Posts Tagged ‘United States’

The atom and the molecule: A one-day symposium on 23 March, 2016 celebrating Gilbert N. Lewis.

Friday, December 11th, 2015

You might have noticed the occasional reference here to the upcoming centenary of the publication of Gilbert N. Lewis’ famous article entitled “The atom and the molecule“.[1] A symposium exploring his scientific impact and legacy will be held in London on March 23, 2016, exactly 70 years to the day since his death. A list of the speakers and their titles is shown below; there is no attendance fee, but you must register as per the instructions below.

Royal Society of Chemistry Historical Group Meeting on 23th March 2016, Burlington House, Piccadilly, London: The atom and the molecule: A symposium celebrating Gilbert N. Lewis.

  • Dr Patrick Coffey (Berkeley, USA): Does Personality Influence Scientific Credit? Simultaneous Priority Disputes: Lewis vs. Langmuir and Langmuir vs. Harkins
  • Professor Robin Hendry (Durham, UK): Lewis on Structure and the Chemical Bond
  • Professor Alan Dronsfield (UK): An organic chemist reflects on the Lewis two-electron bond
  • Dr Julia Contreras-García (UPMC, France): Do bonds need a name?
  • Professor Nick Greeves (Liverpool, UK): The influence of Lewis on organic chemistry teaching, textbooks and beyond
  • Professor Clark Landis (UWM, USA): Lewis and Lewis-like Structures in the Quantum Era
  • Professor Michael Mingos (Oxford, UK): The Inorganic dimension to Lewis and Kossel’s landmark contributions
  • Dr Patrick Coffey (Berkeley, USA): Lewis’ Life, Death, and Missing Nobel Prize

Prior registration is essential. Please email your name and address to Professor John Nicholson,  jwnicholson01 @ gmail.com

References

  1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002

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Posted in Interesting chemistry | 1 Comment »

The chemical Web at 22 and where it might go.

Wednesday, August 19th, 2015

This post is prompted by the appearance of a retrospective special issue of C&E news, with what appears to be its very own Website: internet.cenmag.org. It contains articles and interviews with many interesting people, along with several variations on the historical (albeit rather USA-centric) perspectives and a time-line covers many of the key innovations (again, from a USA-perspective). Some subjects are covered in greater depth, including computational chemistry. The periodic table too gets coverage, but surprisingly that is not of Mark Winter’s WebElements, which carries the impressive 1993-2015 continuous timeline (hence 22 in the title!).  

You can find mention of Tim Berners-Lee at the CEN site (but no interview with Sir Tim), so here I contribute to the historical record by showing the plaque placed in the corridor of offices at CERN where TiMBL and Robert Cailliau worked to set the Web up in 1991.‡

Click to expand

Click to expand

What is not really given much prominence in the C&E news article is DATA. Which arguably is the reason why TimBL set things going back in 1989! Zenodo is (just like the Web before it) a spin-off from the activities at CERN, but now handling just data. Or Code. Or indeed almost any useful outcome of the research process that might be useful to someone else or to posterity. And to put it into context, it comes in two parts:

  1. The data store itself (which CERN are especially good at, since the Large Hadron Collider generates a great deal of data). They add the A to FAIR (Findable, Accessible, interoperable and Reusable). And also a certain confidence that this store will be enduring, not here today and gone tomorrow.
  2. The metadata describing the data, which in fact turns out is stored somewhere else, at DataCite. This organisation serves to add the F to FAIR.

And to show how this works in practice I can do no better than give this link: search.labs.datacite.org/help/examples which shows how you can benefit from the metadata.

I have already demonstrated the use of Zenodo for archiving some old computer code of mine for calculating kinetic isotope effects, but of course it is so much more than that. If the first CERN spin-out, the Web, is already 22 years old (for chemists), then I am confident in asserting that facilities such as Zenodo will play an increasingly important role over the next 22 years (indeed a much shorter timescale than that). 

‡A personal souvenir can be seen here.

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Henry Armstrong: almost an electronic theory of chemistry!

Monday, November 7th, 2011

Henry Armstrong studied at the Royal College of Chemistry from 1865-7 and spent his subsequent career as an organic chemist at the Central College of the Imperial college of Science and technology until he retired in 1912. He spent the rest of his long life railing against the state of modern chemistry, saving much of his vitriol against (inter alia) the absurdity of ions, electronic theory in chemistry, quantum mechanics and nuclear bombardment in physics. He snarled at Robinson’s and Ingold’s new invention (ca 1926-1930) of electronic arrow pushing with the put down “bent arrows never hit their marks“.1  He was dismissed as an “old fogy, stuck in a time warp about 1894.”1 So why on earth would I want to write about him? Read on…

He did worthy (nowadays this could mean dull) chemistry on e.g. naphthalenes, but I want to focus on two articles from the period 1887-1890 (10.1039/CT8875100258  and 10.1039/PL8900600095). Let me set the scene by reminding of an earlier post showing the structure of a bis(stilbyl)ketone, dated 1921. The two aromatic groups (yes, they really are such) are drawn in the manner we would nowadays draw cyclohexane. This practice in fact continued in texts and articles for perhaps 30 more years! Not much sign of electronic accounting there then! And by a professor at Imperial College no less, where Armstrong had been.

Aromatic molecule, circa 1921

So when would you date the diagrams below? So called Clar2 representations, originating from the 1950s? The one on the bottom below cites Clar and dates from 2010, DOI: 10.3390/sym2031653, but the one above it comes from Armstrong’s 1890 article!

Two representations of pyrene, 2010 and 1890.

Clar representations are used to count electrons (as coming in six packs). But there is little doubt that Armstrong’s use of a “C” (or inner circle, which is exactly what it is) means six as well. The evidence I present below, taken from his 1887 article.

Armstrongs six pack

  1. He counts the six carbons as having a total of 24 what he calls affinities (definition: An attraction or force between particles that causes them to combine), or four per carbon. Let us make life easy and equate affinity=electron (remember, the electron itself was not yet discovered or named!). He disposes of 12 affinities/electrons to form what we now call six carbon-carbon σ bonds, and a further six for the  six C-H bonds.
  2. He is left with exactly six affinities/electrons, which he presupposes to act upon each other, in the manner of resultants (the old term for vectors). In fact, he replaces these six vectors by a circle (the inner circle) in his second article of 1890.
  3. He invents delocalization in all but name when he states that any one atom has an influence on other atoms not contiguous to it in the ring (he really did have o/m/p directing influence in mind here).
  4. He compares the introduction of a substituent (R, which comes from the old name Radicle) perturbing the distribution of the affinity to how electric charges perturb each other. So, the affinity behaves as if it might have electrical (from which the name electron came of course) properties? And it might be described by a vector?
  5. Remember, this is a scientist who in later life did not believe in electronic theories of chemistry? Really? Well, again in 1890:

Is this an affinity (=electronic) theory of chemistry?

  1. Here, he is refining his vector representation of affinities, saying that these vectors in effect define a circle, an inner circle no less. One that can be disrupted  (Robinson some 30 years later wrote of how the cycle of six electrons are able to form a group that resists disruption) when an additive compound is formed (his examples are all electrophiles, what we now call electrophilic addition) such that the remaining carbons become merely unsaturated. There seems little doubt he is describing what we now call a Wheland Intermediate.
  2. Is this really a man who did not believe in electronic theories of chemistry? What about that concluding paragraph then? The laws of substitution require a knowledge of the inner structure of (what we now call the aromatic) hydrocarbons?
  3. And that such speculations may suggest fresh lines of experimental inquiry? This all sounds very much like the modern use of quantum mechanics and its electronic eigenvectors to describe the probability distribution of electrons (remember, Armstrong did not approve of this either) to probe the inner structure of molecules and to suggest new experiments.

We have a real mystery. Armstrong got so very close to a modern theory of chemistry. Was he asleep when Stoney named the electron around 1891 and Thomson discovered it in 1897? If only he had followed his own advice! Ah well, just as well he was ignored in the 20th century when he preached against it all.

  1. W. H. Brock, “The case of the Poisonous Socks”, chapter 20, RSC Publishing, 2011, 978-1-84973-324-3
  2. Clar, E. The Aromatic Sextet; Wiley: New York, NY, USA, 1972.

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Computers 1967-2011: a personal perspective. Part 3. 1990-1994.

Tuesday, July 12th, 2011

In 1986 or so, molecular modelling came of age. Richard Counts, who ran an organisation called QCPE (here I had already submitted several of the program codes I had worked on) had a few years before contacted me to ask for my help with his Roadshow. He had started these in the USA as a means of promoting QCPE, which was the then main repository of chemistry codes, and as a means of showing people how to use the codes. My task was to organise a speakers list, the venue being in Oxford in a delightful house owned by the university computing services. Access to VAX computers was provided, via VT100 terminals. Amazingly, these terminals could do very primitive molecular graphics (using delightfully named escape codes, which I learnt to manipulate).

An expert on the use of such codes was George Purvis, who hailed from the quantum theory project at the University of Florida at Gainesville. He had developed QUIPU for VAX/VT100 and together we had much fun setting things up for the participants at these QCPE workshops (which ran 1986-1990). During one session, George asked me whether I thought a properly implemented and reasonably cheap graphical user interface might have commercial potential in chemistry. Remember, the VAX/Evans&Sutherland PS390 system we had acquired in 1987 was NOT cheap. I must have encouraged him, since in 1990 George (now part of the CACHE, or computer assisted chemistry, group at the Tektronix corporation in Beaverton) had brought to market a “shrink-wrapped” system which did just that. This was, in many ways, well ahead of its time. It was based on a then state-of-the-art Macintosh computer, with a co-processor that could crunch floating point numbers quite fast (this was then very rare in so called personal computers, being reserved for supercomputers). It had a unique spherical trackball (almost a haptic device) for rotating molecules, and a liquid crystal polarized screen running at 120Hz (60Hz for the left eye, 60Hz for the right eye). Wearing polarized (passive) glasses, the stereo 3D effect via the 19″ screen (big for its day) was awe inspiring. What is more, two people could sit at it and both see molecules in stereo.

We managed to get a grant to purchase such a system, and I well remember taking it to the 1990 Oxford workshop (I had now taken over from Richard for the UK workshops) in the back of my car. This involved driving to my office on a Saturday, and heaving the thing out. A security guard saw me doing this and arrested me. After much ado, I was forced to take the CACHE to my office and told not to try that again. I waited 30 minutes, and took it out the back door (which nowadays has a black security camera watching it, but in those days was not guarded) and on to Oxford (checking for police sirens all the way). I think I made the trip to Oxford with this thing in the back of the car one more time, where I used it to give a poster at a conference, handing out the 3D glasses to anyone who expressed an interest (and reclaiming them rapidly if they posed no interesting question). I still fancy this was almost unique in the history of posters (which tend, even nowadays, to be printed on paper). Reflecting on this, I realise that my total aversion to Powerpoint probably dates from that time.

At this stage, I will tell you about some of the science we did with the remarkable stereographical 3D CACHE system. The first is our realisation that the Pirkle reagent exhibits a π-facial hydrogen bond from the OH group (DOI: 10.1039/C39910000765). Indeed, I notice that four of the posts here relate to this topic! Once you know what you are looking for, its trivial to spot. But I recollect that the crystallographers who did the structure for us had failed to identify this unusual hydrogen bond; it took the CACHE, and its 3D glasses, for us to notice it.

But the really important breakthrough using CACHE was a different molecule, halofantrine (X=Y=Cl, DOI: 10.1039/C39940001135) an antimalarial pharmaceutical molecule.

Halofantrine.

At this stage, pharmaceutical companies were assiduously resolving chiral compounds into their enantiomers and testing each separately for biological activity. It had been noticed that whereas X=H, Y=Cl could NOT be resolved on a chiral column, replacing X=H by X=Cl suddenly made it possible to do so. But why? Well, in order to inspect this with the CACHE system, we asked for the crystal structure to be done. Back it came and Mike Webb and I sat inspecting the coordinates in full stereoscopic glory, as I recollect for about an hour, twiddling the viewpoint here and there. Each of us would take over the haptic trackball for 10-15 minutes, and we would then discuss what we saw. In one of those magical moments (I can assure you that shivers do run down one’s back at moments like this) we spotted that X=H had a strong hydrogen bond to the OH of another molecule, whereas X=Cl did not. Suppressing that C-H…O interaction forces the molecule to π-π stack instead, and this mode now enables it to better interact with the chiral column and hence resolve.

Halofantrine. Click for 3D.

Some of that magic is recreated above. If you click on the image, the coordinates will be loaded. Now that the relevant interaction is highlighted, it is so easy to spot you might wonder how anyone would have ever missed it!. At any rate, shortly after writing this article, I sat down to write another on a new phenomenon called the World-Wide-Web. And to illustrate why the Web might become important, we highlighted halofantrine, and how the Web could carry such immediately visual information to its readers. This blog, in effect, is a direct descendent of that article (which, by the way, is still available in HTML form here). So, 3D graphics led to the (chemical) Web. What a tangled web indeed.

And to end with 3D. I live in hope that shortly, stereoscopic tablets will make an appearance. Given that the CACHE system noted above was heavy (it was a major struggle moving the monitor into the car, as described above), it will be an amazing evolution to see (almost) pocket sized devices being carried around for the same purpose.

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Posted in Chemical IT, Interesting chemistry | 4 Comments »

Capturing penta-coordinate carbon! (Part 1).

Tuesday, September 22nd, 2009

The bimolecular nucleophilic substitution reaction at saturated carbon is an icon of organic chemistry, and is better known by its mechanistic label, SN2. It is normally a slow reaction, with half lives often measured in hours. This implies a significant barrier to reaction (~15-20 kcal/mol) for the transition state, shown below (X is normally both a good nucleophile and a good nucleofuge/leaving group, such as halide, cyanide, etc.  Y can have a wide variety of forms).

The Sn2 transition state

The Sn2 transition state

This transition state is normally regarded as the only situation in which carbon can sustain penta-coordination (there are some exceptions), and this is often contrasted with the analogous situation for silicon, which demonstrates an abundance of stable penta- (and hexa-)coordinate (crystal) structures. Perhaps inevitably therefore, chemists have set themselves the goal of capturing a penta-coordinate carbon, not as a transition state with fleeting lifetime, but as a stable (and perchance crystalline) species.  The best strategy is to explore potential systems computationally, and the latest report of such an exploration has some suggestions for synthesis (Pierrefixe, S. C. A. H.; van Stralen, S. J. M.; van Strale, J. N. P.; Guerra, C. F.; Bickelhaupt, F. M., “Hypervalent Carbon Atom: “Freezing” the SN2 Transition State,” DOI: 10.1002/anie.200902125). Their suggestion corresponds to Y=CN and X=At (Astatine), a rather esoteric combination it has to be said.  In the manner of the blogosphere, Steve Bachrach has noted this report in his own blog, where a discussion has opened up on the origins of why carbon can be regarded as abnormal (at least compared to silicon), and more particularly whether such a species should be regarded as merely hypercoordinate, or as Bickelhaupt and co-workers suggest, hypervalent.

In fact, such reports are not new. As I note in the discussion of Steve’s blog, a crystalline structure of a hexa-coordinate carbon compound was reported in 2008 (DOI: 10.1021/ja710423d (below), and it is also tentatively described as possibly hexavalent near the end of the article! I shall return to this compound in the second part of this post.

Hexa-coordinate carbon

Hexa-coordinate carbon

The astatine system reported above is unusual, and it really only contains three carbon-carbon bonds surrounding the pentacoordinate carbon. The compound above contains only two such C-C “bonds”. It would be perhaps more interesting to ask if one could design a compound with five C-C bonds surrounding the putative pentacoordinate atom. Whilst mulling over Steve’s post, and pondering my contribution to that blog, a colleague in my department wandered into my office (my door is almost always open) and without saying a word, he wrote a structure on my blackboard (yes, I really do have such).  He then walked out (almost;  I believe he did mutter perhaps two words before leaving). He had sketched the key feature of an article by Ethan L. Fisher and Tristan H. Lambert entitled Leaving Group Potential of a Substituted Cyclopentadienyl Anion Toward Oxidative Addition (DOI: 10.1021/ol901598n). This triggered the following question in my mind: could the aromatic cyclopentadienyl anion act as the X group in the pentacoordinate carbon example above? The essential property of group X is that it must be big!  Well, cyclopentadienyl can be made big! It would also achieve the purpose of forming a penta-coordinate carbon with  five  C…C bonds.

So in it goes for a B3LYP/6-311+G(2df) calculation. Surely, the life of a computational chemist is an easy one; all one  has to do is wait a few hours (or, with a large basis set, days) for an answer. The result is shown below.

The SN2 reaction captured with cyclopentadienyl anion

The SN2 reaction captured with cyclopentadienyl anion

The key vibrational mode (which you can see animated if you click on the image above) has a wavenumber of 194 cm-1 (B3LYP/6-311+G(2df); other basis sets show similar values). It corresponds to the SN2 mode,  and is what we normally think of as the  transition or reaction normal mode for this reaction. But  in this case, it is not an imaginary mode, but a real mode!  The SN2 has been (virtually) captured for a penta-coordinate carbon with five C…C interactions. How does it compare with the astatine system noted in 10.1002/anie.200902125? Well, unfortunately, the umbrella-mode for that system  is only reported as a force constant without mass weighting, so it cannot be compared to the mass-weighted value we have here. The calculation is digitally archived (e.g. as 10042/to-2407 or 10042/to-2415) so you can analyze it for yourself!

An obvious question to ask is what the nature of the  axial bonds for X=cyclopentadienyl is. Is the central carbon hypercoordinate, or hypervalent, or both? But this blog is quite long enough already, and so this will all be discussed in part 2, to follow shortly.

Oh, one final comment. The issue of hypervalency and hypercoordination of carbon has previously been discussed largely in conventional scientific publications (for which DOIs are provided above). The forum moved to Salt Lake  City in the  USA, where some of the results were presented orally at the ACS spring conference in 2009.  Now that it  has been formally published, it has been taken up by Bachrach in his blog, where some of the discussion has continued. So where should I have presented the present result?  In the primary scientific literature? Or perhaps another ACS meeting? Well, here it is in another blog (I have been variously told I am either brave or very foolish for doing so!). And as I write this, of course it is not peer reviewed (but there is nothing to stop people from commenting on this of course, as has happened in Bachrach’s blog). Will it “count” here – in other words, does it (yet) have any scientific respectability? Should  blogs report new scientific results, or merely be reserved for commenting on such results which have been reported in the “proper scientific manner”? Will indeed this result appear in the future in the scientific literature under different authorship, but with no accreditation for this blog? If I do choose to “write it up properly” (assuming the journals now let me), can I cite this blog in the way one can cite the ACS conferences? I do not suppose many people know what the answers are to all these questions. Perhaps the appearance of this post might provide some?

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Posted in Hypervalency, Interesting chemistry | 3 Comments »