Continuing our discussion on whether a chemical strucure diagram is copyrightable.
PMR: “With regard to ring B, the wedges here are actually NOT how it has to be. Note that the carbons of ring B are not stereocenters. ” I don’t know whether this is true or not. Looking at the 3D structure it seems to me that there are two isomers (not conformers) where TS’s wedges show one. It may, however, be that the ring is sufficiently flexible that they interconvert rapidly enough not to be isomers.
More generally, however, there are many reasons why structural diagrams are essential. The diagram above is numbered. The numbers are essential to understand much of the data (spectral assignments, reactivity, etc.) They cannot be held in SMILES, or InChI or, indeed, in anything in common use other than CML (which has support for many sorts of annotation). Neither InChIs nor SMILES are any use for most organometallic compounds, polymers, intermolecules compounds, supermolecules, nanotubes, polymer beads, etc. Many of these things don’t have useful 3D coordinates – we are working on polymers and have developed Polymer Markup Language – and we can generate 3D coordinates very nicely, but not many others can.
So I contend that for much of chemistry diagrams are the only method of primary communication. It’s actually part of the problem of involving machines. How do we get these things into a formal system without losing information.
That’s hard enough without the publishers’ lawyers suing us.
September 24th, 2007 at 9:27 pm ePeter,
I have to take exception to some of your claims. The chemical formula drawing is not the only way of communicating the compound. In fact there are really much better ways of doing this, though not necessarily the best for a human to readily read. The InChI or smiles or 3-D coordinates really capture more information in a more reusable and less likely to be error-ridden way (especially the 3-D coordinates). The chemical formula drawing is not even unique, as we have seen in your examples.
Furthermore, Totally Synthetic had many arbitrary decisions to make in how to represent the structure. I have modified this structure in a few simple ways to make this point:
Note that I have changed the orientation of the terminal isopropyl/OH groups and the way the amide connects to ring A. With regard to ring B, the wedges here are actually NOT how it has to be. Note that the carbons of ring B are not stereocenters. The structure is drawn to try to indicate that ring B sort of π-stacks above ring E. This may or may not be true. Furthermore, the oxygen of the ring could in fact be pointing backwards. In my representation, I decided not to indicate any of this 3-D relationship.
Now I am not claiming that my structure is better than the original. My claim, however, is that Totally Synthetic made some creative decisions in making this presentation, and thus it should be protected.