This story starts with a calixarene, a molecule (suitably adorned with substituents) frequently used as a host to entrap a guest and perchance make the guest do something interesting. Such a calixarene was at the heart of a recent story where an attempt was made to induce it to capture cyclobutadiene in its cavity.
Archive for the ‘Interesting chemistry’ Category
A comparison of left and right handed DNA double-helix models.
Saturday, January 1st, 2011When Watson and Crick (WC) constructed their famous 3D model for DNA, they had to decide whether to make the double helix left or right handed. They chose a right-handed turn, on the grounds that their attempts at left-handed models all “violated permissible van der Waals contacts“. No details of what these might have been were given in their original full article (or the particular base-pairs which led to the observation). This follow-up to my earlier post explores this aspect, using a computer model.
Do marauding electrons go in packs?
Monday, December 27th, 2010Is there a preferred pack size for electrons on the move? Or put less flamboyantly, is there an optimum, and a maximum number of arrows (electron pairs) that one might push in revealing the mechanism of a concerted reaction? A sort of village-instinct for electrons. Consider the following (known, DOI: 10.1016/S0040-4039(00)98289-3) reaction
(re)Use of data from chemical journals.
Wednesday, December 22nd, 2010If 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.
Following one’s nose: a quadruple bond to carbon. Surely I must be joking!
Thursday, December 16th, 2010Do you fancy a story going from simplicity to complexity, if not absurdity, in three easy steps? Read on! The following problem appears in one of our (past) examination questions in introductory organic chemistry. From relatively mundane beginnings, one can rapidly find oneself in very unexpected territory.
Janus mechanisms (the past and the future): Reactions of the diazonium cation.
Saturday, December 11th, 2010Janus was the mythological Roman god depicted as having two heads facing opposite directions, looking simultaneously into the past and the future. Some of the most ancient (i.e. 19th century) known reactions can be considered part of a chemical mythology; perhaps it is time for a Janus-like look into their future.
(anti)aromaticity avoided: a tutorial example
Tuesday, December 7th, 2010More inspiration from tutorials. In a lecture on organic aromaticity, the 4n+2/4n Hückel rule was introduced (in fact, neither rule appears to have actually been coined in this form by Hückel himself!). The simplest examples are respectively the cyclopropenyl cation and anion. The former has 2 π-electrons exhibiting cyclic delocalisation, and the 4n+2 (n=0) rule predicts aromaticity. Accordingly, all three C-C distances are the same (1.363Å).
Morphing an arrow-pushing tutorial into a dihydrogen bond
Thursday, December 2nd, 2010My university tutorial yesterday covered selective reductions of functional groups in organic chemistry. My thoughts on that topic have now morphed into something rather different. Scientific research has a habit of having this sort of thing happen.
Anatomy of an arrow-pushing tutorial: reducing a carboxylic acid.
Wednesday, December 1st, 2010Arrow pushing (why never pulling?) is a technique learnt by all students of organic chemistry (inorganic chemistry seems exempt!). The rules are easily learnt (supposedly) and it can be used across a broad spectrum of mechanism. But, as one both becomes more experienced, and in time teaches the techniques oneself as a tutor, its subtle and nuanced character starts to dawn. An example of such a mechanism is illustrated below, and in this post I attempt to tease out some of these nuances.