Posts Tagged ‘spin-off’

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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The conformation of 1,2-difluoroethane

Tuesday, April 6th, 2010

Here I offer another spin-off from writing a lecture course on conformational analysis. This is the famous example of why 1,2-difluoroethane adopts a gauche rather than antiperiplanar conformation.

The gauche and antiperiplanar conformations of 1,2-difluoroethane

One major contribution to the greater stability of the gauche is the stereoelectronic interactions, and this is best probed using the NBO (Natural Bond Orbital) approach of Weinhold (DOI: 10.1021/ja00501a009). The process is approximately described as first reducing the wavefunction down to a set of orbitals which have been localized (using appropriate algorithms) down to two or one centres (corresponding to two-centre covalent bonds, or one-centre electron lone pairs). Perturbation theory is then used to evaluate the interaction energy between any filled and any empty combination. For the molecule above, six such combinations are inspected, involving any one of the six filled C-H or C-F σ-orbitals, and the best-overlapping σ* orbital which turns out to be located on the C-H or C-F bond anti-periplanar to the filled orbital.

Filled C-H NBO orbital. Click for 3D to superimpose empty C-F anti bonding orbital.

Empty C-F antibonding NBO orbital. Click for 3D

A filled C-H orbital is shown above on the left, accompanied by an empty C-F σ* orbital on the right which is anti-periplanar to the first. This alignment allows the phases of the two orbitals to overlap maximally (blue-blue on the top, red-red beneath).

The interaction energy between this pair is determined not only by the efficacy of the overlap, but by the energy gap between the two. The smaller the gap, the better the interaction energy (referred to as E2, in kcal/mol). For the gauche conformation, the six pairs of orbitals have the following interaction energies; two σC-H/σ*C-F interactions (illustrated above), 4.9; two σC-H/σ*C-H 2.6 and two σC-F/σ*C-H 0.8 kcal/mol. For the anti-periplanar conformation, the terms are four σC-H/σ*C-H 2.5 and two σC-F/σ*C-F 1.8 kcal/mol. The two totals (16.6 vs 13.6) indicate that gauche is stabilized more by such interactions.

There is of course a bit more to this story, but I have documented the above here, since I can include an explicit (and rotatable) illustration of the orbitals involved (which  I have not seen elsewhere). If you want a recipe for generating these orbitals, go here.

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Posted in Interesting chemistry | 14 Comments »