The Mastery of The Pyramids

“Hard to believe, Sy.”

“What’s hard to believe, Vinnie?”

“What you said back there, about all molecules being tetrahedron-shaped.”

“Whoa, that’s not what I said.  What I did say was that the tetrahedron is the fundamental structural building block for most of the Universe’s molecules. To put a finer point on it, it’s the building block for most kinds of molecules.”

“What kinds are you leaving out?”

“Molecular hydrogen, for instance.  It’s probably the most common molecule in the Universe but it’s got only two atoms and two electrons and it doesn’t do tetrahedra.  I was talking about almost all the other flavors.  Molecules can have all kinds of shapes, from spherical to long and skinny.  Say, Eddie, do your kids play with Legos?”

“Geez, yes.  My feet find blocks all over the house.  Only thing worse is glitter.”

“You can build just about any shape from those rectangular blocks, right?  Pegs on one block plug into holes on other blocks and pretty soon you’ve got a rocket ship or something.  Atoms can work the same way.  Four bonding orbitals pointing out to those pyramid corners, ready to share with whatever comes along.”

“Not just with hydrogen like with that CH4 stuff?”

“Depends on the atom, but in general, yeah.  Except for the outermost columns of the Periodic Table, most of the elements in the upper rows can be persuaded to share at least one bond with most of the others.  Carbon’s the champ that links with practically everything.”Tetrahedral bonding

“Even carbon?”

“Especially carbon, Vinnie.  Linking to carbon is carbon’s best thing.  It’s even got three and a fraction different ways to do it.  Here’s a sketch.  It boils down to the different ways you can have two tetrahedra match up points.”

“Lemme look at this for a minute… OK, that point-to-point one at the top —”

“It’s called a single bond.”

“Whatever, you’re saying that could be like two –CH3 pieces tied together.”

“Mm-hm.  The –CH3‘s are methyl groups, and with two of them you’ve got ethane.  Or link a methyl to a –CH2CH3 and you’ve got propane, or link it to an –OH to get methyl alcohol.  At least in principle you can pop a methyl onto any other atom or molecule that started off with only one unit of charge in an unshared orbital.”

“So it’s like my daughter’s bead necklace where she can pop it apart and add all different kinds of beads.”

“Exactly, Eddie, except her beads probably have their two links in a straight line.  These atoms support four links at 109° angles to each other.”

“That picture reminds me of one of my kids’ toys that’s like a top spinning on top of another top.  Is there anything that locks the two sides together so they can’t do that?”

“One way is if the two sides are each linked to bulky groups that get in each other’s way.  Hydrogens don’t much.  Scientists have measured methyl group rotation rates above 10 million cycles per second.”

“Hey, I’m still looking over here.  These other diagrams say that the tetrahedron things can link along an edge —”

“That’d be a double bond, Vinnie.”

“Looks to me like those double-bond shapes are locked in.  No rotation there, right?”

“Right.  In fact, rotational stability across a double bond is so strong that different arrangements operate like different compounds.  Switching A\B:C\D to A\B:D\C can be the difference between a useful med and something that’s inert or even toxic.”

“And I suppose when they match up whole triangles that’s a triple bond?”

“You got it.”

“Well, that can’t spin, for sure.”

“Nah, Vinnie, that’s like the atom-in-a-field thing, no difference between x- and y- axes.  Spinning like crazy except you can’t see it.”

“Eddie’s right, Vinnie.  The four atoms in a triple-bond structure are in a line.  The charge of three electron pairs mushes into a barrel-shaped region between the two carbons.”

“All that pent-up charge, I bet it’s reactive as hell.”

“Uh-huh.  With hydrogen atoms at both ends that’s acetylene gas.  Let that stuff touch copper and you get explosive decomposition.”

“So that’s why they say don’t run acetylene through copper tubing or brass fittings.”

“Believe it, Vinnie.  Believe it.”

~~ Rich Olcott

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To Bond Or Not To Bond, That Is The Question

Vinnie’s pushing pizza crumbs around his plate, watching them clump together.  “These molecular orbitals gotta be pretty complicated.  How do you even write them down?”

“Combinations.  There’s a bunch of different strategies, but they all go back to Laplace’s spherical harmonics.  Remember, he showed that every possible distribution around a central attractor could be described as a combination of his patterns.  Turn on a field, like from another atom, and you just change what combination is active.  Here’s a sketch of the simplest case, two hydrogen atoms — see how the charge on each one bulges toward the other?  The bulge is a combination of a spherical orbital and a dumbbell one.  The molecular orbitals are combinations of orbitals from both atoms, describing how the charges overlap, or not.”Hydrogen molecule

“What’s that blue in the other direction?”

“Another possible combination.  You can combine atomic orbitals with pluses or minuses.  The difference is that the minus combination will always have an additional node in between.  Extra nodes mean higher energy, harder to activate. When the molecule’s in the lowest energy state, charge will be between the atoms where that extra node isn’t.”

“So the overlapped charge here is negative, right, and it pulls the two positive nucleusses —”

“Nuclei”

“Whatever, it pulls ’em together.  Why don’t they just merge?”

“Positive-positive repulsion counts, too.  At the equilibrium bond distance, the nuclei repel each other exactly as much as the shared charge pulls them together.”

Eddie’s still hovering by our table.  “You said that there’s this huge number of possible atomic orbitals.  Wouldn’t there be an even huger number of molecular orbitals?”

“Sure.  The trick is in figuring out which of them are lowest-energy and activated and how that relates to the molecule’s configuration.  Keep track of your model’s total energy as you move the atoms about, for instance, and you can predict the equilibrium distance where the energy is a minimum.  In principle you can calculate configuration changes as two molecules approach each other and react.”

“Looks like a lot of work.”

“For sure, Eddie.  Even a handful of atoms has lots of atomic orbitals to keep track of.  That can burn up acres of compute time.”

Vinnie pushes three crumbs into a triangle.  “You got three distances, you can figure their angles.  So you got the whole shape of the thing.”

“Right, but like Eddie said, that’s a lot of computer work.  Chemists had to come up with shortcuts.  As a matter of fact, they had the shortcuts way before the computers came along.”

“They used, like, abacuses?”

“Funny, Vinnie.  No, no math at all.  And it’s why they still show school-kids those Bohr diagrams.”

“Crazy Eights.”

“Eddie, you got games on the brain.  But yeah, eights.  Or better, quartets of pairs.  One thing I’ve not mentioned yet is that even though they’ve got the same charge, electrons are willing to pair up.”

“How come?”

“That’s the thing of it, Vinnie.  There’s a story about Richard Feynman, probably the foremost physicist of the mid-20th Century.  Someone asked him to explain the pairing-up without using math.  Feynman went into his office for a week, came back out and said he couldn’t do it.  The math demands pairing-up, but outside of the math all we can say is experiments show that’s how it works.”

“HAH, that’s the reason for the ‘two charge units per orbital’ rule!”

“Exactly, Eddie.  It’s how charge can collect in that bonding molecular orbital in the first place.  It’s also the reason that helium doesn’t form molecules at all.  Imagine two helium atoms, each with two units of charge.  Suppose they come close to each other like those hydrogens did.  Where would the charge go?”

“OK, you got two units going into that in-between space, ahh, and the other two activating that blue orbital and pulling the two atoms apart.  So that adds up to zero?”

“Uh-huh.  They just bounce off and away.”

“Cool.”

“Hey, I got a question.  Your sketch has a ball orbital combining with a dumbbell.  But they’ve got different node counts, one and two.  Can you mix things from different shells?”

“Sure, Vinnie, if there’s enough energy.  The electron pair-up can release that much.”

“Cool.”

~~ Rich Olcott

  • A friend pointed out that I’m doing my best to avoid saying the word “electron.” He’s absolutely right.  At least in this series I’m taking Bohr’s side in his debate with Einstein — electrons in atoms don’t act like little billiard balls, they act like statistical averages, smeared-out ones at that.  It’s closer to reality to talk about where the charge is so that’s how I’m writing it.