Discussion

This question is more for any of the chemical search engines, even though this particular sub-section was on PubChem. Chemical search engines are getting extremely complex and this seems to be a great thing for researchers to save time. My question is that when doing my background research on something and later publishing it, should I be keeping really detailed notes on every single option used in my chemical searches to be included into the citations or would this be overdoing things? In the past, it may have only been necessary to include which search engine was used and the keyword, but with replicating an exact search being very complex, it seems there is a big need for this in the science community in regards to publications.

If you know the structure of a molecule (in the form of xyz coordinates, molecular graph, etc.), you can generate a fingerprint from it. Therefore, if you have correct/valid structure-based chemical identifiers (e.g., InChI, SMILES, and so on) that have information on molecular structures, you can generate molecular fingerprints from them. Molecular fingerprints represent the presence or absence of a particular functional group in a molecule, and one can use fingerprints to encode the number of a particular functional group. Therefore, they can be used to identify functional groups in molecules and how many, using the approach that you suggested in your post. However, in essence, what you are trying to do is “substructure” search, which is discussed in Section 2.4 of Module 6 (<a href="http://olcc.ccce.divched.org/2015OLCCModule6P1TLO-2-4">http://olcc.ccce.divched.org/2015OLCCModule6P1TLO-2-4</a>). What you are trying to do can also be done by substructure search with a SMARTS string (that represents a functional group) as a query. (Of course, you will need to convert InChI to SMILES before the substructure search).

I am not able to reproduce the results you said you got. I've uploaded a pdf file that contains a step-by-step instruction about how to perform a similarity search in question 3. Please follow the steps in the pdf file. If you do the same things as shown in the pdf file and still have the same problem, you can try two additional things: (1) Delete all histories/caches of your browser, and re-run the search again, or (2) Re-run the search using a different browser (e.g., any of IE, Safari, Google, FireFox, Opera, and so on). Please let me know whether you can reproduce what's seen in the pdf file.