Christopher Maloney (“a brother blogger“) has commented recently on a herb from india which is known to contain a substance called Withaferin A which can be isolated from a plant named “winter cherry” or “ashwagandha“. Now this herb is thought to have some useful medical properties, I have looked and in the Cambridge data base an entry for this substance exists.
P. Bandhoria, V.K. Gupta, P. Kumar, N.K. Satti, P. Dutt and K.A. Suri, Anal. Sci. :X-Ray Struct. Anal. Online, 2006, 22, x89 is a paper which reports the strucutre of the compound.
The compound is a steroid which has an epoxide group and a lactone group in it. One paper suggests that the compound is an antiestrogen (E-R. Hahm, J. Lee, Y. Huang and S.V. Singh, Molecular Carcinogenesis, 2011, 50, pages 614 to 624). I have looked at the strucutre of the drug and here it is as a 2D drawing.
In real life the molecule has a 3D shape, I looked at it using my trusty copy of ORTEP. I have done a few POVray files for you good people to look at. For those of you at home who have copies of POVray I am tempted just to give the code, but for those of you who are not into POVray art here is the the picture.
While a spacefilling model is very useful to be able to hold in your hand and view, it has oftein hard to see the wood for the trees. For that reason we tend to use the ball and stick view of a molecule. Here is the ball and stick view of it.
It is interesting to note that back in 1968, A.T. McPhail and G.A. Sim published (J. Chem. Soc. B, page 962) a strcutre of the para-bromobenzoate / acetate ester of withaferin A. I think that the reason that the para-bromobenzoate was used was that it includes a heavy atom which is more easy to find in X-ray crystallography than a carbon, oxygen or hydrogen atom. The idea of the Patterson method is that you solve the crystal strcutre for the very heavy atom only at first and then during the refinement you can locate the carbons, oxygens and hydrogens using electron density maps. What happens is that the crystallographer looks at the difference in the electron densities obtained from the data with the predictions made from the locations of the atoms which have already been found. In this way new (lighter) atoms can be located which improves the quaility of the result.
Before cheap and powerful computers were avaiable to crystallographers the direct methods (which is more computationally intense) was less popular than it is today. Today crystallographers can use both dirrect and Patterson methods, but I know a lot of crystallographers still like to use the Patterson method when they have a heavy atom in a solid.
Well keep tuned, and if you find any interesting herbs then please tell me. I may be able to look them up to see what interesting chemicals they might contain.