Most visitors to London use the famous underground trains (the “tube”) or a double-decker bus to see the city (one can also use rivers and canals). So I thought, during the tourism month of August, I would show you an alternative overground circumnavigation of the city using the metaphor of benzene.
A tourist trip around London Overground with a chemical theme.
August 29th, 2015Mesomeric resonance in substituted benzenes: a crystallographic reality check.
August 26th, 2015Previously, I showed how conjugation in dienes and diaryls can be visualised by inspecting bond lengths as a function of torsions. Here is another illustration, this time of the mesomeric resonance on a benzene ring induced by an electron donating substituent (an amino group) or an electron withdrawing substituent (cyano).
A visualisation of the effects of conjugation; dienes and biaryls.
August 25th, 2015Here is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds?
A (light) introductory tutorial on Research Data Management (in chemistry).
August 20th, 2015Management of research (data) outputs is a hot topic in the UK at the moment, although the topic has been rumbling for five years or more. Most research-active higher educational establishments have or are about to publish general guidelines, which predominantly take the form of aspirational targets rather than actionable examples or use-cases.‡ Because the concepts remain somewhat abstract, one can encounter questions from researchers such as “how should I go about achieving such RDM (research data management)?” I thought it might be useful for me to here summarise some key features in the form of an FAQ that can help answer that question. I will concentrate purely on the sub-set chemistry about which I know most.
The chemical Web at 22 and where it might go.
August 19th, 2015This post is prompted by the appearance of a retrospective special issue of C&E news, with what appears to be its very own Website: internet.cenmag.org. It contains articles and interviews with many interesting people, along with several variations on the historical (albeit rather USA-centric) perspectives and a time-line covers many of the key innovations (again, from a USA-perspective). Some subjects are covered in greater depth, including computational chemistry. The periodic table too gets coverage, but surprisingly that is not of Mark Winter’s WebElements, which carries the impressive 1993-2015 continuous timeline (hence 22 in the title!).
Intermolecular atom-atom bonds in crystals? The O…O case.
July 25th, 2015I recently followed this bloggers trail; link1 → link2 to arrive at this delightful short commentary on atom-atom bonds in crystals[cite]10.1107/S2052252515002006[/cite] by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis,[cite]10.1021/ja02261a002[/cite] we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack's article: "The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions" I thought I might explore this point a bit further in this post.
The structure of naphthalene: 1890-1925, and a modern twist.
July 18th, 2015This is a little historical essay into the electronic structure of naphthalene, presented as key dates (and also collects comments made which were appended to other posts).
Reproducibility in science: calculated kinetic isotope effects for cyclopropyl carbinyl radical.
July 11th, 2015Previously on the kinetic isotope effects for the Baeyer-Villiger reaction, I was discussing whether a realistic computed model could be constructed for the mechanism. The measured KIE or kinetic isotope effects (along with the approximate rate of the reaction) were to be our reality check. I had used ΔΔG energy differences and then HRR (harmonic rate ratios) to compute[cite]10.5281/zenodo.19272[/cite] the KIE, and Dan Singleton asked if I had included heavy atom tunnelling corrections in the calculation, which I had not. His group has shown these are not negligible for low-barrier reactions such as ring opening of cyclopropyl carbinyl radical.[cite]10.1021/ja1055593[/cite] As a prelude to configuring his suggested programs for computing tunnelling (GAUSSRATE and POLYRATE), it was important I learnt how to reproduce his KIE values.[cite]10.1021/ja1055593[/cite] Hence the title of this post. Now, read on.