May 10, 2004
Structural molecular orbital diagrams: some tools and a method
The advice below can easily be applied to many different academic endeavors, including use in non-science classes. Here's a recipe. First, buy these pens:
- The Bic brite liner, of course. Avoid excessive markup with this. Really. Some of you may need to be told this, so here goes: what good is text that is mostly highlighted?
- The classic Bic "4-color pen": you can't survive without this!
- At least one Sharpie pen (keep one in your labcoat pocket) for marking test tubes and centrifuge vessels. I know, these have nothing to do with the method below, but a good lab geek always has one in her pocket anyway.
- A set of colored pencils. I use the erasable Sanford Col-Erase, but non-erasable Crayola colored pencils are cheaper and color adequately too.
The classic Bic 4-color pen should be in any student's pocket anyway. Annotating your own notes is so much easier when you use different colors. Here's an application to chemistry: you can draw much more easily understandable molecular orbital "balloon diagrams" (using the 90% probability surface standard or other representation of choice) if you assign colors to orbitals and stick with those colors.
The "balloon diagram method" I use:
Before placing any of these pens to paper, first visualize where on that paper you'll place your molecule's constituent atoms, bearing in mind that you'll usually be converting a flattened Lewis dot diagram to a projection of some angle of a 3-dimensional structure. I strongly recommend therefore that you do the full Lewis diagram first, taking into account resonance, where applicable.
Draw the central atoms first, e.g. the backbone carbons in most organic structures, then place the peripheral atoms next, populating with hydrogens as the very last step (since they're invariably peripheral).
Using the medium-point 4-color pen, draw circles in your color of choice for those species (almost always only hydrogen) whose atomic orbitals do not hybridize. In other words, the 1s orbital around the hydrogens.
Assuming you're not working with d-block elements - that is, you're dealing only with s-block and d-block elements but not funky transition metals - move to the central atoms and, referring to your Lewis dot diagram, ask yourself about the hybridization of the atom's atomic orbitals, e.g. sp, sp2, sp3. Draw the outlines of the orbitals using a different lobe color for each hybridization type.
Using a closely matching color for each orbital type (to match your pen color outlines), lightly shade your orbitals with a the side edge of a colored pencil. Your structural orbital diagram should be very clear by this time. If you've done this step right, you should have axial bonding overlaps between neighboring 1s (unhybridized) and sp, sp2, or sp3 orbital lobes.
At this point, again consult your Lewis dot diagram and identify any pi bonds. There's more than one way of representing the electron cloud manually. Don't try to reproduce the printed textbook "pi sandwich" style of orbital: you don't have the tools at hand. Instead, I recommend picking yet another color and schematically representing, by overlay, the pi bond by drawing a line from the tip of one unhybridized p-orbital to its atomic neighbor, making sure to indicate the signs of the wavefunction of each p-orbital lobe (hint: bonding orbitals match in signs; pick an arbitrary sign and make sure it's matched with its neighbor). Do the same for the opposing lobes. Label all pi bonds as such.
Your instructor may have a different standard for handwritten orbitals. Consult first.
Draw short, black lines across (perpendicular to) the sigma bonds, labelling sigma bonds as such. Revisit all the atoms and, again using another color, write the hybridization type near the atom. Here's an important step many students forget: indicate resonance in whatever manner your instructor will accept, again in another color, in a manner that clearly indicates electron delocalization. Label the line (what I use) as "resonance".
Hope someone finds this useful... this started as a rant on colored pens and mutated into a set of recommendations on drawing molecular structural orbital diagrams.
Posted by Russell Whitaker at May 10, 2004 03:31 PM | TrackBack