A scalemic molecule is the term used by Eliel to describe any non-racemic chiral compound. Synthetic chemists imply it when they describe a synthetic product with an observable enantiomeric excess or ee (which can range from close to 0% to almost 100%). There are two cheminformatics questions of interest to me: (more…)
Archive for the ‘Chemical IT’ Category
Scalemic molecules: a cheminformatics challenge!
Wednesday, July 6th, 2011Molecular 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).
Hafnium and Niels Bohr
Sunday, June 5th, 2011In 1923, Coster and von Hevesy[cite]10.1038/111079a0[/cite] claimed discovery of the element Hafnium, atomic number 72 (latin Hafnia, meaning Copenhagen, where the authors worked) on the basis of six lines in its X-ray spectrum. The debate had long raged as to whether (undiscovered) element 72 belonged to the rare-earth group 3 of the periodic table below yttrium, or whether it should be placed in group 4 below zirconium. Establishing its chemical properties finally placed it in group 4. Why is this apparently arcane and obscure re-assignment historically significant? Because, in June 1922, in Göttingen, Niels Bohr had given a famous series of lectures now known as the Bohr Festspiele on the topic of his electron shell theory of the atom. Prior to giving these lectures he had submitted his collected thoughts in January 1922[cite]10.1007/BF01326955[/cite].
Blogs, Twitter, Wikis and other on-line tools: the movie!
Friday, May 27th, 2011Libraries (and librarians) are evolving rapidly. Thus a week or so ago one of our dynamic librarians here, approached some PhD students and academics to ask them how they used “Web 2.0” (thanks Jenny!). The result was edited (thanks John!) and uploaded, where you can see it below (embedded in this post, I might add, using HTML5). No doubt there is more of this genre to come. Libraries nowadays it seems, are not just about books and journals, but about the full digital experience (not to mention sustenance; ours is now one of the more popular places for students to eat!).
Chemicalizing a blog.
Wednesday, March 30th, 2011I am at the ACS meeting, attending a session on chemistry and the Internet. This post was inspired by Chemicalize, a service offered by ChemAxon, which scans a post like this one, and identifies molecules named. I had previously used generic post taggers, which frankly did not work well in identifying chemical content. So this is by way of an experiment. I list below some of the substances about which I have blogged, to see how the chemicalizer works. (more…)
Embedding molecules in blogs: ChemDoodle, WebGL and SVG
Friday, December 24th, 2010If you get a small rotatable molecule below, then ChemDoodle/HTML5/WebGL is working. Why might this be important? Well, the future is mobile, in other words, devices that rely on batteries or other sources of built-in power. This means the power guzzling GPU cards of the past (some reach ~400 Watts!) cannot be used. Rather than using e.g. a full power OpenGL library, one will use Web-based graphics libraries, which (to quote Wikipedia) extends the capability of the JavaScript programming language to allow it to generate interactive 3D graphics within any compatible web browser. A typical target device might be for example Apple’s iPad (for which the redoubtable Jmol, which is based on Java, is unlikely to ever work).
(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.
Data-round-tripping: moving chemical data around.
Saturday, November 20th, 2010For those of us who were around in 1985, an important chemical IT innovation occurred. We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the clipboard, paste it into a word processor (it was called a Macintosh). Perchance even print the result on a laserprinter. Most students of the present age have no idea what we used to do before this innovation! Perhaps not in 1985, but at some stage shortly thereafter, and in effect without most people noticing, the return journey also started working, the so-called round trip. It seemed natural that a chemical structure diagram subjected to this treatment could still be chemically edited, and that it could make the round trip repeatedly. Little did we realise how fragile this round trip might be. Years later, the computer and its clipboard, the chemistry software, and the word processor had all moved on many generations (it is important to flag that three different vendors were involved, all using proprietary formats to weave their magic). And (on a Mac at least) the round-tripping no longer worked. Upon its return to (Chemdraw in this instance), it had been rendered inert, un-editable, and devoid of semantic meaning unless a human intervened. By the way, this process of data-loss is easily demonstrated even on this blog. The chemical diagrams you see here are similarly devoid of data, being merely bit-mapped JPG images. Which is why, on many of these posts, I put in the caption Click for 3D, which gives you access to the chemical data proper (in CML or other formats). And I throw in a digital repository identifier for good measure should you want a full dataset.