Spectral Full House

So, all of the isomers of C4H11O are in NMRShiftDB and here are all the experimental and predicted carbon spectra:

It's not obvious from this picture, but not all of the predicted spectra are unique matches for their experimental partners. In other words, you could not pick out the right molecule by comparing the predicted and experimental spectra.

The situation is more difficult still for larger isomer spaces, where the predicted spectra may be exactly the same for sub-sets of the isomers. There are still many with unique predictions, but the rest follow a sort of power-law distribution of spectral-equivalent sets.

EDIT: As per a suggestion by egon, here is a table of top hits (a yellow square indicates the top match):


Nice example.

1. Now, the next step is to express the proper similarity of the predicted versus experimental spectrum. A 7x7 matrix. If you color the cells of that matrix by similarity, you should immediately see a trace on on the diagonal (if matches are properly found). You'll notice that not every similarity measure is equally sensitive for this data. (Check bc_seneca for my suggested measure :)

2. I also would like to see if it works out nicely for the oxygens... since these are much more alike, I expect two group: hydroxyl and ether, but am interested in seeing the results for that too... just out of curiosity...
cic said…
Very nice indeed.
It will be interesting to see how this does statistically develop over a larger number of test sets. Since we have already demonstrated that a-pinene can be found in a C10H16 chemical space, it is not safe to assume that the number of degenerate cases grows in some clear way with the number of atoms in the molecular formular.
CIC, what information was used for that, only 1D 13C data, and what 13NMR prediction software?

Christoph's SENECA code can easily find a-pinene too, particularly when hydrogen count info for the carbons is included (DEPT experiment).

CIC, I noted that your blog is empty? Do you have yet to start blogging? And, at which university is your fachgruppe? CIC, as in the former Gasteiger group?
Gilleain, the matrix is interesting. You mentioned as there are a few clearly off-diagonal hits. Which similarity measure did you use there? Can you please try the WCC too? Source code can be found in the Bioclipse1 repository.
gilleain said…
Hei Egon,

I used the simplest possible similarity measure, which is the sum of the differences between pairs of equivalent peaks, where equivalence is based on respective order in the peak lists.

I don't know what the WCC code is weighting by, I should look at it again (and get Mark to translate the code comments, some of which are in Dutch :)