Author Archive
Wednesday, December 29th, 2010
Science is about making connections. Plenty are on show in Watson and Crick’s famous 1953 article on the structure of DNA[1] 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!).
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References
- J.D. WATSON, and F.H.C. CRICK, "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid", Nature, vol. 171, pp. 737-738, 1953. https://doi.org/10.1038/171737a0
Tags:Bijvoet, chemist, chiroptical, d(CGCG), Derek Barton, dispersion forces, DNA duplex, Historical, Marcus du Sautoy, Note, Odile Crick, professional artist, Tartaric Acid, van der Waals, watoc11, Watson Crick, Web sense, Z-DNA
Posted in Interesting chemistry | 8 Comments »
Friday, December 24th, 2010
If 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).
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Tags:3D graphics, Apple, GPU, HTML5, iPad, Java, JavaScript, OpenGL library, SVG, typical target device, Web browser, Web-based graphics libraries, WebGL
Posted in Chemical IT | 3 Comments »
Wednesday, December 22nd, 2010
If 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.
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Tags:chemical, chemical journals, chemist, opendata, RDF, semantic web, software tools, suitable processing programs, XML
Posted in Chemical IT, Interesting chemistry | 7 Comments »
Sunday, December 19th, 2010
Chemistry gets complex very rapidly. Consider the formula CH3NO as the topic for a tutorial in introductory chemistry. I challenge my group (of about 8 students) to draw as many different molecules as they can using exactly those atoms. I imply that perhaps each of them might find a different structure; this normally brings disbelieving expressions to their faces.
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Tags:/RT, anomeric effects, arrow pushing, configurational isomer, conformational somer, double bond equivalent, electron octet, entwined systems, free energy barrier, Jan Jensen, optical isomerism, pericyclic reaction, resonance isomer, stereochemical, stereoelectronic, tautomers
Posted in General | No Comments »
Thursday, December 16th, 2010
Do 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.
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Tags:Henry Rzepa, Jahn-Teller, pence, TfO, tutor
Posted in Hypervalency, Interesting chemistry | 19 Comments »
Saturday, December 11th, 2010
Janus 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.
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Tags:activation free energy, benzonitrile product, chemical mythology, coloured solutions, cyano, diazo, diazonium, free energy, Henry Rzepa, Historical, Ion-Pair Mechanisms, L. A., nitrogen gas
Posted in Interesting chemistry | 3 Comments »
Tuesday, December 7th, 2010
More 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).
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Tags:energy, free energy, Huckel, Interesting chemistry, Pretty straight forward, Tutorial material
Posted in Interesting chemistry | 12 Comments »
Tuesday, December 7th, 2010
Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say ChemDraw) and the Word processor used to place them into a context (say Microsoft office), via an intermediate storage area known as the clipboard. The round trip between the Macintosh (OS X) versions of these programs had been broken a little while, but it is now fixed! A small victory. This blog reports what happened when such a Mac-created Word document is sent to someone using Microsoft Windows as an OS (or vice versa).
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Tags:Android, cellular telephone, chemical, chemical information, Chemical IT, content carrier, HTML, iPad, JPEG, Mac OS X, Macintosh, Microsoft, Microsoft Windows, opendata, operating systems, search engines, Web browser, word processor, XML
Posted in Chemical IT | No Comments »