Henry Rzepa's Blog Chemistry with a twist

September 17, 2010

Solid carbon dioxide: hexacoordinate carbon?

Carbon dioxide is much in the news, not least because its atmospheric concentration is on the increase. How to sequester it and save the planet is a hot topic. Here I ponder its solid state structure, as a hint to its possible reactivity, and hence perhaps for clues as to how it might be captured. The structure was determined (DOI 10.1103/PhysRevB.65.104103) as shown below.

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September 14, 2010

The oldest reaction mechanism: updated!

Unravelling reaction mechanisms is thought to be a 20th century phenomenon, coincident more or less with the development of electronic theories of chemistry. Hence electronic arrow pushing as a term. But here I argue that the true origin of this immensely powerful technique in chemistry goes back to the 19th century. In 1890, Henry Armstrong proposed what amounts to close to the modern mechanism for the process we now know as aromatic electrophilic substitution [1]. Beyond doubt, he invented what is now known as the Wheland Intermediate (about 50 years before Wheland wrote about it, and hence I argue here it should really be called the Armstrong/Wheland intermediate). This is illustrated (in modern style) along the top row of the diagram.

The mechanism of aromatic electrophilic substitution

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References

  1. "Proceedings of the Chemical Society, Vol. 6, No. 85", Proceedings of the Chemical Society (London), vol. 6, pp. 95, 1890. http://dx.doi.org/10.1039/PL8900600095

August 8, 2010

Reactions in supramolecular cavities – trapping a cyclobutadiene: ! or ?

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!

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July 24, 2010

Bio-renewable green polymers: Stereoinduction in poly(lactic acid)

Lactide 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!

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July 21, 2010

The weirdest bond of all? Laplacian isosurfaces for [1.1.1]Propellane.

In 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?

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July 15, 2010

Non-covalent interactions (NCI): revisiting Pirkle

Filed under: Interesting chemistry — Tags: , , — Henry Rzepa @ 8:50 am

NCI (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.

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July 11, 2010

Tunable bonds looked at in a different way

Filed under: Interesting chemistry — Tags: , , , — Henry Rzepa @ 9:31 am

The 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.

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July 6, 2010

Looking at bonds in a different way: the Laplacian.

The 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).

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July 3, 2010

Tunable bonds

Car 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.

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July 1, 2010

The mysteries of stereoinduction.

Stereo-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.

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