The properties of electrons are studied by both chemists and physicists. At the boundaries of these two disciplines, sometimes interesting differences in interpretation emerge. One of the most controversial is that due to Bader (for a recent review, see DOI: 10.1021/jp102748b) a physicist who brought the mathematical rigor of electronic topology to bear upon molecules. The title of his review is revealing: “Definition of Molecular Structure: By Choice or by Appeal to Observation?”. He argues that electron density is observable, and that what chemists call a bond should be defined by that observable (with the implication that chemists instead often resort to arbitrary choice). Here I explore one molecule which could be said to be the focus of the differences between physics and chemistry; cis-but-2-ene.
Posts Tagged ‘chemist’
Are close H…H contacts bonds?
Friday, October 7th, 2011Breakdowns in communication: the two cultures
Tuesday, August 2nd, 2011In his famous lecture in 1959, C. P. Snow wrote about the breakdown in communications between the “two cultures” of modern society — the sciences and the humanities (arts). That was then. This is now, and the occasion of my visit to a spectacular “city of arts and sciences complex” in Europe. An un-missable exhibit representing science and life was the 15m high model of DNA. Now to be fair this is styled an artist’s impression, and one presumes that an artist is allowed license. But how much license? And at how much expense to the science? And is there a counterbalance to the art where the science is fastidiously (but artistically) preserved?
Molecular illusions and deceptions. Ascending and Descending Penrose stairs.
Wednesday, June 15th, 2011It 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).
(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.
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.