Building Blocks

So, when you’re a young chemist you have to take classes in all the various versions of chemistry – analytical, organic, inorganic, physical, biochemistry are the “typical” way that the field is broken up.

And one of the first things you learn in Physical Chemistry, is Atomic Theory.  That molecules are made up of atoms.  Atoms, in turn, are composed of a nucleus (where the protons and neutrons reside) and an electron cloud.  Atoms bond to one another (to make molecules) by sharing their electron clouds.

Most of this work was done in the 19th and early 20th century (for the past century, most work has been on subatomic particles), which is pretty remarkable, given the lack of sophisticated instrumentation available at that time.  But atomic and molecular theory has stood the test of time because (as you’d suppose) experimental support continues to support the conclusion that matter forms up this way.

As students, we’d draw molecules as lines, or balls and sticks – approximations of the way atoms are bonded to one another.  We’d draw the shape of different electronic orbitals — “s” orbitals are spheres,  “p” orbitals are like squashed dumbbells.  Why?  Well, again, that’s what the math and thousands of indirect experiments made you conclude.  As a student, you just sort of accepted it and moved on – after all, this stuff was old news.

Well – even though I went on and became an organic biochemist type, there was plenty of work going on in the P-chem world – especially in microscopy.  And two papers that came out in the last month demonstrate how.

The first is a paper from a group at IBM Zurich that imaged – down to single atoms – a small organic molecule – pentacene.  The picture shows a typical ball and stick diagram of pentacene and below it is ACTUAL PENTACENE.  Not a structure you deduce based on disparate data.  That’s IT.  Right there.

Not to be outdone, another group has figured out a way to image the electron clouds of individual atoms.  And here, the images look just like the ones I had to draw on Chem111 tests.


Now, I guess I shouldn’t be surprised that these molecules and electron orbitals look like “they’re supposed to” – as I said, there’s a couple of centuries of data to back it up.  But to see it – not just deduce it – is remarkable to me.

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7 thoughts on “Building Blocks

  1. Actually that is rather remarkable that the representation we have been using actually looks like the real thing….Not that I ever liked any Chemistry at all though, sad to admit, its the one subject I just never really warmed up to.

  2. Chemistry is a lovely subject, and I think if it were taught correctly, there would be far fewer people who despised it. I never did enjoy the drawing part though, I think that electron clouds deserve more of a paint splatter than a sketch. ;)

  3. Awesome! Some of the stuff logged in my head is still good. I'm happy for that, I'd hate to go back, forget everything and then have to learn it again. I love the images. That is truly amazing.

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