Skip to main content

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):
Labels:

Comments

Egon Willighagen said…
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...
30 January 2009 at 09:55
Unknown 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.
30 January 2009 at 22:42
Egon Willighagen said…
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?
31 January 2009 at 13:14
Egon Willighagen said…
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.
31 January 2009 at 13:15
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 :)
31 January 2009 at 17:05
Post a Comment

Popular posts from this blog

Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin
2 comments
Read more

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the
2 comments
Read more

General Graph Layout : Putting the Parts Together

An essential tool for graph generation is surely the ability to draw graphs. There are, of course, many methods for doing so along with many implementations of them. This post describes one more (or perhaps an existing method - I haven't checked). Firstly, lets divide a graph up into two parts; a) the blocks, also known as ' biconnected components ', and b) trees connecting those blocks. This is illustrated in the following set of examples on 6 vertices: Trees are circled in green, and blocks in red; the vertices in the overlap between two circles are articulation points. Since all trees are planar, a graph need only have planar blocks to be planar overall. The layout then just needs to do a tree layout  on the tree bits and some other layout on the embedding of the blocks. One slight wrinkle is shown by the last example in the image above. There are three parts - two blocks and a tree - just like the one to its left, but sharing a single articulation point. I had
2 comments
Read more