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!

7 Responses to “Ugly Organometallics and the Challenge of Structure Depiction”

  1. Gary says:

    The clean up algorithms, at least in my experience, have given rather variable results and don’t always yield a structure of “beauty.” When those algorithms fail, they seem to fail ugly. Generally, however, you can clean up a portion of a structure successfully.

  2. Chris Singleton says:

    Can anyone point to a blog or site which details inorganic structure clean-up? I’m curious as to why the algorithms are available for organics but ones for inorganics aren’t as effective. Is is just a matter of scale, more demand for organic structure clean-up?

  3. Andrew Dalke says:

    Organic structures typically have 4 or fewer bonds and many are so-called “planar graphs”. That’s a graph that can be drawn in 2D without overlapping bonds. Doing layout of these isn’t easy, but it is a lot easier than doing inorganic structures with 5 bonds to a metal and more complicated 3D structure. These can’t easily be flattened to 2D.

    Organic structures are not immune to these problems. Fullerenes are a simple example. Take a look at CID 21039425 from PubChem. It’s C53H50 so no inorganics there. But the depiction is very ugly. (Or look at CID 20675583: It’s a triangle (?!) with formula C42H54). By comparison, buckminsterfullerene has hand-assigned coordinates. See CID 123591. It looks very nice.

  4. Adam Ehad says:

    Ok. I typed “beauty” into google images and the above picture you used (of the African woman) came up as the first image. I thought it was a glitch, but tried again several months later (now) and it is still first. What is going on? What trick have you used to bring this up first?

  5. Antony Williams says:

    I didn’t do anything but maybe its as simple as this blog gets a lot of traffic and since it references the image is moves to the top?

  6. jeberti says:

    please remove the ” African woman” its offensive

  7. letters says:

    Remember guys, “beauty is in the eye of the beholder” so in Africa, this might be considered pretty and beautiful. Some African women stretch their necks out like a giraffe and that is considered beautiful.

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