I am currently refactoring Nick Day’s code that has supported “NMREye” – the collection of Open experiments and Data that he has generated as part of his thesis and have been trailed on this blog ( View post). One intention of this – which got lost in some of the other discussion is to be able to see whether published results are “correct”. This is, of course, not new to us – students here developed the OSCAR toolkit for checking experimental data (View post). The NMREye work suggest that it should be possible to validate the actual 13C NMR values reported in a scientific experiment.
Nick will take it as a compliment that I am refactoring his code. It was written on a very strict timescale – he had to write the code, collect and analyse the results in little more than a month. And his work has a wider applicability within our group. So I am trying to design a library system that supports his ideas while being generally re-usable. And this has very useful consequences for CML – the main question as always is “does CML support enough chemistry in a simple fashion and can it be coded?”. As an example here’s an example of data from a thesis we are analyzing in the SPECTRaT project:
13C (150 MHz) d 138.4 (Ar-ipso-C), 136.7 (C-2), 136.1 (C-1), 128.3, 127.6, 127.5 (Ar‑ortho-C, Ar-meta-C, Ar-para-C), 87.2 (C-3), 80.1 (C-4), 72.1 (OCH2Ph), 69.7 (CH2OBn), 58.0 (C-5), 26.7 (C-6), 20.9 ((CH3)AC-6), 17.9 ((CH3)BC-6), 11.3 (CH3C‑2), 0.5 (Si(CH3)3).
(the “d” is a delta but I think everything has been faithfully copied from the Word document. Note that OSCAR can :
- understand that this is a 13C spectrum
- extract the frequency
- identify the peak values (shiofts) and identify the comments
Try to think how you would explain this to a robot and what additional information you would need. Indeed try to explain this to a non-chemist – it’s a useful exercise.
What OSCAR and the other tools cannot do yet is:
- extract the solvent (this is mentioned elsewhere in the thesis)
- understand the comments
- manage the framework symmetry group of the phenyl ring
- understand peakGroup (the aromatic ring)
So the toolchain has to cover this and much more. However the open source chemistry community (in this case all Blue Obelisk) has provided most of the components. More on this later.