Archive for the ChemSpider Integrations Category

When ChemSpider went live earlier this year all chemical structures had systematic names generated. These were later removed. We are happy to announce that OpenEye have been kind enough to provide us with a copy of their Lexichem. This software will allow us to generate systematic names for structures across the database. The structures are presently being named in batches and you will see them show up as we publish them to the database. An example systematic name is shown below.

ChemSpider users are aware of the fact that we have supported the deposition of spectra to ChemSpider so that structure-spectra association is in place. We have described this in previous posts (1,2) and a technical note about depositing spectral data is available online.

Thanks to the valiant efforts of Bob Lancashire it appears that he has resolved the issues regarding Java versions 1.5 onwards. In order to see spectral viewing in place please visit the cocaine structure here and see the five associated spectra. Thanks Bob!

A blog posting last night discussed the fact that we had not yet implemented a 3D optimization engine under Jmol and that the structures displayed are 2D FLAT molecules. Well I’m happy to report that less than 24 hours later (actually it was done before I woke up this morning) the optimization of 3D structures under JMol is incorporated.

Rajarshi Guha pointed us to smi23d and we have embedded this under JMol now. This is of course, beta (we stay in constant beta) and there are a couple of bugs…we’re not sure whether these are on our side or in the Optimizer and are awaiting feedback. In the previous posting on Diazonamide A I commented on the six hits. The top two do NOT optimize while the bottom 4 do. I think it’s about the fact that the structure might be TOO far away from a starting point for optimization. I’ve opened an email dialog with Rajarshi to discuss.

Please note that the 3D coordinates are calculated in real time and the JMol screen might stay empty for a while during the optimization process. Here’s what it looks like for Diazonamide A.

Diazonamide A 3D in Jmol

The InChI Key has recently been released in a beta form (version 1.02) and is discussed in more detail over on the ChemSpider Blog. As of today these InChIs have been made searchable on the ChemSpider site and  our investigations have shown that there are no collisions between the InChI Keys – that is that there are no two keys which are the same but representing different structures. This is as to be expected based on other discussions.

The InChi and InChIKey for caffeine are shown below:
InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
InChIKey=RYYVLZVUVIJVGH-UHFFFAOYAW