To (mis)quote Oscar Wilde again, ““To lose one methyl group may be regarded as a misfortune; to lose both looks like carelessness.” Here, I refer to the (past) tendency of molecular modellers to simplify molecular structures. Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset by lost groups. One of my early efforts (DOI: 10.1021/ja00465a005) was selected for study because it had nothing left to lose; the mass spectrometric fragmentation of the radical cations of methane and ethane. Methyl, phenyl and other “large” groups were routinely replaced by hydrogen in order to enable the study. Cations indeed were always of interest to modellers; the relative lack of electrons almost always meant unusual or interesting structures and reactions (including this controversial species, DOI: 10.1021/ja00444a012). Inured to such functional loss, we modellers forgot that (unless in a mass spectrometer), cations have to have a counter anion. Here I explore one example of the model being complete(d).
Archive for the ‘Interesting chemistry’ Category
The importance of being complete.
Monday, September 26th, 2011Molecular Matryoshka dolls
Tuesday, September 20th, 2011A Matryoshka doll is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here for a good candidate for making a three-layered example (the inside layer is C60, which itself might encapsulate a small molecule. See also DOI: 10.1021/ja991747w). These molecular dolls can be created out of quite simple molecules. Here I explore just one, and focus on what is happening inside!
Some fun with no-go areas of chemistry: cyclobutadiene.
Sunday, September 18th, 2011Organic chemistry has some no-go areas, where few molecules dare venture. One of them is described by a concept known as anti-aromaticity. Whereas aromatic molecules are favoured species, their anti-equivalent is avoided. I previously illustrated this (Hückel rule) with cyclopropenium anion. Now I take a look at cyclobutadiene, for which the π-system is said to be iso-electronic (where two electrons in a double bond have replaced the carbanion lone pair).
A stable borylene. An exercise in lateral thinking.
Sunday, August 7th, 2011I have often heard the question posed “how much of chemistry has been discovered?” Another might be “has most of chemistry, like low-hanging fruit, already been picked?“. Well, time and time again, one comes across examples which are only a simple diagram or so away from what might be found in any introductory chemistry text, and which would tend to indicate the answers to these questions is a resounding no. Take for example the three reactions shown below.
Extreme chemical intimacy: the Xe2@C60 ion-pair.
Wednesday, August 3rd, 2011Unusual bonds are always intriguing, and the Xe-Xe bond is no exception. It was first reported (10.1002/anie.199702731) for the species Xe2+. Sb4F21– and its length (3.09Å) was claimed as “unsurpassed in length in main group chemistry by any other element -element bond”. Krapp and Frenking then creatively tweaked the bond (in a computer). The counterion was replaced by C60, and the two xenon atoms placed inside! Buckyballs have a fascinating ability to absorb electrons, up to six in fact, from whatever is placed inside the cavity, and so this assembly acts as a rather intriguing ion-pair. So the issue reduces to how many electrons does C60 manage to scavenge from two Xenon atoms, and what is the nature of any resulting bonding formed between these two atoms?
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).
The stereochemistry of [8+2] pericyclic cycloadditions.
Sunday, July 10th, 2011Steve Bachrach has blogged on the reaction shown below. If it were a pericyclic cycloaddition, both new bonds would form simultaneously, as shown with the indicated arrow pushing. Ten electrons would be involved, and in theory, the transition state would have 4n+2 aromaticity. In fact Fernandez, Sierra and Torres have reported that they can trap an intermediate zwitterion 2, and in this sense therefore, the reaction is not pericyclic but nucleophilic addition from the imine lone pair to the carbonyl of the ketene (it finds the half way stage convivial). But this got me thinking. Does this reaction have any pericyclic character at all? And if so, could it be enhanced by design?
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).