ChemSpider Blog

Recently a new website connecting chemicals to synthesis references went online. The site is ChemSynthesis and as well as synthesis references the database also contains physical properties for many of the listed substances. There are currently more than 40 000 compounds and more than 45 000 synthesis references in the database and there is an intention to keep the database growing with contributions from the community. Presently ChemSynthesis is indexing information from quite an extensive list of journals given below.

The Journal of the American Chemical Society, Canadian Journal of Chemistry, Chemical and Pharmaceutical Bulletin, Chemistry Letters, Journal of Heterocyclic Chemistry, Journal of Medicinal Chemistry, The Journal of Organic Chemistry, Organic Syntheses, Synthesis, Synthetic Communications, Tetrahedron Letters, Tetrahedron

An example record can be found here and a list of hits from a text search is shown below.

Linking_from ChemSpider to ChemSynthesis seemed like a natural way to help our users source potential synthesis details. So, that’s done. Also we have exchanged the appropriate information with ChemSynthesis so that we have completed the loop. Users searching ChemSynthesis can navigate directly to the ChemSpider record with one click.

To review the entire ChemSynthesis dataset on ChemSpider simply follow this link. It is >40,000 molecules so might take a while to load. Another contribution to the community of connected chemists….

Something good is happening in regards to ChemSpiders reputation it seems. I’ve chosen to interpret it as an indication that we are doing a stellar job at running our website and contributing to the community of chemistry. I’ll take it as kudos for the quality of what we do. Maybe it’s just an indication that the world is in economic turmoil and people are looking for jobs? In any case, the weekly requests coming in now to join ChemSpider, here’s my resume etc is very interesting. In the past 48 hours I have had to respond to 4 people that while we ARE a professionial organization (i.e. we’re all professionals and good at our jobs) we are not hiring at present and actually don’t have any of us gainfully “employed” by ChemSpider per se.

Despite this situation at present we DO have plans as to how to start to recoup some of the investments we have made over the past year and a half. We are discussing the ChemSpider Appliance with some organizations at present. The ChemSpider Appliance is what exactly? It will be a stripped down and read only version of ChemSpider installed INSIDE a company’s firewall with daily synchronization between the public server and the company’s system. We will not be able to provide the entire database to a company, especially for predicted properties etc because that might damage the business of some of our collaborators. All of this is presently under discussion. Watch this space…

We’ve been working on structure depictions on ChemSpider and overall we are very happy with where we have got to. These structure depictions are going to be showing up in various parts of our system now.

However, we should qualify the difference between structure images and structure layout. The depictions and the layout are governed by different algorithms.While a structure image can be attractive the layout may not be perfect. it is possible to improve the layout of the molecule deposited on ChemSpider. Notice for the structure on the left that there is overlap with the methyl group.

For details on how to CLEAN structures on ChemSpider please read the Technical Note here: Interactive Cleaning of Molecules During Curation and Deposition.

The result of performing cleaning is shown below. This layout may also not be the perfect layout but there is no overlap. The user can continue to manually optimize the structure for the preferred layout.