Monday, November 28, 2005

new blog for molecules

I have created a new blog at

The aim of this blog is to keep track of information on the compounds we wish to synthesize and the reagents necessary to do so.

For example the target compound in the previous synthesis is listed as UC0001 in usefulchem-molecules. Everything is cross-linked between the blogs so it should be easy to follow.

The key to tracking molecules is the SMILES code. You can get that from ChemSketch under tools->generate SMILES code for any highlighted molecule. The name can be generated in a similar way from ChemSketch.

The SMILES code is the most versatile way of inputing a structure into a database, like Chmoogle. Unfortunately, Chmoogle's database is not as extensive as I had hoped. But you can input the SMILES code into company catalogues, like Sigma-Aldrich to find reagents. Doing this I found the Aldrich number for Reagent A and a price of about $25/5 grams.

Other databases that will take SMILES and format conversions can be found here

For Reagent B, I just put the jpeg, the SMILES code and links to the relevant post in UsefulChem. I want to see if others can understand what I am saying and add the rest of the info. The most useful info is of course the commercial availability and the cost. Ask me to add you as member to this blog if you wish to contribute.

Yes, we are using a blog as a database. That is certainly not the most efficient way to store and retrieve information but with relatively few compounds I think the advantages are significant. The blog is accessible by anyone and is archived quickly by search engines, especially Blogsearch. This is a free and hosted solution so anyone can replicate this model immediately in other fields. The blog provides an intuitive environment for both humans and autonomous agents. Since Word now has a plug-in to update Blogger, we might consider VBA as a quick hack to carry out some of the automation.

And perhaps most importantly, a blog represents an easy to way to create an RSS-CML (Chemical Markup Language) feed so autonomous agents can read the feed as chemical information. See Rzepa and Murray-Rust references here for more info on CML. ChemSketch can export CML but I have been able to have that output interpreted correctly by the RSS-CML reader mentioned in those references. This would be a useful thing for the programmers to figure out.

Thanks everyone!


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