Copyright©2009 Antony Williams
Beauty is in the eye of the beholder. Something I see as stunningly beautiful can just as easily be unattractive to my peers. Such is the nature of Chemistry too. Some might find a particular reaction particularly elegant while others would argue it is mundane. I judge that when it comes to the depiction of chemical structures we would all have fairly consistent views of what are attractive and appropriate chemical structure depictions or “layouts”.
Structure layout is hard to do well and there is still a need for THE optimal layout algorithm. We still find some nightmare organic structure layouts on ChemSpider. When we push them through the layout algorithm we use now they are easily resolved so we’re not sure why some escape the layout algorithm first time but such it is. We have provided the ability to clean these individual records as we find them and it takes just a couple of seconds. The technical note explaining how is here.
Such an operation was applied here. The structure on the left is the “ugly” structure (does anyone think it’s pretty?) and the one on the right is the cleaned version using the online process.
Unfortunately it is NOT so easy to obtain such improved layouts for the MAJORITY of organometallic compounds. This can be seen on PubChem (here) and, similarly, on ChemSpider here. The example is shown below. Are we working on this problem? Not really…the layout for such complex systems has been a challenge for many years and the appropriate way to deal with such situations is to use the CIF file, if its available, and display in JMol as we have enabled here. We are however still working on cleaning up the structures of organic molecules as we see them and still searching for the ultimate layout tool…Stumble it!