In 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 3. 1990-1994.
July 12th, 2011The stereochemistry of [8+2] pericyclic cycloadditions.
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?
Computers 1967-2011: a personal perspective. Part 1. 1967-1985.
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. Read the rest of this entry »
Scalemic molecules: a cheminformatics challenge!
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: Read the rest of this entry »
Hexavalent carbon revisited (and undecavalent boron thrown in).
June 26th, 2011A little while ago, I speculated (blogs are good for that sort of thing) about hexavalent carbon, and noted how one often needs to make (retrospectively) obvious connections between two different areas of chemistry. That post has attracted a number of comments in the two years its been up, along the lines: what about carboranes? So here I have decided to explore that portal into boron chemistry. The starting point is the reported crystal structure of a molecule containing a CH12B11– anion (DOI: 10.1021/ja00201a073). This differs from the molecule I previously reported in having not so much 5C-C + 1C-H bonds around a single carbon, but instead 5B-C + 1C-H bonds. The basic cluster is much in fashion (as B12Cl122-) for its properties as a non-coordinating counterion.
Molecular illusions and deceptions. Ascending and Descending Penrose stairs.
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).
Buses (and dyotropic rearrangements) always come in threes.
June 12th, 2011The last two posts have played a game of find the electrons. We saw how the dyotropic rearrangement of ethane borrowed electrons from the C-C bond, and how 1,2,dibromoethane went ionic on us. How about this mixed system, in which a hydrogen and a BH2 swap their positions?
More is more: the dyotropic rearrangement of 1,2-dibromoethane.
June 12th, 2011In the previous post, I discussed what we could learn from ethane by forcing it into a pericyclic dyotropic rearrangement. We saw how it voraciously scavenged two electrons from the C-C bond to achieve this. What if we give it more electrons? Thus 1,2-dibromoethane undergoing the same reaction.
Less is more: the dyotropic rearrangement of ethane
June 11th, 2011In a time when large (molecules) are considered beautiful (or the corollary that beauty must be big), it is good to reflect that small molecules may teach us something as well. Take ethane. Is there anything left which has not been said about it already? Well, consider the reaction below, in which two hydrogen atoms mutually hop from one carbon to the other.