Cavities promote reactions, and they can also trap the products of reactions. Such (supramolecular) chemistry is used to provide models for how enzymes work, but it also allows un-natural reactions to be undertaken. A famous example is the preparation of P4 (see blog post here), an otherwise highly reactive species which, when trapped in the cavity is now sufficiently protected from the ravages of oxygen for its X-ray structure to be determined. A colleague recently alerted me to a just-published article by Legrand, van der Lee and Barboiu (DOI: 10.1126/science.1188002) who report the use of cavities to trap and stabilize the notoriously (self)reactive 1,3-dimethylcyclobutadiene (3/4 in the scheme below). Again sequestration by the host allowed an x-ray determination of the captured species!
Bio-renewable green polymers: Stereoinduction in poly(lactic acid)
July 24th, 2010Lactide is a small molecule made from lactic acid, which is itself available in large quantities by harvesting plants rather than drilling for oil. Lactide can be turned into polymers with remarkable properties, which in turn degrade down easily back to lactic acid. A perfect bio-renewable material!
The weirdest bond of all? Laplacian isosurfaces for [1.1.1]Propellane.
July 21st, 2010In this post, I will take a look at what must be the most extraordinary small molecule ever made (especially given that it is merely a hydrocarbon). Its peculiarity is the region indicated by the dashed line below. Is it a bond? If so, what kind, given that it would exist sandwiched between two inverted carbon atoms?
Non-covalent interactions (NCI): revisiting Pirkle
July 15th, 2010NCI (non-covalent interactions) is the name of a fascinating new technique for identifying exactly these. Published recently by Johnson, Keinan, Mori-Snchez, Contreras-Garca, Cohen and Yang, it came to my attention at a conference to celebrate the 20th birthday of ELF when Julia Contreras-Garcia talked about the procedure. It is one of those methods which may seem as if it merely teases out the obvious about a molecule, but it is surprising how difficult seeing the obvious can be sometimes. I have blogged about this previously, in discussing the so-called Pirkle reagent. On that occasion, I used the QTAIM technique to identify so-called critical points in the electron density. NCI goes one stage further in identifying surfaces of interaction rather than just single points, the idea being that this focuses attention on regions in molecules which are primarily responsible for binding, stereoselection and other aspects of molecular selectivity.
Tunable bonds looked at in a different way
July 11th, 2010The title of this post merges those of the two previous ones. The tunable C-Cl bond brought about in the molecule tris(amino)chloromethane by anomeric effects will be probed using the Laplacian of the electronic density.
Looking at bonds in a different way: the Laplacian.
July 6th, 2010The Cheshire cat in Alice’s Adventures in Wonderland comes and goes at will, and engages Alice with baffling philosophical points. Chemical bonds are a bit like that too. In the previous post, we saw how (some) bonds can be tuned to be strong or weak simply by how a lone pair of electrons elsewhere in the molecule is oriented with respect to the bond. Here I explore another way of looking at bonds. To start, we must introduce a quantity known as ∇2ρ(r), henceforth termed the Laplacian of the electron density ρ(r).
Tunable bonds
July 3rd, 2010Car transmissions come in two types, ones with fixed ratio gears, and ones which are continuously variable. When it comes to chemical bonds, we tend to think of them as being very much of the first type. Bonds come in fixed ratios; single, aromatic, double, triple, etc. OK, they do vary, but the variations are assumed as small perturbations on the basic form. Take for example the molecule shown below. The bonds as shown are all clearly single (the wedge and hashed bond are merely stereochemical notations). No-one would really think of drawing this molecule in any other way, and this idea of the transferability of bonds between molecules (all double bonds react in specific ways which are different from single bonds, and they also have characteristic spectroscopic properties, etc) is what allows molecules to be classified.
The mysteries of stereoinduction.
July 1st, 2010Stereo-induction is, lets face it, a subtle phenomenon. The ratio of two stereoisomers formed in a reaction can be detected very accurately by experiment, and when converted to a free energy difference using ΔG = -RT Ln K, this can amount to quite a small value (between 0.5 – 1.5 kcal/mol). Can modelling reproduce effects originating from such small energy differences? Well one system that has been argued about now for several decades is shown below as 1.
Chemistry with a super-twist: A molecular trefoil knot, part 2.
June 1st, 2010A conjugated, (apparently) aromatic molecular trefoil might be expected to have some unusual, if not extreme properties. Here some of these are explored. Read the rest of this entry »