NMR Prediction through nmrdb.org

Chemspider recently reported (NMR Prediction Now Available Via ChemSpider) a new NMR service at nmrdb.org. Our OSCAR tool is able to extract large numbers of NMR peak lists to I thought I’d try it out. Since our new software can also extract structures we can create files for input into nmrdb. It seems necessary to use MOL file input and get the answer in the inline format used in many journals (this is referred to as “ACS” but I’m not sure whether this is actually specified by the ACS. So I took the first molecule from one of our theses, used JUMBO to convert to a MOL file (with 2-D coordinates) and input it manually
Here’s the result:
7.254 (4, 1H, dddd, J=7.718, J=7.710, J=1.682, J=1.681), 7.473 (5, 1H, dddd, J=7.874, J=7.710, J=5.054, J=1.760), 7.278 (6, 1H, dddd, J=7.723, J=7.718, J=5.199, J=1.760), 7.304 (7, 1H, dddd, J=7.723, J=5.054, J=1.682, J=1.521), 7.304 (9, 1H, dddd, J=7.874, J=5.199, J=1.681, J=1.521), 3.039 (11, 1H), 3.040 (11, 1H), 3.015 (13, 1H, ddd, J=12.296, J=9.880, J=1.750), 3.289 (13, 1H, ddd, J=12.296, J=4.300, J=1.760), 1.823 (14, 1H, dtt, J=13.309, J=4.300, J=1.750), 1.804 (14, 1H, dtt, J=13.309, J=9.880, J=1.760), 3.289 (15, 1H, ddd, J=12.296, J=4.300, J=1.760), 3.015 (15, 1H, ddd, J=12.296, J=9.880, J=1.750), 2.187 (16, 3H)
It appears that the numeric labels refer to the atom to which the H is attached. Since I have the experimental values (which are not all assigned by the author) we can write something like:
obs 7.20
7.254 (4, 1H, dddd, J=7.718, J=7.710, J=1.682, J=1.681),
obs 7.94, 7.40 (2*2H not assigned)
7.473 (5, 1H, dddd, J=7.874, J=7.710, J=5.054, J=1.760),
7.278 (6, 1H, dddd, J=7.723, J=7.718, J=5.199, J=1.760),
7.304 (7, 1H, dddd, J=7.723, J=5.054, J=1.682, J=1.521),
7.304 (9, 1H, dddd, J=7.874, J=5.199, J=1.681, J=1.521),
obs: 3.15
3.039 (11, 1H),
3.040 (11, 1H),
obs 2.74:
3.015 (13, 1H, ddd, J=12.296, J=9.880, J=1.750),
3.015 (15, 1H, ddd, J=12.296, J=9.880, J=1.750),
3.289 (13, 1H, ddd, J=12.296, J=4.300, J=1.760),
3.289 (15, 1H, ddd, J=12.296, J=4.300, J=1.760),
obs 1.96
1.823 (14, 1H, dtt, J=13.309, J=4.300, J=1.750),
1.804 (14, 1H, dtt, J=13.309, J=9.880, J=1.760),
obs 1.85:
2.187 (16, 3H)
There is no exact symmetry in the result (we would expected 13 and 15 to be identical for example) although there is approximate symmetry. It would have been useful for the machine to label the couplings. Overall the RMS is about 0.3 Hz which is probably quite useful for high-throughput assignment and for checking for major errors.
There are similar observations on the Chemspider blog.
If the service can provide an API, and if it persists, that would be of considerable value.

This entry was posted in Uncategorized. Bookmark the permalink.

Leave a Reply

Your email address will not be published. Required fields are marked *