Bonds are a good example of something all chemists think they can recognise when they see them. But they are also remarkably dependent on context. We are running a molecular modelling course at the moment, and I found myself explaining to someone how very context-sensitive they can be. I thought it might be useful to collect my thoughts here. (more…)
Archive for the ‘Chemical IT’ Category
Bonds.
Thursday, October 13th, 2011Steve Jobs and chemistry: a personal recollection.
Sunday, October 9th, 2011Steve Jobs death on October 5th 2011 was followed by a remarkable number of tributes and reflections on the impact the company he founded has had on the world. Many of these tributes summarise the effect as a visionary disruption. Here I describe from my own perspective some of the disruptions to chemistry I experienced (for another commentary, see here).
Hunt the charge: the Cheshire cat of chemistry
Thursday, September 29th, 2011Charges in chemistry, like the grin on Lewis Carroll’s cat, can be mysterious creatures. Take for example the following structure, reported by Paul Lickiss and co-workers (DOI: 10.1039/b513203g).
Computers 1967-2011: a personal perspective. Part 3. 1990-1994.
Tuesday, July 12th, 2011In 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).
Computers 1967-2011: a personal perspective. Part 1. 1967-1985.
Thursday, July 7th, 2011Computers and I go back a while (44 years to be precise), and it struck me (with some horror) that I have been around them for ~62% of the modern computing era (Babbage notwithstanding, ~1940 is normally taken as the start of the modern computing era). So indulge me whilst I record this perspective from the viewpoint of the computers I have used over this 62% of the computing era. (more…)
Scalemic molecules: a cheminformatics challenge!
Wednesday, July 6th, 2011A 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…)
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).
Hafnium and Niels Bohr
Sunday, June 5th, 2011In 1923, Coster and von Hevesy[1] 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[2].
References
- D. COSTER, and G. HEVESY, "On the Missing Element of Atomic Number 72", Nature, vol. 111, pp. 79-79, 1923. https://doi.org/10.1038/111079a0
- N. Bohr, "Der Bau der Atome und die physikalischen und chemischen Eigenschaften der Elemente", Zeitschrift f�r Physik, vol. 9, pp. 1-67, 1922. https://doi.org/10.1007/bf01326955
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!).