Molecule of the Month: Retinal Imine

...this page requires Chime to view properly

This may look like a pretty complicated molecule, depending on how much chemistry you have had. It's a pretty important molecule, though: without its cousin, rhodopsin, you wouldn't be able to see the display or page that you are viewing.

The line-segment structure of this molecule looks like this:

This is the so-called 11-cis retinal form, which is found in the active visual pigment called opsin. You might notice that it has a cis configuration of the double bond near the little 11 in the diagram. The retinal is the part that absorbs the photon of light to initiate the process of vision. In less than a picosecond (that's 10-12 second), the 11 cis bond has isomerized to the trans form, causing the protein enclosing it to change shape and start the cascade of the nerve response. [I might point out that in 1999, Ahmad Zewail was awarded the Nobel Prize for work done gathering information about extremely fast reactions. While he was not the only person to work on the ultrafast spectroscopy of the visual process, he has made extraordinary contributions in the field.]

The diagram below shows a lot more about the molecule. Created in Spartan, this is a complex picture showing the actual 3D shape of the molecule, as calculated by a semi-empirical molecular orbital approach. It also shows three electron-distribution issues. First, the cloud surrounding the entire molecule is the surface which encloses virtually all of the electrons in the molecule. This shows the general overall shape of the molecule. Second, the dark red and blue blobs on the inside are the shape of the highest occupied molecular orbital (HOMO). If you could correlate the blobs with the structure above, you would note that these blobs follow the "double bonds" in the valence bond representation. There is considerable resonance along the polyene chain. Note also that the red and blue blobs are all parts of one orbital, not separate orbitals. This is the molecular orbital representation of delocalized electrons, which are the source of the electron that is promoted during the absorption of light..

The red and blue mesh blobs show another orbital crucial to the absorption of light. These show the shape of the lowest unoccupied molecular orbital (LUMO). This is the destination of the electron which gets promoted when the photon of light is absorbed. Note that the mesh blobs are not found where we draw the double bonds, but instead are found where the single bonds are drawn.

That is the molecular event which allows the release of the pent-up strain in the retinal, and allows the cis-trans isomerization. When an electron is promoted from the pi-bonding orbital (HOMO), to the pi-antibonding orbital (LUMO), it negates that part of the bond, and makes it easy to twist. If you can see the structure in 3D (try the Chime viewer below), you'll notice that the molecule is already twisted partway. (Try looking at the spacefilling display to figure out why it twists) It makes a very lovely mousetrap for light.

A historical note. When I was working in the vision group of Koji Nakanishi at Columbia University (over 20 years ago), the calculations required to produce the picture below were done only by specialized theorists, Barry Honig and his group in our case. They used hours of calculation time on mainframe computers. While I was not quite using the same level of theory, I finished my calculation in less than 10 minutes on my Macintosh G3 using MacSpartan.