In 1993-1994, when the Web (synonymous in most minds now with the Internet) was still young, the pace of progress was so rapid that some wag worked out that one “web-year” was like a dog-year, worth about 7 years of normal human time. So in this respect, 1994 is now some 133 web-years ago. Long enough for an archaeological excavation.
Posts Tagged ‘chemical’
The transient π-complex formed during the “[5,5]” sigmatropic rearrangement of protonated N,O-diphenyl hydroxylamine can be (formally) represented as below, namely the interaction of a six-π-electron aromatic ring (the phenoxide anion 2) with a four-π-electron phenyl dication-anion pair 1. Can one analyse this interaction in terms of aromaticity?
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).
It is not often that an article on the topic of illusion and deception makes it into a chemical journal. Such is addressed (DOI: 10.1002/anie.201102210) in no less an eminent journal than Angew Chemie. The illusion (or deception if you will) actually goes to the heart of how we represent three-dimensional molecules in two dimensions, and the meanings that may be subverted by doing so. A it happens, it is also a recurring theme of this particular blog, which is the need to present chemistry with data for all three dimensions fully intact (hence the Click for 3D captions which often appear profusely here).
If you visit this blog you will see a scientific discourse in action. One of the commentators there notes how they would like to access some data made available in a journal article via the (still quite rare) format of an interactive table, but they are not familiar with how to handle that kind of data (file). The topic in question deals with various kinds of (chemical) data, including crystallographic information, computational modelling, and spectroscopic parameters. It could potentially deal with much more. It is indeed difficult for any one chemist to be familiar with how data is handled in such diverse areas. So I thought I would put up a short tutorial/illustration in this post of how one might go about extracting and re-using data from this one particular source.
Unravelling reaction mechanisms is thought to be a 20th century phenomenon, coincident more or less with the development of electronic theories of chemistry. Hence electronic arrow pushing as a term. But here I argue that the true origin of this immensely powerful technique in chemistry goes back to the 19th century. In 1890, Henry Armstrong proposed what amounts to close to the modern mechanism for the process we now know as aromatic electrophilic substitution (10.1039/PL8900600095). Beyond doubt, he invented what is now known as the Wheland Intermediate (about 50 years before Wheland wrote about it, and hence I argue here it should really be called the Armstrong/Wheland intermediate). This is illustrated (in modern style) along the top row of the diagram.
The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it yourself. Even after 15 years of the (chemical) Web, this can be distressingly difficult to achieve (or can it be that it is only myself who wishes to view molecules in their native mode?). Thus the standard mechanism is to seek out on journal pages that disarming little entry entitled supporting information and to hope that you might find something useful embedded there. Embedded is the correct description, since the information is often found within the confines of an Acrobat file, and has to be extracted from there. Indeed, that is what I had to resort to in order to write one of the blog entries below. I ground my teeth whilst doing so.
So is there a better way? We think so! The digital repository. If you click on this you should see the entry directly. What can you do there? Well, if you have suitable programs, you can download eg a Checkpoint file of the calculation that created the molecule model and re-activate it there. Or you can download just the CML file for viewing in any CML-compliant program (such as e.g. Jmol). Or you can check up on the InCHi string or the InChI Key of the molecule.