Science is about making connections. Plenty are on show in Watson and Crick’s famous 1953 article on the structure of DNA[cite]10.1038/171737a0[/cite] but often with the tersest of explanations. Take for example their statement “Both chains follow right-handed helices“. Where did that come from? This post will explore the subtle implications of that remark (and how in one aspect they did not quite get it right!).
Archive for the ‘Interesting chemistry’ Category
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.
Gravitational fields and asymmetric synthesis
Saturday, November 20th, 2010Our understanding of science mostly advances in small incremental and nuanced steps (which can nevertheless be controversial) but sometimes the steps can be much larger jumps into the unknown, and hence potentially more controversial as well. More accurately, it might be e.g. relatively unexplored territory for say a chemist, but more familiar stomping ground for say a physicist. Take the area of asymmetric synthesis, which synthetic chemists would like to feel they understand. But combine this with gravity, which is outside of their normal comfort zone, albeit one we presume is understood by physicists. Around 1980, one chemist took such a large jump by combining the two, in an article spectacularly entitled Asymmetric synthesis in a confined vortex; Gravitational fields and asymmetric synthesis[cite]10.1021/ja00521a067[/cite]. The experiment was actually quite simple. Isophorone (a molecule with a plane of symmetry and hence achiral) was treated with hydrogen peroxide and the optical rotation measured.
Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?
Friday, November 19th, 2010On 8th August this year, I posted on a fascinating article that had just appeared in Science[cite]10.1126/science.1188002[/cite] in which the crystal structure was reported of two small molecules, 1,3-dimethyl cyclobutadiene and carbon dioxide, entrapped together inside a calixarene cavity. Other journals (e.g. Nature Chemistry[cite]10.1038/nchem.823[/cite] ran the article as a research highlight (where the purpose is not a critical analysis but more of an alerting service). A colleague, David Scheschkewitz, pointed me to the article. We both independently analyzed different aspects, and first David, and then I then submitted separate articles for publication describing what we had found. Science today published both David’s thoughts[cite]10.1126/science.1195752[/cite] and also those of another independent group, Igor Alabugin and colleagues[cite]10.1126/science.1196188[/cite]. The original authors have in turn responded [cite]10.1126/science.1195846[/cite]. My own article on the topic will appear very shortly[cite]10.1039/C0CC04023A[/cite]. You can see quite a hornet’s nest has been stirred up!