistently reproducible. Other inconsistencies were found relating to the nature of the chemical bonding — the silicon tetrachloride produced in Seyferth and Pudvin’s experiment had longer Si–C bond lengths than would be expected based on other literature reports and they also exhibited an increased stretching frequency compared with commercial samples.

This led to the following (remarkable) conclusion, which I reproduce in full from the original paper:

The conditions of our tetramethylsilane pyrolysis were sufficient not only to break all Si–C bonds, but also to strip all of the unoccupied 3d orbitals from the gaseous silicon atoms which were generated at the high temperatures used. These then condensed and were isolated in the form of a dense amber liquid.

This is what d orbitals look like really close up. Image taken from the UC Davis ChemWiki (http://chemwiki.ucdavis.edu/). CC BY-NC-SA 3.0 US

This is what d orbitals look like really close up. Image taken from the UC Davis ChemWiki (http://chemwiki.ucdavis.edu/). CC BY-NC-SA 3.0 US

And this astounding finding explains all of the anomalous observations described earlier in the paper. Because compound 1 is simply made up of vacant 3d orbitals, there would be no NMR signal (there are no nuclei to resonate) and there is no elemental composition to even be determined. Moreover the induced NMR shifts observed for hydrocarbon solvents can be explained by the interaction of these 3d orbitals with the carbon atoms of the solvents and the subsequent effect on their valence electrons.

The reactivity of solutions of compound 1 in carbon tetrachloride are rationalized by Seyferth and Pudvin in terms of what they call ‘orbital grafting’. Whereas carbon tetrachloride is resistant to hydrolysis because there are no empty orbitals on the carbon atom of sufficiently low energy for uncharged nucleophiles (such as water) to attack, the grafting of unoccupied 3d orbitals to the carbon atom makes nucleophilic attack much easier — and hence the formation of carbon dioxide and hydrogen chloride from solutions of 1 in carbon tetrachloride proceeds readily under ambient conditions.

This hypothesis also explains the unusual properties of the silicon tetrachloride formed from the silicon residues following the initial pyrolysis. Because the silicon atoms in this form of silicon tetrachloride have been stripped of their 3d orbitals, this compound is much more resistant to hydrolysis. Furthermore, the absence of 3d orbitals also explains the unusually long (and weaker) Si–C bonds than would typically be expected. The donation of electrons from the Cl atoms into the 3d orbitals on Si is no longer possible and so there are no resonance contributions from a putative Cl=Si species.

Seyferth and Pudvin go on to calculate their isolated yield of 3d orbitals (using the rest mass of a 3d orbital reported in an earlier study) as 87%, which they say, “…attests to the efficiency of our pyrolysis process.” Not content with simply identifying the amber liquid, however, they go on to show how the availability of free 3d orbitals could have a huge impact in chemistry.

The first demonstration described in the paper is truly remarkable. Although tetraalkylammonium salts have no valence orbitals left free for further bonding, it is shown that in the presence of a stoichiometric amount of unoccupied 3d orbitals obtained from silicon, the tetramethylammonium ion can be reacted with methyllithium to give pentamethylnitrogen. This compound can be isolated as a liquid, although it is pointed out that it, “…rivals mercuric fulminate in its propensity for unexpected and violent detonation.”

As well as using the vacant 3d orbitals to create chemical curiosities, Seyferth and Pudvin show us a glimpse of the real-world potential too. Taking advantage of the orbital grafting phenomenon described earlier, the persistent environmental hazards posed by chlorinated and fluorinated hydrocarbons become less of a problem because these pollutants can now be more easily broken down by water. Moreover, it is shown that when nitrogen gas is added to an aqueous solution of 1 at 80 °C, it is possible to form ammonium nitrite — so vacant 3d orbitals can solve the problem of nitrogen fixation too!

The paper ends with a discussion of future directions, suggesting that the process is not just limited to silicon. In theory it should be possible to obtain vacant 5d orbitals from tetramethyltin, although initial experiments were unsuccessful. It is thought that the more reactive 5d orbitals could be grafting on to the silicon atoms present in the glass traps in the experimental apparatus. Intriguingly, although the hydrolysis of tetramethylsilane is assumed to give equal amounts of the five different types of d orbitals, Seyferth and Pudvin speculate that it should be possible to strip specific d orbitals from suitable transition metals that have partially filled shells. It is surely only a matter of time before pure samples of dxy or dz2 orbitals are obtained and put into bottles.

And finally, it is suggested that this procedure may not be limited to just d orbitals. Pure pz orbitals could be obtained from the pyrolysis of trimethylborane and an appropriate lanthanide or actinide compound could be the source of pure f orbitals. To reiterate the final sentence of the paper, “It is clear that a vast new area of chemistry has been opened.” Amazing. And who would have thought that d orbitals were amber in colour; I’d always assumed red and blue…

————————–

*Today is probably a slightly more appropriate choice than any of the other 364 days this year come to think about it.

**There will be a follow-up post soon with a bit more background to this one (it’s here).

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How to make sloe gin… and a little bit of chemistry

First, the recipe.

Making sloe gin really is as easy as 1, 2, 3… – it only requires three ingredients (a fourth is optional) and the particular ratio my recipe uses is 1:2:3 (sugar:sloes:gin). The recipe is easily scaled depending on the size of the container you plan to use.

For a 1.5 litre Kilner jar, I use the following:

250 g caster sugar
500 g sloes
750 mL gin

(a splash of almond extract is optional; make sure you use an alcohol-based one rather than oil-based).

I usually sterilize the Kilner jar with a sterilizing solution made up with the tablets that you can buy in any supermarket – I’m not sure this is absolutely necessary, but better safe than sorry. I leave the jar upside-down on some kitchen roll and let it air dry.

Once you’ve gotten hold of the sloes (more on that later), I get rid of any leaves/stalks, wash them in water, dry them, and then put them in the freezer in a plastic bag. Leave them in there for a day or two and this should split the skins. If when you take them out of the freezer the sloes haven’t split, just prick each one with a sharp knife (it’s less messy if you do it while they are still frozen… and it doesn’t take as long as you think it will). Some sloe-gin folklore tells you that you need to prick the sloes with a thorn from the blackthorn bush you picked the fruit from; alternatively you should use a silver needle. This is stupid, you don’t need to do it – a knife is fine.

Simply weigh 500 g of the frozen sloes into the Kilner jar, add the sugar, then the gin, and finally the splash of almond essence if you plan on including it. Close the jar lid and then give the whole thing a good shake. Store the jar in a dark cupboard and give it a shake each day until the sugar completely dissolves – this shouldn’t take more than a few days. After that, invert the jar once a week (or just whenever you happen to remember). Then wait. The longer the better.

Just add time.

Just add time.

If you don’t have weighing scales or a measuring jug then the following is a good approximation: pick the container you want to make your sloe gin in and fill it half full with sloes. Add sugar until it fills the gaps between the fruit and reaches the same level in the container as the sloes, and then fill the container to the top with gin (add your almond extract if you want). You don’t need to use Kilner jars; just something that forms a pretty good seal – old gin bottles or even plastic drinking water bottles will do. Some people say you shouldn’t use plastic, but I couldn’t tell the difference between a batch made in a plastic bottle and one made in a glass Kilner jar.

16 months (11 over fruit, 5 after filtering) from hedgerow to glass.

16 months (11 over fruit, 5 after filtering) from hedgerow to glass.

Whichever method you use, you’ll notice the gin take on a light pink colour quite quickly and it will get darker over time until it reaches a deep ruby red colour. Of the first batch I ever made, I filtered one jar after 3 months, another after 6 months and the final one after 11 months (I couldn’t hang on for the full year). As with the whole glass/plastic debate, you will see varying opinions on just how long you should leave the sloes steeping in the gin. All I can tell you is that the stuff filtered after 3 months was good, the 6-month vintage was great and the 11-month batch was amazing (that stuff in the glasses over there is some of the 11-month batch). I’d probably draw the line at 12 months; it may well be a case of diminishing returns at that point in terms of what additional flavour can be extracted from the sloes.

In terms of filtering, no fancy lab equipment is required, we use a kitchen funnel and coffee filters – and we simply filter into the gin bottles that we emptied at the start of the whole process. At this point, you’re desperate for a taste, and you should have one, but just a small one. If you can, put the lid back on the bottle, put it into a dark cupboard and try to forget about it for as long as possible. It will certainly be drinkable right away, but the taste improves with age and it just gets better and better.

So, that’s the process. Simple really. If you search for sloe gin recipes on the web you will find many different variations (amazing for something with so few ingredients), but this one works for us. These proportions give a fairly sweet liqueur (although I wouldn’t say syrupy), and if you don’t want it to be quite so sweet just add less sugar at the start (you can always add more if you taste it during the steeping process and decide it’s not sweet enough; what you can’t do is remove any sugar, so best to err on the side of adding less rather than more at the outset). Similarly, if you want a stronger sloe flavour, increase the proportion of sloes. You can also get a hint of the almond flavour straight from the stones in the sloes without needing to add the almond extract, but adding the extract enhances the flavour. Just experiment – do batches with and without almond extract (we do), and vary the 1:2:3 ratio to see what you like best. Play with the timings too; it’s hard to really do anything wrong.

Oh, and when it comes to the gin, we usually use Gordon’s (just keep an eye on when it’s on offer throughout the year and buy it when it is at its cheapest; a litre for £18 is not bad). Having said that, the batch I did with supermarket-brand gin tasted just as good and even though we didn’t do a blind taste test, I don’t think we would have been able to tell the difference. Just don’t waste money on anything too fancy – any delicate flavours in the original gin will be well and truly overpowered by the sloes – but on the other hand, don’t use dirt-cheap stuff either.

Whereas the sugar and gin are easily acquired at your local supermarket, you’ll need to get your walking boots on to get the sloes, but they are really not that difficult to find. Sloes are the fruit of the blackthorn bush, which is commonly used for hedges in the countryside; be careful when you go picking, however, because the thorns can be vicious (that’s why blackthorn makes for good hedges). Sloes are roughly 1 cm in diameter (or just a little larger) and are blue-ish/purple-ish/black-ish in colour. If you come across something similar, but are a little larger and are growing on a bush that has no thorns, you’ve probably found some bullace – see the photo below. Sloes, bullace and damsons are all types of small wild plum and it may well be that bullace developed over time from the sloe and, in turn, the damson developed from the bullace (or so Wikipedia tells me). And just to make things more complicated, there may well be hybrids of these growing out there in the wild too.

Sloes on the left, bullace on the right (I think).

Sloes on the left, bullace on the right (I think).

So, when do you pick the sloes? As with every other step of the process, there are myths and legends associated with this aspect too. The most common one is that you should wait until the first frost. If we had waited for the first frost, we wouldn’t have picked any this time around until December/January and there wouldn’t have been many left. I suspect in years gone by the first frost just happened to coincide with when the sloes were ripe, but we start picking any time from early September onwards. The answer to the question of when to pick the sloes is simply when they are ripe.

Warning – for those not interested in the chemistry, skip to the last paragraph, but for those who are, keep on reading. Sloes are really very bitter; you wouldn’t want to eat them or make any kind of dessert from them. The reason for this astringency is the presence of a variety of polyphenol compounds, some of which are shown below.

The compounds that make sloe gin taste like sloe gin.

The compounds that make sloe gin taste like sloe gin.

I found these in a 2014 paper entitled ‘Phenolic composition, antioxidant and antimicrobial activity of the extracts from Prunus spinosa L. fruit’ (PDF here) where an ethanol/water extract of sloes was analysed by HPLC. The phenolic compounds identified in the extracts were neochlorogenic acid (1), quercetin (2), caffeic acid (3), myricetin (4), peonidin-3-O-glucoside (5), antirrhinin (6) and chrysanthemin (7). It is also presumably the reactions of these compounds (oxidation, oligomerization, esterification and maybe others) that leads to the change in taste of the sloe gin as it ages.

If you don’t want to try making your own sloe gin, there are commercial versions available. Be warned, however. Of the three I’ve tried, Gordon’s sloe gin is probably good for stripping paint but little else; Sipsmith sloe gin isn’t bad, but by far the best (at least to my taste) is that made by SLOEmotion. Their sloe whisky is also quite special too (I’m making some of my own this year). When I get a chance, I’ll post recipes for damson gin and cherry plum gin too… the damson gin probably won’t last long this year!

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A quantitative analysis of how often Nature gives a fuck

After seeing this tweet the other evening:

I started to wonder just how sweary Nature has been over the years. For the purposes of this exercise, I’m just counting words that have been printed in the hardcopy of the journal (online-only mentions don’t count, sorry).

It turns out that the instance of ‘bollocks’ referred to in the tweet above is actually its sixth mention in Nature over the years. The first time ‘bollocks’ dropped into the journal was on April 16, 1998 in a piece by Martin Kemp about some photographs that had appeared in Nature’s pages the previous autumn. Kemp’s article was quoting what a postgraduate student was heard to have said (“What’s this bollocks doing in Nature?”) in the biology department’s tea room at Leicester University in response to Cornelia Parker’s pictures of navel fluff from (i) a sailor (while at sea), (ii) a farmer and (iii) an architect.

Kemp’s article soon prompted some critical correspondence from Ian Smith, who opened his letter with, “How lovely to see the word “bollocks” appearing, perhaps for the first time, in Nature,” before going on to suggest that Parker would not be any less eligible to evaluate the Leicester University student’s work than that student would be to evaluate hers – and so perhaps she should be invited to be an external examiner for his PhD thesis.

And so, this initimately related pair of ‘bollocks’ appeared in Nature within the space of two weeks.

The third, fourth and fifth appearances of the word ‘bollocks’ came in a single letter published in 2001, penned by *that* Leicester University student responding to the bollocking dished out by Smith in the pages of Nature almost 3 years beforehand. Although Magnus Johnson lamented the fact that his contribution to Kemp’s article would likely be the closest he would get to publishing in Nature, he described being responsible for the first time ‘bollocks’ appeared in the journal as possibly the pinnacle of his scientific career.

Anyway, never mind the bollocks, what about other swear words?

First of all, if we’re going to survey swear words used in Nature, we need some sort of classification of sweary-ness. This led me to a wonderful set of guidelines from the BBC categorizing different swear words according to whether they are likely to cause most offense, moderate offense or simply mild offense. Just imagine the posh radio 4 lady reading those guidelines out loud.

I think a more widely known (and in-depth) analysis of swear words is George Carlin’s seven dirty words – if you’ve never heard/watched the sketch, you can find it here (NSFW, not without headphones anyway). Of those 7 dirty words, only 4 have appeared in Nature, and the one that has appeared the most (more than 650 times) is in an ornithological context rather than any swear-y sense. So that leaves fuck, piss and shit (and variations thereof). I’ve found 48 shits (including 13 bullshits, 1 shit-stirrer and 1 nano-shit), 26 piss-derived expressions, and a grand total of 10 fucks. And this is how those fucks breakdown over time.

fuck2

The 1937 ‘fuck’ appears in a section entitled ‘Societies and Academies’ and seems to list the titles of presentations made to them. Under the heading ‘Rome’, there is an entry that reads:

G. BORZINI: Observations on the parasitism of Sclerotinia libertiana sclerotiorum Fuck associated with other fungi.

From a little digging on Google, it seems that the thing in italics is a plant fungus and it was named for Karl Wilhelm Gottlieb Leopold Fuckel – the Wikipedia entry helpfully points out that in non-English-speaking countries, Fuckel was sometimes abbreviated as ‘Fuck.’ – although the fullstop is missing in this case in Nature.

The 1985 ‘fuck’ is similarly innocent. One of the authors of reference 11 cited in the paper Andean-trending mobile belts in the Brazilian Shield is one ‘R. A. Fuck’.

It’s only in 1989 that ‘fuck’ is first used in anger. While reviewing Stephen Jay Gould’s Wonderful Life, Richard Fortey repeats a quote (“Oh fuck, another new phylum”) featured in the book. The remaining 7 instances of ‘fucked’, ‘fuck’ and ‘fucking’ are also found in quotes rather than being the authors’ own words, and appear in news stories, news features or the Books & Arts section. So, that’s 8 deliberate fucks in roughly 145 years; one every 18 years or so, although it’s clearly not an even distribution. If the rate of usage continues to pick up as it has done over the past few years, expect to see more clusters of fucks in the near future.

Do note, however, that this level of sweary-ness is not a patch on just a single article published in the journal Chemical Communications. It might not sound terribly risqué, but the paper Electrochemical synthesis of metal and semimetal nanotube–nanowire heterojunctions and their electronic transport properties mentions perhaps the most offensive of Carlin’s 7 dirty words more than 50 times – there’s even a bunch of them shown in the graphical abstract that accompanies the article. Perhaps a different abbreviation for copper nanotubes would have been a better choice?

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